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The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology
Open accessAbstract
In recent years, mass spectrometry has emerged as a core component of fundamental discoveries in virology. As a consequence of their coevolution, viruses and host cells have established complex, dynamic interactions that function either in promoting virus replication and dissemination or in host defense against invading pathogens. Thus, viral infection triggers an impressive range of proteome changes. Alterations in protein abundances, interactions, posttranslational modifications, subcellular localizations, and secretion are temporally regulated during the progression of an infection. Consequently, understanding viral infection at the molecular level requires versatile approaches that afford both breadth and depth of analysis. Mass spectrometry is uniquely positioned to bridge this experimental dichotomy. Its application to both unbiased systems analyses and targeted, hypothesis-driven studies has accelerated discoveries in viral pathogenesis and host defense. Here, we review the contributions of mass spectrometry–based proteomic approaches to understanding viral morphogenesis, replication, and assembly and to characterizing host responses to infection.
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- Interpretationreasoning
Mass spectrometry has become a central tool in fundamental virology discoveries.
“In recent years, mass spectrometry has emerged as a core component of fundamental discoveries in virology.”
Quote in the paperSubstantial claim - Premisecitation
Deeper proteomic analyses have been conducted on mammalian herpesviruses including human and murine cytomegaloviruses, herpes simplex viruses, Epstein-Barr virus, and pseudorabies virus.
“Subsequently, deeper proteomic analyses have been conducted on mammalian herpesviruses, such as human (8) and murine (5) cytomegaloviruses, herpes simplex viruses (7, 9, 15), Epstein–Barr virus (EBV) (4), and pseudorabies virus (PRV) (6).”
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- Premisecitation
Most virion compositional mass spectrometry studies have focused on viruses with high proteomic complexity, including Herpesviridae and Poxviridae.
“For compositional analysis, most studies have focused on viruses with high proteomic complexity, including those in the families Herpesviridae (4–9) and Poxviridae (10–12).”
Quote in the paperNot a substantial claim0 of 9 sources checked- cites [4] Johannsen E, Luftig M, Chase MR, Weicksel S, Cahir-McFarland E, 2004 Proteins of purified Epstein–Barr virus. Proc. Natl. Acad. Sci. USA 101: 16286– 91 15534216 PMC528973 source
- cites [5] Kattenhorn LM, Mills R, Wagner M, Lomsadze A, Makeev V, 2004 Identification of proteins associated with murine cytomegalovirus virions. J. Virol 78: 11187– 97 15452238 PMC521832 source
- cites [6] Kramer T, Greco TM, Enquist LW, Cristea IM. 2011 Proteomic characterization of pseudorabies virus extracellular virions. J. Virol 85: 6427– 41 21525350 PMC3126529 source
- cites [7] Loret S, Guay G, Lippé R. 2008 Comprehensive characterization of extracellular herpes simplex virus type 1 virions. J. Virol 82: 8605– 18 18596102 PMC2519676 source
- cites [8] Varnum SM, Streblow DN, Monroe ME, Smith P, Auberry KJ, 2004 Identification of proteinsin human cytomegalovirus (HCMV) particles: the HCMV proteome. J. Virol 78: 10960– 66 15452216 PMC521840 source
- cites [9] Vidick S, Leroy B, Palmeira L, Machiels B, Mast J, 2013 Proteomic characterization of murid herpesvirus 4 extracellular virions. PLoS ONE 8: e83842 PMC3875534 24386290 source
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- Interpretationreasoning
Applying mass spectrometry to unbiased and targeted studies has sped up discoveries about viral pathogenesis and host defense.
“Its application to both unbiased systems analyses and targeted, hypothesis-driven studies has accelerated discoveries in viral pathogenesis and host defense.”
Quote in the paperNot a substantial claim - Interpretationnone given
Mass spectrometry has been a powerful method for characterizing the detailed protein composition and macromolecular structures of virions.
“MS has provided a powerful means for characterizing their detailed protein composition and macromolecular structures (Figure 2).”
Quote in the paperSubstantial claim
- Premisecitation
Mass spectrometry analysis of purified channel catfish virus virions provided amino acid sequence data supporting a common evolutionary origin with other herpesviruses.
“MS analysis of purified channel catfish virus virions provided amino acid sequence data to support the common evolutionary origin of this virus with other herpesviruses (14), a hypothesis previously based only on capsid and virion morphology.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [14] Davison AJ, Davison MD. 1995 Identification of structural proteins of channel catfish virus by mass spectrometry. Virology 206: 1035– 43 7856078 source
- Premisecitation
Native mass spectrometry and atomic force microscopy demonstrated that the single-stranded RNA genome of Triatoma virus stabilizes or triggers uncoating of the capsid in a pH-dependent fashion through electrostatic genome-capsid interactions.
“For example, native MS and atomic force microscopy have demonstrated that the single-stranded RNA genome of the picorna-like Triatoma virus stabilizes or triggers uncoating of the capsid in a pH-dependent fashion through electrostatic genome-capsid interactions (29).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [29] Snijder J, Uetrecht C, Rose RJ, Sanchez-Eugenia R, Marti GA, 2013 Probing the biophysical interplay between a viral genome and its capsid. Nat. Chem 5: 502– 9 23695632 Native MS and atomic force microscopy reveal the constraints of Triatoma virus capsid packaging and uncoating. source
- Premisecitation
These developments helped establish that virions contain host proteins.
“These developments have helped establish that virions contain host proteins and have triggered the expansion of MS studies to the proteomes of filoviruses, HIV, influenza, and respiratory syncytial virus (16–22).”
Quote in the paperSubstantial claim0 of 7 sources checked- cites [16] Spurgers KB, Alefantis T, Peyser BD, Ruthel GT, Bergeron AA, 2010 Identification of essential filovirion-associated host factors by serial proteomic analysis and RNAi screen. Mol. Cell. Proteomics 9: 2690– 703 20702783 PMC3101857 source
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- cites [20] Saphire AC, Gallay PA, Bark SJ. 2006 Proteomic analysis of human immunodeficiency virus using liquid chromatography/tandem mass spectrometry effectively distinguishes specific incorporated host proteins. J. Proteome Res 5: 530– 38 16512667 source
- cites [21] Shaw ML, Stone KL, Colangelo CM, Gulcicek EE, Palese P. 2008 Cellular proteins in influenza virusparticles. PLoS Pathog. 4: e1000085 PMC2390764 18535660 source
- cites [22] Stegen C, Yakova Y, Henaff D, Nadjar J, Duron J, Lippé R. 2013 Analysis of virion-incorporated host proteins required for herpes simplex virus type 1 infection through a RNA interference screen. PLoS ONE 8: e53276 PMC3536771 23301054 source
- Premisecitation
Native mass spectrometry enables detection of complexes of several million daltons.
“An emerging biomolecular technique, termed native MS, enables the detection of complexes of several million daltons (23,24).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [23] Uetrecht C, Barbu IM, Shoemaker GK, van Duijn E, Heck AJR. 2011 Interrogating viral capsid assembly with ion mobility–mass spectrometry. Nat. Chem 3: 126– 32 21258385 source
- cites [24] Pease LF III. 2012 Physical analysis of virus particles using electrospray differential mobility analysis. Trends Biotechnol. 30: 216– 24 22172689 source
- Interpretationcitation
Native mass spectrometry combined with ion mobility is valuable for determining the size and shape of intermediate and mature capsid structures.
“When combined with ion mobility, a gas phase–based separation, native MS becomes a valuable technique for structural virologists to determine the size and shape of intermediate and mature capsid structures (Figure 2) (25–27).”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [25] Alexander CG, Jürgens MC, Shepherd DA, Freund SMV, Ashcroft AE, Ferguson N. 2013 Thermo-dynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein. Proc. Natl. Acad. Sci. USA 110: E2782–91 PMC3725087 23824290 source
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- cites [27] Shepherd DA, Holmes K, Rowlands DJ, Stonehouse NJ, Ashcroft AE. 2013 Using ion mobility spectrometry–mass spectrometry to decipher the conformational and assembly characteristics of the hepatitis B capsid protein. Biophys. J 105: 1258– 67 24010669 PMC3762345 source
- Premisecitation
Hydrogen/deuterium exchange mass spectrometry has been used as a complementary strategy for characterizing the assembly of viral capsids.
“In addition to native ion mobility MS, hydrogen/deuterium (H/D) exchange MS has been used as a complementary strategy for characterizing the assembly of viral capsids (30).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [30] Tuma R, Coward LU, Kirk MC, Barnes S, Prevelige PE Jr. 2001 Hydrogen-deuterium exchange as aprobe of folding and assembly in viral capsids. J. Mol. Biol 306: 389– 96 11178899 source
- Premisecitation
Native ion mobility mass spectrometry can monitor the dynamics of capsid morphology and stability as a function of pH and ionic strength.
“As many capsid proteins self-assemble in vitro, native ion mobility MS can monitor the dynamics of capsid morphology and stability as a function of pH and ionic strength (28, 29).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [28] Shoemaker GK, van Duijn E, Crawford SE, Uetrecht C, Baclayon M, 2010 Norwalk virus assembly and stability monitored by mass spectrometry. Mol. Cell. Proteomics 9: 1742– 51 20418222 PMC2938053 source
- cites [29] Snijder J, Uetrecht C, Rose RJ, Sanchez-Eugenia R, Marti GA, 2013 Probing the biophysical interplay between a viral genome and its capsid. Nat. Chem 5: 502– 9 23695632 Native MS and atomic force microscopy reveal the constraints of Triatoma virus capsid packaging and uncoating. source
- Premisereasoning
Hydrogen/deuterium exchange mass spectrometry allows determination of amino acid sequence regions that change conformation or intermolecular contacts during infection.
“For the study of macromolecular virus structures, this technique allows determination of amino acid sequence regions that undergo changes in conformation and/or modification of intermolecular contacts during infection.”
Quote in the paperSubstantial claim - Premisecitation
In a large-scale interactome study, all HIV-encoded proteins were individually expressed in 293 and Jurkat cells and subjected to tandem affinity purification-mass spectrometry.
“For example, in a large-scale interactome study, all the viral proteins encoded by the HIV genome were individually expressed in 293 and Jurkat cells and subjected to TAP AP-MS analysis (61).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [61] Jäger S, Cimermančič P, Gulbahce N, Johnson JR, McGovern KE, 2012 Global landscape of HIV-human protein complexes. Nature 481: 365– 70 PMC3310911 22190034 First interactome of all proteins encoded by a viral genome using individually expressed viral proteins. source
- Premisecitation
Components of SWI/SNF and ISWI chromatin-remodeling complexes were coisolated with the single-stranded DNA-binding protein ICP8.
“Interestingly, components of SWI/SNF and ISWI chromatin-remodeling complexes were coisolated with the single-stranded DNA–binding protein ICP8.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [34] Fontaine-Rodriguez EC, Taylor TJ, Olesky M, Knipe DM. 2004 Proteomics of herpes simplex virus infected cell protein 27: association with translation initiation factors. Virology 330: 487– 92 15567442 source
- cites [35] Taylor TJ, Knipe DM. 2004 Proteomics of herpes simplex virus replication compartments: association of cellular DNA replication, repair, recombination, and chromatin remodeling proteins with ICP8. J. Virol 78: 5856– 66 15140983 PMC415816 source
- Premisenone given
Most affinity purification-mass spectrometry studies have focused on interactions at one given time point of infection.
“Most studies have focused on interactions at one given time point of infection.”
Quote in the paperNot a substantial claim - Premisecitation
The Knipe laboratory used affinity purification-mass spectrometry to study virus-host protein complexes containing ICP27 or ICP8 at an early stage of herpes simplex virus 1 infection in human Hep2 cells.
“For example, the Knipe laboratory (34, 35) used AP-MS to study virus-host protein complexes containing the immediate-early proteins ICP27 or ICP8 at an early stage of herpes simplex virus 1 (HSV-1) infection in human Hep2 cells.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [34] Fontaine-Rodriguez EC, Taylor TJ, Olesky M, Knipe DM. 2004 Proteomics of herpes simplex virus infected cell protein 27: association with translation initiation factors. Virology 330: 487– 92 15567442 source
- cites [35] Taylor TJ, Knipe DM. 2004 Proteomics of herpes simplex virus replication compartments: association of cellular DNA replication, repair, recombination, and chromatin remodeling proteins with ICP8. J. Virol 78: 5856– 66 15140983 PMC415816 source
- Premisecitation
Use of fluorescent probes for affinity purification by Cristea and coworkers demonstrated the applicability of affinity purification-mass spectrometry for isolating protein complexes at different stages of viral infection.
“it was not until the use of fluorescent probes for AP by Cristea and coworkers (37) that the applicability of AP-MS was demonstrated for the isolation of protein complexes at different stages of a viral infection (38).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [37] Cristea IM, Williams R, Chait BT, Rout MP. 2005 Fluorescent proteins as proteomic probes. Mol. Cell. Proteomics 4: 1933– 41 16155292 source
- cites [38] Cristea IM, Carroll JW, Rout MP, Rice CM, Chait BT, MacDonald MR. 2006 Tracking and elucidating Alphavirus-host protein interactions. J. Biol. Chem 281: 30269– 78 16895903 The first temporal AP-MS study of virus-host protein interactions during the progression of an infection. source
- Premisecitation
Chromatin-remodeling complexes are now established as important players during infection.
“chromatin-remodeling complexes are now established as important players during infection (reviewed, e.g., in 36).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [36] Guise AJ, Budayeva HG, Diner BA, Cristea IM. 2013 Histone deacetylases in herpesvirus replication and virus-stimulated host defense. Viruses 5: 1607– 32 23807710 PMC3738950 source
- Premisecitation
Affinity purification coupled to mass spectrometry allows a protein's interacting partners to be identified with little to no prior knowledge.
“Their integration with MS (AP-MS) (Figure 2) has allowed a protein’s interacting partners to be identified with little to no a priori knowledge (33).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [33] Rowles DL, Terhune SS, Cristea IM. 2013 Discovery of host-viral protein complexes during infection. Methods Mol. Biol 1064: 43– 70 23996249 PMC4162421 source
- Premisecitation
Affinity purification-mass spectrometry has been used to identify host proteins in replication complexes at viral promoters in herpesviruses, influenza virus polymerases, and HIV-1 preintegration complexes.
“AP-MS has been employed to determine the identity of such host proteins, for instance, proteins in replication complexes at viral promoters in herpesviruses (67–69), viral polymerases of influenza virus (53), and preintegration complexes in HIV-1 (70).”
Quote in the paperSubstantial claim0 of 5 sources checked- cites [67] Gao Y, Colletti K, Pari GS. 2008 Identification of human cytomegalovirus UL84 virus-and cell-encoded binding partners by using proteomics analysis. J. Virol 82: 96– 104 17959680 PMC2224362 source
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- cites [69] Lester JT, DeLuca NA. 2011 Herpes simplex virus 1 ICP4 forms complexes with TFIID and mediatorin virus-infected cells. J. Virol 85: 5733– 44 21450820 PMC3126299 source
- cites [53] Mayer D, Molawi K, Martínez-Sobrido L, Ghanem A, Thomas S, 2007 Identification of cellular interaction partners of the influenza virus ribonucleoprotein complex and polymerase complex using proteomic-based approaches. J. Proteome Res 6: 672– 82 17269724 PMC2577182 source
- cites [70] Raghavendra NK, Shkriabai N, Graham RL, Hess S, Kvaratskhelia M, Wu L. 2010 Identification of host proteins associated with HIV-1 preintegration complexes isolated from infected CD4+ cells. Retrovirology 7: 66 20698996 PMC2924840 source
- Premisecitation
After binding to cell surface receptors, Kaposi sarcoma-associated herpesvirus is rapidly translocated in a c-Cbl-dependent manner to lipid rafts and internalized into macropinosomes.
“after initial binding to cell surface receptors, Kaposi sarcoma–associated herpesvirus (KSHV) is rapidly translocated in a c-Cbl-dependent manner to lipid rafts and internalized into macropinosomes (65).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [65] Raghu H, Sharma-Walia N, Veettil MV, Sadagopan S, Chandran B. 2009 Kaposi’s sarcoma–associated herpesvirus utilizes an actin polymerization–dependent macropinocytic pathway to enter human dermal microvascular endothelial and human umbilical vein endothelial cells. J. Virol 83: 4895– 911 19279100 PMC2682094 source
- Premisecitation
IFI16 was identified as the first known nuclear DNA sensor.
“The subsequent identification of IFI16 as the first known nuclear DNA sensor (70a, 71, 72)”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites 70a, 71, 72
- Premisecitation
Almost 200 interactions were identified in both cell types in the HIV interactome study.
“Almost 200 interactions were identified in both cell types.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [61] Jäger S, Cimermančič P, Gulbahce N, Johnson JR, McGovern KE, 2012 Global landscape of HIV-human protein complexes. Nature 481: 365– 70 PMC3310911 22190034 First interactome of all proteins encoded by a viral genome using individually expressed viral proteins. source
- Premisecitation
A pUL83-dependent inhibition of the IFI16 sensing function was identified.
“and of the pUL83-dependent inhibition of this sensing function (73)”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [73] Li T, Chen J, Cristea IM. 2013 Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion. Cell Host Microbe 14: 591– 99 Host-mediated phosphorylation of a viral protein during infection inhibits its function in viral immune evasion. 24237704 PMC3876934 source
- Study design and conductcitation
In the HIV interactome study, 97 of 127 selected interactions were confirmed by reciprocal isolations.
“Moreover, 97 of 127 selected interactions were confirmed by reciprocal isolations, highlighting the confidence of this data set.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [61] Jäger S, Cimermančič P, Gulbahce N, Johnson JR, McGovern KE, 2012 Global landscape of HIV-human protein complexes. Nature 481: 365– 70 PMC3310911 22190034 First interactome of all proteins encoded by a viral genome using individually expressed viral proteins. source
- Premisenone given
In human cytomegalovirus infection, the virion protein pUL83 induces transcription from the viral major immediate-early promoter.
“In HCMV infection, the virion protein pUL83 was found to induce transcription from the viral major immediate-early promoter (MIEP).”
Quote in the paperSubstantial claim - Interpretationnone given
Expression of single viral proteins in cellular systems cannot fully recapitulate the diversity and temporality of signaling pathway modulation during infection.
“In general, one drawback of the expression of single viral proteins within cellular systems is that it cannot fully recapitulate the diversity and temporality of signaling pathway modulation during an infection.”
Quote in the paperSubstantial claim - Premisecitation
Metabolic labeling with stable isotopes, I-DIRT, was developed to address contaminants that bind to isolated proteins.
“To address this issue, an approach using metabolic labeling with stable isotopes was developed (I-DIRT; see Figure 2) (91, 92).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [91] Tackett AJ, DeGrasse JA, Sekedat MD, Oeffinger M, Rout MP, Chait BT. 2005 I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J. Proteome Res 4: 1752– 56 16212429 source
- cites [92] Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, 2013 The functional interactome landscape of the human histone deacetylase family. Mol. Syst. Biol 9: 672 23752268 PMC3964310 Integrated label-free and metabolic labelling approaches measure the relative stability and specificity of protein interactions. source
- Premisecitation
Affinity purification-mass spectrometry approaches have been adapted to identify proteins that bind viral RNA, most often to the 5' or 3' untranslated regions thought to function in initial stages of viral RNA replication and translation.
“AP-MS approaches have been adapted to identify proteins that bind viral RNA (vRNA), most often to the 5′ or 3′ untranslated regions thought to function in the initial stages of vRNA replication and translation (80).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [80] Galán C, Sola I, Nogales A, Thomas B, Akoulitchev A, 2009 Host cell proteins interacting with the 3′ end of TGEV coronavirus genome influence virus replication. Virology 391: 304– 14 19580983 PMC7118768 source
- Premisecitation
Sequences of uncharacterized proteins and transcripts mapped to nonannotated or overlapping annotated human cytomegalovirus genomic loci and corresponded with alternative splicing or translation sites within known viral gene transcripts.
“Sequences of uncharacterized proteins and transcripts could be mapped to nonannotated or overlapping annotated HCMV genomic loci and corresponded with alternative splicing or translation sites within known HCMV gene transcripts.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [101] Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, 2012 Decoding human cytomegalovirus. Science 338: 1088– 93 23180859 PMC3817102 Combination of transcriptomics and proteomics identifies novel viral translation products during HCMV infection. source
- Premisecitation
In latent HCMV infection, the viral protein pUL138 degrades the PM drug transporter MRP1.
“More recently, during latent HCMV infection, the degradation of the PM drug transporter MRP1 by the viral protein pUL138 was discovered by SILAC-MS after PM enrichment (110).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [110] Weekes MP, Tan SY, Poole E, Talbot S, Antrobus R, 2013 Latency-associated degradation of the MRP1 drug transporter during latent human cytomegalovirus infection. Science 340: 199– 202 23580527 PMC3683642 source
- Premisecitation
Differentially regulated Golgi-resident and vesicle trafficking factors, including SEC22B and LAMTOR1, were shown to affect MHV virion assembly in RNAi and overexpression assays.
“selected differentially regulated Golgi-resident and vesicle trafficking factors, such as SEC22B and the Ragulator complex protein LAMTOR1, were shown to alter MHV virion assembly using RNA interference and overexpression assays.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [102] Vogels MW, van Balkom BW, Kaloyanova DV, Batenburg JJ, Heck AJ, 2011 Identification of host factors involved in coronavirus replication by quantitative proteomics analysis. Proteomics 11: 64– 80 21182195 PMC7167679 source
- Premisecitation
Inhibiting XIAP and Mcl-1 with drugs sensitized latently HIV-1-infected cells to apoptosis.
“Interestingly, drug inhibition of XIAP and Mcl-1 expression sensitized latently infected cells to apoptosis.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [109] Berro R, de la Fuente C, Klase Z, Kehn K, Parvin L, 2007 Identifying the membrane proteome of HIV-1 latently infected cells. J. Biol. Chem 282: 8207– 18 17237230 source
- Premisecitation
In mouse hepatitis virus-infected hepatocytes, SILAC measured virus-induced expression changes in Golgi-enriched fractions.
“metabolic labeling using stable isotope labeling in cell culture (SILAC; see Figure 2) was employed to quantify virus-induced expression changes in Golgi-enriched fractions from mouse hepatitis virus (MHV)-infected hepatocytes (102).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [102] Vogels MW, van Balkom BW, Kaloyanova DV, Batenburg JJ, Heck AJ, 2011 Identification of host factors involved in coronavirus replication by quantitative proteomics analysis. Proteomics 11: 64– 80 21182195 PMC7167679 source
- Premisereasoning
SILAC is particularly suitable for reducing quantification variance in multistep proteomic workflows.
“Overall, SILAC is well suited for minimizing quantification variance from multistep proteomic approaches.”
Quote in the paperNot a substantial claim - Premiseown data
LRP1 is strongly upregulated early in HCMV infection.
“The low-density lipoprotein receptor LRP1, which negatively regulates cholesterol influx into cells (15), was strongly upregulated early in infection.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [111] Gudleski-O’Regan N, Greco TM, Cristea IM, Shenk T. 2012 Increased expression of LDL receptor–related protein 1 during human cytomegalovirus infection reduces virion cholesterol and infectivity. Cell Host Microbe 12: 86– 96 22817990 PMC3405916 source
- Premisecitation
In HIV-1 latently infected lymphocytes, differentially expressed integral and membrane-associated proteins, including XIAP and Mcl-1, were identified and validated by orthogonal methods.
“Differentially expressed integral and membrane-associated proteins, including the antiapoptotic proteins XIAP and Mcl-1, were identified and validated by orthogonal techniques.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [109] Berro R, de la Fuente C, Klase Z, Kehn K, Parvin L, 2007 Identifying the membrane proteome of HIV-1 latently infected cells. J. Biol. Chem 282: 8207– 18 17237230 source
- Interpretationcitation
Mass spectrometry approaches are necessary to reveal the true genetic complexity and protein diversity of even well-studied viruses.
“This study highlighted the necessity of MS approaches to reveal the true genetic complexity and protein diversity of even well-studied viruses.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [101] Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, 2012 Decoding human cytomegalovirus. Science 338: 1088– 93 23180859 PMC3817102 Combination of transcriptomics and proteomics identifies novel viral translation products during HCMV infection. source
- Premisecitation
Cholesterol depletion reduced infectivity of other enveloped viruses, including HIV-1, hepatitis B and C viruses, and influenza.
“Similar to our HCMV studies, depletion of cholesterol was observed to compromise infectivity of other enveloped viruses, such as HIV-1, hepatitis B and C viruses, and influenza (112–115).”
Quote in the paperSubstantial claim0 of 4 sources checked- cites [112] Pollock S, Nichita NB, Böhmer A, Radulescu C, Dwek RA, Zitzmann N. 2010 Polyunsaturated liposomes are antiviral against hepatitis B and C viruses and HIV by decreasing cholesterol levels in infected cells. Proc. Natl. Acad. Sci. USA 107: 17176– 81 20855621 PMC2951407 source
- cites [113] Sun X, Whittaker GR. 2003 Role for influenza virus envelope cholesterol in virus entry and infection. J. Virol 77: 12543– 51 14610177 PMC262566 source
- cites [114] Campbell SM, Crowe SM, Mak J. 2002 Virion-associated cholesterol is critical for the maintenance of HIV-1 structure and infectivity. AIDS 16: 2253– 61 12441796 source
- cites [115] Guyader M, Kiyokawa E, Abrami L, Turelli P, Trono D. 2002 Role for human immunodeficiency virus type 1 membrane cholesterol in viral internalization. J. Virol 76: 10356– 64 12239312 PMC136590 source
- Premisecitation
MRP1 loss made latently HCMV-infected monocytes and hematopoietic progenitors sensitive to cytotoxic MRP1 substrates.
“Loss of MRP1 conferred sensitivity to cytotoxic MRP1 drug substrates in latently infected monocytes and hematopoietic progenitors.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [110] Weekes MP, Tan SY, Poole E, Talbot S, Antrobus R, 2013 Latency-associated degradation of the MRP1 drug transporter during latent human cytomegalovirus infection. Science 340: 199– 202 23580527 PMC3683642 source
- Premisecitation
Isobaric tagging and tandem MS quantified more than 400 secreted proteins from HSV-1-infected macrophages.
“In one study, isobaric tagging and tandem MS (Figure 2 and Table 1) quantified the secretion of >400 proteins from HSV-1-infected macrophages (121).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [121] Miettinen JJ, Matikainen S, Nyman TA. 2012 Global secretome characterization of herpes simplex virus 1–infected human primary macrophages. J. Virol 86: 12770– 78 22973042 PMC3497699 Multiplexed, quantitative MS analysis of the HSV-1-stimulated macrophage secretome identifies interferon-inducible proteins. source
- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Premisecitation
Chronic inflammation from persistent lifelong HCMV infection contributes to vascular pathologies, including atherosclerosis and allograft rejection.
“Accruing data suggest that chronic inflammation triggered by persistent, lifelong HCMV infection contributes to vascular pathologies, including atherosclerosis and allograft rejection (125–127).”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [125] Vliegen I, Duijvestijn A, Grauls G, Herngreen S, Bruggeman C, Stassen F. 2004 Cytomegalovirus infection aggravates atherogenesis in apoE knockout mice by both local and systemic immune activation. Microbes Infect. 6: 17– 24 14738889 source
- cites [126] Merigan TC, Renlund DG, Keay S, Bristow MR, Starnes V, 1992 A controlled trial of ganciclovir to prevent cytomegalovirus disease after heart transplantation. N. Engl. J. Med 326: 1182– 86 1313549 source
- cites [127] Vliegen I, Herngreen SB, Grauls GE, Bruggeman CA, Stassen FR. 2005 Mouse cytomegalovirus antigenic immune stimulation is sufficient to aggravate atherosclerosis in hypercholesterolemic mice. Atherosclerosis 181: 39– 44 15939052 source
- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Premisecitation
The influenza A-induced secretome significantly overlaps with HSV-1 and HCMV secretomes in cytokines, cathepsin proteases, and danger-associated signals.
“Interestingly, the influenza A–induced secretome (120) exhibited significant overlap with those of HSV-1 (121) and HCMV (124) in cytokines, cathepsin proteases, and danger-associated signals, suggesting the activation of common downstream signaling pathways in response to different viruses.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [120] Lietzén N, Ohman T, Rintahaka J, Julkunen I, Aittokallio T, 2011 Quantitative subcellular proteome and secretome profiling of influenza A virus–infected human primary macrophages. PLoS Pathog. 7: e1001340 PMC3093355 21589892 source
- cites [121] Miettinen JJ, Matikainen S, Nyman TA. 2012 Global secretome characterization of herpes simplex virus 1–infected human primary macrophages. J. Virol 86: 12770– 78 22973042 PMC3497699 Multiplexed, quantitative MS analysis of the HSV-1-stimulated macrophage secretome identifies interferon-inducible proteins. source
- cites [124] Dumortier J, Streblow DN, Moses AV, Jacobs JM, Kreklywich CN, 2008 Human cytomegalovirus secretome contains factors that induce angiogenesis and wound healing. J. Virol 82: 6524– 35 18448536 PMC2447085 source
- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Interpretationcitation
HSV-1 antagonizes inflammasome activity.
“These results implicated an HSV-1 mechanism for antagonizing inflammasome activity, which was subsequently demonstrated (123).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [123] Johnson KE, Chikoti L, Chandran B. 2013 Herpes simplex virus 1 infection induces activation and subsequent inhibition of the IFI16 and NLRP3 inflammasomes. J. Virol 87: 5005– 18 23427152 PMC3624293 source
- Interpretationreasoning
The HSV-1-induced macrophage secretome is exported through nonconventional, vesicle-mediated pathways.
“Interestingly, bioinformatic analyses revealed that 80% of these are exosomal proteins, suggesting export through nonconventional, vesicle-mediated pathways.”
Quote in the paperSubstantial claim- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Interpretationreasoning
Quantitative MS-based subproteomic profiling improves understanding of host-virus dynamics by providing sensitivity and spatial resolution during infection.
“Altogether, quantitative MS–based subproteomic profiling heightens our understanding of host-virus dynamics by providing sensitivity and spatial resolution during infection.”
Quote in the paperSubstantial claim - Premisecitation
Virus-induced secretion of signaling factors mediates the onset of innate and adaptive immunity.
“This is critical from the host perspective, as the virus-induced secretion of signaling factors mediates the onset of innate and adaptive immunity (116).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [116] Bonjardim CA, Ferreira PC, Kroon EG. 2009 Interferons: signaling, antiviral and viral evasion. Immunol. Lett 122: 1– 11 19059436 PMC7112942 source
- Premisecitation
Of those secreted proteins from HSV-1-infected macrophages, 80% are exosomal proteins.
“Interestingly, bioinformatic analyses revealed that 80% of these are exosomal proteins, suggesting export through nonconventional, vesicle-mediated pathways.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [121] Miettinen JJ, Matikainen S, Nyman TA. 2012 Global secretome characterization of herpes simplex virus 1–infected human primary macrophages. J. Virol 86: 12770– 78 22973042 PMC3497699 Multiplexed, quantitative MS analysis of the HSV-1-stimulated macrophage secretome identifies interferon-inducible proteins. source
- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Interpretationreasoning
Different viruses activate common downstream signaling pathways, as suggested by secretome overlap.
“Interestingly, the influenza A–induced secretome (120) exhibited significant overlap with those of HSV-1 (121) and HCMV (124) in cytokines, cathepsin proteases, and danger-associated signals, suggesting the activation of common downstream signaling pathways in response to different viruses.”
Quote in the paperSubstantial claim- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Premisecitation
HSV-1-infected macrophages secrete no interleukin-1β.
“Finally, the authors found no secretion of the proinflammatory cytokine interleukin-1β, a process known to depend on the inflammasome—a caspase-1-containing complex (122).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [121] Miettinen JJ, Matikainen S, Nyman TA. 2012 Global secretome characterization of herpes simplex virus 1–infected human primary macrophages. J. Virol 86: 12770– 78 22973042 PMC3497699 Multiplexed, quantitative MS analysis of the HSV-1-stimulated macrophage secretome identifies interferon-inducible proteins. source
- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Premisecitation
Angiogenesis is implicated in HCMV-associated vasculopathies.
“Considering recent evidence implicating angiogenesis in HCMV-associated vasculopathies (128), Dumortier et al. (124) profiled the secretome of HCMV-infected human dermal fibroblasts.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [128] Streblow DN, Dumortier J, Moses AV, Orloff SL, Nelson JA. 2008 Mechanisms of cytomegalovirus-accelerated vascular disease: induction of paracrine factors that promote angiogenesis and wound healing. Curr. Top. Microbiol. Immunol 325: 397– 415 18637518 PMC2699259 source
- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Premisecitation
A phosphorylation within the influenza A nucleoprotein is necessary for efficient viral replication.
“Here, an identified phosphorylation within the influenza A nucleoprotein was found to be necessary for efficient viral replication.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [131] Hutchinson EC, Denham EM, Thomas B, Trudgian DC, Hester SS, 2012 Mapping the phosphoproteome of influenza A and B viruses by mass spectrometry. PLoS Pathog. 8: e1002993 PMC3493474 23144613 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Premisecitation
Analysis of HSV-1 phosphorylation sites revealed great sequence degeneracy.
“Analysis of these phosphorylation sites revealed great sequence degeneracy, suggesting that the kinases mediating these phosphorylation events either have altered behavior during infection or have not yet been characterized.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [129] Bell C, Desjardins M, Thibault P, Radtke K. 2013 Proteomics analysis of herpes simplex virus type 1–infected cells reveals dynamic changes of viral protein expression, ubiquitylation, and phosphorylation. J. Proteome Res 12: 1820– 29 23418649
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Premisecitation
Multiple acetylations within OAS2, TRIM25, IRAK4, and RIG-I were identified using anti-acetyllysine antibody enrichment and MS.
“Interestingly, multiple acetylations within other innate immunity signaling components—OAS2, TRIM25, IRAK4, and RIG-I—were identified using anti-acetyllysine antibody enrichment and MS (138).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [138] Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, 2009 Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325: 834– 40 19608861 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Interpretationcitation
MS is effective for understanding immunological and pathophysiological consequences of viral infection through characterization of cellular secretion patterns.
“Together, these studies substantiate the effectiveness of MS in understanding the immunological and pathophysiological consequences of viral infection through characterization of cellular secretion patterns.”
Quote in the paperSubstantial claim- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Premisecitation
Bell et al. discovered 95 phosphorylations and 10 ubiquitinations within HSV-1 proteins enriched for cellular trafficking and immune evasion functions.
“For example, Bell et al. (129) discovered 95 phosphorylations and 10 ubiquitinations within HSV-1 proteins enriched for cellular trafficking and immune evasion functions.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [129] Bell C, Desjardins M, Thibault P, Radtke K. 2013 Proteomics analysis of herpes simplex virus type 1–infected cells reveals dynamic changes of viral protein expression, ubiquitylation, and phosphorylation. J. Proteome Res 12: 1820– 29 23418649
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Premisereasoning
Immunoaffinity isolation of a protein of interest allows simultaneous detection of various PTMs within the target protein, aiding investigation of PTM-dependent function.
“As an alternative to PTM-specific enrichment, immunoaffinity isolation of a protein of interest allows the simultaneous detection of various PTMs within the target protein, aiding the investigation of PTM-dependent protein function.”
Quote in the paperSubstantial claim- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Premisecitation
Eight phosphosites were identified within immunoaffinity-isolated HCMV pUL83.
“Recently, we identified eight phosphosites within immunoaffinity-isolated pUL83 and established that one phosphorylation, under the control of host kinases, functions to block pUL83-dependent dispersal of cellular innate immunity effectors (73).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [73] Li T, Chen J, Cristea IM. 2013 Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion. Cell Host Microbe 14: 591– 99 Host-mediated phosphorylation of a viral protein during infection inhibits its function in viral immune evasion. 24237704 PMC3876934 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Interpretationreasoning
Profiling modifications within purified mature virions may distinguish PTMs important for virion structure, entry, and dissemination from those added de novo to regulate intracellular viral protein functions.
“This strategy may distinguish PTMs important for virion structure, entry, and dissemination from those added de novo to regulate intracellular viral protein functions over the course of infection.”
Quote in the paperSubstantial claim- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Premisecitation
Several identified phosphorylations within HSV-1 ICP0 modulate its ubiquitin ligase, transactivation, and localization activities.
“Similarly, several identified phosphorylations within the multifunctional HSV-1 protein ICP0 were found to modulate its ubiquitin ligase, transactivation, and localization activities using an AP-MS/mutagenesis approach (133).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [133] Davido DJ, von Zagorski WF, Lane WS, Schaffer PA. 2005 Phosphorylation site mutations affect herpes simplex virus type 1 ICP0 function. J. Virol 79: 1232– 43 15613350 PMC538545 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Premisecitation
The HCMV-specific secretome is enriched for proangiogenic and wound healing factors.
“Pathway analysis revealed that the HCMV-specific secretome was enriched for proangiogenic and wound healing factors.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [124] Dumortier J, Streblow DN, Moses AV, Jacobs JM, Kreklywich CN, 2008 Human cytomegalovirus secretome contains factors that induce angiogenesis and wound healing. J. Virol 82: 6524– 35 18448536 PMC2447085 source
- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
- Premisecitation
One phosphorylation of HCMV pUL83, under host kinase control, blocks pUL83-dependent dispersal of cellular innate immunity effectors.
“Recently, we identified eight phosphosites within immunoaffinity-isolated pUL83 and established that one phosphorylation, under the control of host kinases, functions to block pUL83-dependent dispersal of cellular innate immunity effectors (73).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [73] Li T, Chen J, Cristea IM. 2013 Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion. Cell Host Microbe 14: 591– 99 Host-mediated phosphorylation of a viral protein during infection inhibits its function in viral immune evasion. 24237704 PMC3876934 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Study design and conductcitation
The Bell et al. study did not functionally assess the identified PTMs.
“Although this study did not functionally assess the identified PTMs, it highlights the sensitivity and breadth of modern MS-based proteomics with respect to PTM identification and the scarcity of information regarding viral PTMs in the context of infection.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [129] Bell C, Desjardins M, Thibault P, Radtke K. 2013 Proteomics analysis of herpes simplex virus type 1–infected cells reveals dynamic changes of viral protein expression, ubiquitylation, and phosphorylation. J. Proteome Res 12: 1820– 29 23418649
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Premisecitation
TiO2 phospho-enrichment was successfully applied for mapping the phosphoproteome of influenza A-infected human cell lines.
“Recently, TiO2 phospho-enrichment was successfully applied for mapping the phosphoproteome of influenza A–infected human cell lines (131).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [131] Hutchinson EC, Denham EM, Thomas B, Trudgian DC, Hester SS, 2012 Mapping the phosphoproteome of influenza A and B viruses by mass spectrometry. PLoS Pathog. 8: e1002993 PMC3493474 23144613 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Interpretationreasoning
Advances in MS instrumentation, sample preparation, and bioinformatics have allowed researchers to elucidate molecular details of viruses and their interactions with hosts.
“The sensitivity, speed, accuracy, and analytical breadth conferred by recent advances in MS instrumentation, sample preparation, and bioinformatics have allowed researchers to successfully elucidate the molecular details of viruses and their interactions with hosts.”
Quote in the paperSubstantial claim - Premisecitation
Activities of several DUBs are strongly upregulated in EBV-infected lymphocytes.
“By using AP of active DUBs and MS analysis, the activities of several DUBs were found to be strongly upregulated in EBV-infected lymphocytes (145).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [145] Ovaa H, Kessler BM, Rolén U, Galardy PJ, Ploegh HL, Masucci MG. 2004 Activity-based ubiquitin-specific protease (USP) profiling of virus-infected and malignant human cells. Proc. Natl. Acad. Sci. USA 101: 2253– 58 14982996 PMC356937 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Premisecitation
Drug inhibition of cellular deacetylases strongly attenuates pathogen- and immunogen-induced immune responses.
“As drug inhibition of cellular deacetylases strongly attenuates pathogen-and immunogen-induced immune responses (139–141), it is tempting to speculate that acetylation plays a key role in modulating immune signaling pathways.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [139] Halili MA, Andrews MR, Labzin LI, Schroder K, Matthias G, 2010 Differential effects of selective HDAC inhibitors on macrophage inflammatory responses to the Toll-like receptor 4 agonist LPS. J. Leukoc. Biol 87: 1103– 14 20200406 source
- cites [140] Roger T, Lugrin J, Le Roy D, Goy G, Mombelli M, 2011 Histone deacetylase inhibitors impair innate immune responses to Toll-like receptor agonists and to infection. Blood 117: 1205– 17 20956800 source
- cites [141] Mombelli M, Lugrin J, Rubino I, Chanson AL, Giddey M, 2011 Histone deacetylase inhibitors impair antibacterial defenses of macrophages. J. Infect. Dis 204: 1367– 74 21921209 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Study design and conductnone given
Functional interaction networks from single affinity purifications cannot differentiate direct and indirect protein interactions within complexes.
“Furthermore, because functional interaction networks constructed from single affinity purifications cannot differentiate direct and indirect protein interactions within complexes, improvements in chemical cross-linking reagents and bioinformatic tools will accelerate the definition of protein interface topologies, as elegantly demonstrated for virus-plant interactions (147).”
Quote in the paperSubstantial claim - Interpretationnone given
Global proteome studies have provided quantitative information about intracellular protein identifications and abundances during viral infection.
“Thus far, global proteome studies have provided a wealth of quantitative information regarding intracellular protein identifications and abundances during viral infection.”
Quote in the paperSubstantial claim - Premisecitation
Metabolic labeling coupled with AP of cellular kinases via immobilized inhibitors quantified cellular kinome changes during HCMV infection.
“Taking advantage of this concept, metabolic labeling was effectively coupled with AP of cellular kinases via immobilized inhibitors to quantify cellular kinome changes during HCMV infection (142).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [142] Hutterer C, Wandinger SK, Wagner S, Muller R, Stamminger T, 2013 Profiling of the kinome of cytomegalovirus-infected cells reveals the functional importance of host kinases Aurora A, ABL and AMPK. Antivir. Res 99: 139– 48 23648710 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Study design and conductnone given
The dynamic range and spatial-temporal insight of current MS-based proteomic approaches are limiting factors.
“However, the dynamic range and spatial-temporal insight of current MS-based proteomic approaches are still limiting factors.”
Quote in the paperNot a substantial claim - Premisecitation
AMPK is upregulated during HCMV infection.
“The authors demonstrated that drug inhibition of AMPK, a kinase found to be upregulated during infection, decreased virus growth, in agreement with a previous RNA interference screen of kinases during HCMV infection (143).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [142] Hutterer C, Wandinger SK, Wagner S, Muller R, Stamminger T, 2013 Profiling of the kinome of cytomegalovirus-infected cells reveals the functional importance of host kinases Aurora A, ABL and AMPK. Antivir. Res 99: 139– 48 23648710 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- Interpretationreasoning
Modern MS-based proteomics, with orthogonal approaches, is suited for systems understanding of virus-host dynamics.
“For this reason, modern MS-based proteomics, in conjunction with orthogonal approaches, is perfectly suited for acquiring a systems understanding of virus-host dynamics.”
Quote in the paperNot a substantial claim- Rests on an assumption: Intimate virus-host coevolution has shaped viruses in every facet.
- Rests on an assumption: Viruses must induce complex alterations in intracellular protein abundance and activity to dismantle host functions and promote propagation.
- Interpretationnone given
Immunoaffinity isolation coupled with MS has provided insights into dynamic functions and components of viral and cellular protein complexes during infection.
“Apart from global and subproteome studies, immunoaffinity isolation coupled with MS has provided invaluable insights into the dynamic functions and components of viral and cellular protein complexes during infection.”
Quote in the paperSubstantial claim - Interpretationreasoning
Organelle enrichment across multiple time points can partly mitigate dynamic range and spatial-temporal limitations, offering temporal kinetics, subcellular localizations, and increased sensitivity for subtle changes.
“These issues can be partly mitigated using organelle enrichment strategies performed across multiple time points of infection, which offer not only protein temporal kinetics and subcellular localizations but also increased sensitivity for subtle proteomic changes otherwise undetected in global analyses.”
Quote in the paperSubstantial claim - Premisecitation
Drug inhibition of AMPK decreases HCMV growth.
“The authors demonstrated that drug inhibition of AMPK, a kinase found to be upregulated during infection, decreased virus growth, in agreement with a previous RNA interference screen of kinases during HCMV infection (143).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [142] Hutterer C, Wandinger SK, Wagner S, Muller R, Stamminger T, 2013 Profiling of the kinome of cytomegalovirus-infected cells reveals the functional importance of host kinases Aurora A, ABL and AMPK. Antivir. Res 99: 139– 48 23648710 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
- It may state two separate claims as one. 32
- Probably not a substantial claim. 17
It may state two separate claims as one.
PremisecitationTechnological advances in mass spectrometry instrumentation improved sensitivity, providing near-complete proteome coverage and access to low-abundance virion components.
“Technological advances in MS instrumentation have improved the sensitivity of detection, providing near-complete proteome coverage and access to low-abundance virion components (6, 7, 16).”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [6] Kramer T, Greco TM, Enquist LW, Cristea IM. 2011 Proteomic characterization of pseudorabies virus extracellular virions. J. Virol 85: 6427– 41 21525350 PMC3126529 source
- cites [7] Loret S, Guay G, Lippé R. 2008 Comprehensive characterization of extracellular herpes simplex virus type 1 virions. J. Virol 82: 8605– 18 18596102 PMC2519676 source
- cites [16] Spurgers KB, Alefantis T, Peyser BD, Ruthel GT, Bergeron AA, 2010 Identification of essential filovirion-associated host factors by serial proteomic analysis and RNAi screen. Mol. Cell. Proteomics 9: 2690– 703 20702783 PMC3101857 source
Probably not a substantial claim. The paper may give no reason why it holds.
PremisereasoningViral infection causes a broad range of changes in the cellular proteome.
“Thus, viral infection triggers an impressive range of proteome changes.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper may give no reason why it holds.
Premisenone givenDuring infection, changes in protein abundance, interactions, posttranslational modifications, localization, and secretion are regulated over time.
“Alterations in protein abundances, interactions, posttranslational modifications, subcellular localizations, and secretion are temporally regulated during the progression of an infection.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Interpretationnone givenMass spectrometry studies have characterized virion composition and structure, virus-host protein interactions, global and subcellular proteome changes, infection-induced secretomes, and posttranslational modification functions.
“As discussed in this review, MS studies have characterized virion composition and structure, virus-host protein interactions, global and subcellular proteome changes, infection-induced secretomes, and viral and cellular protein PTM functions.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
PremisecitationHydrogen/deuterium exchange rates supported increased protection in the beta-hairpin and NTD-CTD interface in mature virions, which had not formed in the Gag/CA5 structural intermediate.
“H/D exchange rates supported increased protection in the β-hairpin and the NTD-CTD interface in mature virions, which interestingly had yet to form in the Gag/CA5 structural intermediate.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [31] Monroe EB, Kang S, Kyere SK, Li R, Prevelige PE Jr. 2010 Hydrogen/deuterium exchange analysis of HIV-1 capsid assembly and maturation. Structure 18: 1489– 91 PMC2982214 21070947 source
It may state two separate claims as one.
PremisereasoningTwo-step tandem affinity purification reduces background contaminants and identifies stable interactions, but unlike single-step affinity purification it often cannot retain transient interactions.
“Overall, the two-step TAP system reduces background contaminants and identifies stable interactions, but unlike single-step AP, it often cannot retain transient interactions.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationCryogenic cell lysis and fast isolations on magnetic beads helped preserve complexes close to their original state, maximized viral bait isolation, and reduced nonspecific interactions.
“Further advancements introduced through this AP-MS strategy were cryogenic cell lysis of infected cells and fast isolations on magnetic beads, which helped preserve complexes close to their original state in the cell, maximized viral bait isolation, and reduced nonspecific interactions (38).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [38] Cristea IM, Carroll JW, Rout MP, Rice CM, Chait BT, MacDonald MR. 2006 Tracking and elucidating Alphavirus-host protein interactions. J. Biol. Chem 281: 30269– 78 16895903 The first temporal AP-MS study of virus-host protein interactions during the progression of an infection. source
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationTandem affinity purification uses a dual epitope tag for successive immunoaffinity isolations and has been applied to interactions within virus-infected cells.
“As the name implies, TAP uses a dual epitope tag for successive immunoaffinity isolations and has been applied to interactions within virus-infected cells (51–54).”
Quote in the paperNot a substantial claim0 of 4 sources checked- cites [51] Wagenaar TR, Moss B. 2007 Association of vaccinia virus fusion regulatory proteins with the multicomponent entry/fusion complex. J. Virol 81: 6286– 93 17409143 PMC1900102 source
- cites [52] Tanaka M, Sata T, Kawaguchi Y. 2008 The product of the herpes simplex virus 1 UL7 gene interacts with a mitochondrial protein, adenine nucleotide translocator 2. Virol. J 5: 125 18940012 PMC2577096 source
- cites [53] Mayer D, Molawi K, Martínez-Sobrido L, Ghanem A, Thomas S, 2007 Identification of cellular interaction partners of the influenza virus ribonucleoprotein complex and polymerase complex using proteomic-based approaches. J. Proteome Res 6: 672– 82 17269724 PMC2577182 source
- cites [54] Yamayoshi S, Noda T, Ebihara H, Goto H, Morikawa Y, 2008 Ebola virus matrix protein VP40 uses the COPII transport system for its intracellular transport. Cell Host Microbe 3: 168– 77 18329616 PMC2330329 source
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationThe tandem affinity purification tag system was originally applied to yeast and subsequently extended to mammalian systems.
“the tandem affinity purification (TAP) tag system, originally applied to characterizing multiprotein complexes inyeast(49)and subsequently extended to mammalian systems(50).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [49] Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Séraphin B. 1999 A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol 17: 1030– 32 10504710 source
- cites [50] Ikura T, Ogryzko VV, Grigoriev M, Groisman R, Wang J, 2000 Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102: 463– 73 10966108 source
It may state two separate claims as one.
PremisecitationThe COPII complex component Sec24C was identified and validated by colocalization and reciprocal isolations, and its contribution to virus-like particle formation was demonstrated by knockdown.
“The COPII complex component Sec24C was identified and validated by colocalization and reciprocal isolations, and its contribution to virus-like particle formation was demonstrated by knockdown studies (54).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [54] Yamayoshi S, Noda T, Ebihara H, Goto H, Morikawa Y, 2008 Ebola virus matrix protein VP40 uses the COPII transport system for its intracellular transport. Cell Host Microbe 3: 168– 77 18329616 PMC2330329 source
It may state two separate claims as one.
PremisecitationpUL83 interacts with the interferon-inducible protein IFI16 and co-opts it for regulation of immediate-early gene expression.
“Interestingly, pUL83 not only sequestered IFI16 but also co-opted it for regulation of immediate-early gene expression.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [43] Cristea IM, Moorman NJ, Terhune SS, Cuevas CD, O’Keefe ES, 2010 Human cytomegalovirus pUL83 stimulates activity of the viral immediate-early promoter through its interaction with the cellular IFI16 protein. J. Virol 84: 7803– 14 20504932 PMC2897612 source
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
InterpretationreasoningpUL99 associates with the ESCRT/TGN pathway, whereas pUL32 traffics in clathrin-coated vesicles.
“The existing functional knowledge regarding these factors led to the model that pUL99 associates with the ESCRT/TGN pathway, whereas pUL32 traffics in clathrin-coated vesicles.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [42] Moorman NJ, Sharon-Friling R, Shenk T, Cristea IM. 2010 A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation. Mol. Cell. Proteomics 9: 851– 60 20023299 PMC2871419 source
It may state two separate claims as one.
PremisecitationEphA2 was found in a functional complex with integrins, c-Cbl, and myosin IIA and was shown to impact macropinocytic entry and Kaposi sarcoma-associated herpesvirus trafficking.
“EphA2 was found in a functional complex with integrins, c-Cbl, and myosin IIA and was further shown to impact macropinocytic entry and KSHV trafficking (64).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [64] Chakraborty S, Veettil MV, Bottero V, Chandran B. 2012 Kaposi’s sarcoma–associated herpesvirus interacts with EphrinA2 receptor to amplify signaling essential for productive infection. Proc. Natl. Acad. Sci. USA 109: E1163–72 Mechanistic insight into macropinocytic entry facilitated by AP-MS of viral entry complexes at 5 min postinfection. PMC3358903 22509030 source
It may state two separate claims as one.
PremisecitationHuman cytomegalovirus pUL11 binds the receptor tyrosine phosphatase CD45, reduces tyrosine phosphorylation, and inhibits T cell proliferation.
“pUL11 binding reduced tyrosine phosphorylation, leading to inhibition of T cell proliferation (66).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [66] Gabaev I, Steinbrück L, Pokoyski C, Pich A, Stanton RJ, 2011 The human cytomegalovirus UL11 protein interacts with the receptor tyrosine phosphatase CD45, resulting in functional paralysis of T cells. PLoS Pathog. 7: e1002432 PMC3234252 22174689 source
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationVirus-centric repositories have been established, including ViralZone and VirusMINT, and GPS-Prot focuses on HIV-host interactions.
“Virus-centric repositories have also been established, including ViralZone(97) and VirusMINT (98), as well as GPS-Prot, which focuses on HIV-host interactions (99).”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [97] Hulo C, de Castro E, Masson P, Bougueleret L, Bairoch A, 2011 ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res. 39: D576– 82 20947564 PMC3013774 source
- cites [98] Chatr-aryamontri A, Ceol A, Peluso D, Nardozza A, Panni S, 2009 VirusMINT: a viral protein interaction database. Nucleic Acids Res. 37: D669– 73 18974184 PMC2686573 source
- cites [99] Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, 2011 GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. BMC Bioinform. 12: 298 PMC3213248 21777475 source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationBioinformatic network tools including STRING and GeneMania can score direct and indirect protein functional relationships using public database repositories such as IntAct and Reactome.
“Bioinformatic network tools, including STRING and GeneMania (93, 94), can score direct and indirect protein functional relationships using public database repositories, such as IntAct and Reactome (95, 96).”
Quote in the paperNot a substantial claim0 of 4 sources checked- cites [93] Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, 2013 GeneMANIA prediction server 2013 update. Nucleic Acids Res. 41: W115– 22 23794635 PMC3692113 source
- cites [94] Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, 2013 STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41: D808– 15 23203871 PMC3531103 source
- cites [95] Croft D, Mundo AF, Haw R, Milacic M, Weiser J, 2014 The Reactome pathway knowledgebase. Nucleic Acids Res. 42: D472– 77 24243840 PMC3965010 source
- cites [96] Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, 2010 The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38: D525– 31 19850723 PMC2808934 source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationMiST distinguished high-confidence virus-host protein interactions of epitope-tagged HIV proteins individually expressed in human cells.
“Another interaction specificity predictor, MiST, distinguished high-confidence virus-host protein interactions of epitope-tagged HIV proteins individually expressed in human cells (61).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [61] Jäger S, Cimermančič P, Gulbahce N, Johnson JR, McGovern KE, 2012 Global landscape of HIV-human protein complexes. Nature 481: 365– 70 PMC3310911 22190034 First interactome of all proteins encoded by a viral genome using individually expressed viral proteins. source
It may state two separate claims as one.
PremisecitationDuring human cytomegalovirus infection, viral glycoprotein gB localized to endosomes, and all three proteins merged within a large virion assembly structure late in infection.
“Interestingly, at the same time, the viral glycoprotein gB localized to endosomes, and it was not until late in infection that all three proteins merged within a large virion assembly structure (42).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [42] Moorman NJ, Sharon-Friling R, Shenk T, Cristea IM. 2010 A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation. Mol. Cell. Proteomics 9: 851– 60 20023299 PMC2871419 source
It may state two separate claims as one.
PremisecitationMass spectrometry and ribosome occupancy profiling identified and temporally resolved more than 50 previously unreported human cytomegalovirus polypeptides and more than 550 transcripts during infection.
“Recently, MS and ribosome occupancy profiling were used to identify and temporally resolve unique, previously unreported HCMV polypeptides (>50) and transcripts (>550) during infection (101).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [101] Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, 2012 Decoding human cytomegalovirus. Science 338: 1088– 93 23180859 PMC3817102 Combination of transcriptomics and proteomics identifies novel viral translation products during HCMV infection. source
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationPeptide nucleic acid was developed to replace the phosphate backbone with amide bonds, providing reduced nonspecific binding.
“To address this issue, a DNA mimic, termed peptide nucleic acid, was developed to replace the phosphate backbone with amide bonds, providing reduced nonspecific binding (83).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [83] Upadhyay A, Dixit U, Manvar D, Chaturvedi N, Pandey VN. 2013 Affinity capture and identification of host cell factors associated with hepatitis C virus (+) strand subgenomic RNA. Mol. Cell. Proteomics 12: 1539– 52 23429521 PMC3675812 A novel peptide nucleic acid–neamine conjugate for in situ capturing of viral RNA–host interactions. source
It may state two separate claims as one.
PremisecitationIn a study of HSV-1 pUL46 interactions, the viral E3 ubiquitin ligase ICP0 triggered proteasome-dependent degradation of pUL46, the first example of virus-induced degradation of a viral protein.
“One notable pUL46 interaction was the viral E3 ubiquitin ligase ICP0, which triggered a proteasome-dependent degradation of pUL46—a first example of virus-induced degradation of a viral protein.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [45] Lin AE, Greco TM, Döhner K, Sodeik B, Cristea IM. 2013 A proteomic perspective of inbuilt viral¨ protein regulation: pUL46 tegument protein is targeted for degradation by ICP0 during herpes simplex virus type 1 infection. Mol. Cell. Proteomics 12: 3237– 52 23938468 PMC3820936 source
Probably not a substantial claim.
PremisecitationThe SAINT scoring algorithm models protein spectral counts between experimental and control affinity purifications.
“we have used the Significance Analysis of INTeractome (SAINT) scoring algorithm (90), which models protein spectral counts between experimental and control affinity purifications (Figure 2)”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [90] Choi H, Larsen B, Lin ZY, Breitkreutz A, Mellacheruvu D, 2011 SAINT: probabilistic scoring of affinity purification–mass spectrometry data. Nat. Methods 8: 70– 73 21131968 PMC3064265 source
It may state two separate claims as one.
Premiseown dataDisrupting LRP1 activity raised intracellular and progeny HCMV envelope cholesterol levels, which correlated with higher virion infectivity.
“Disruption of LRP1 activity increased intracellular and progeny HCMV envelope cholesterol levels, which was correlated with greater virion infectivity.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [111] Gudleski-O’Regan N, Greco TM, Cristea IM, Shenk T. 2012 Increased expression of LDL receptor–related protein 1 during human cytomegalovirus infection reduces virion cholesterol and infectivity. Cell Host Microbe 12: 86– 96 22817990 PMC3405916 source
It may state two separate claims as one.
PremisereasoningCombining biochemical fractionation or affinity isolation with mass spectrometry boosts sensitivity and yields finer molecular detail about host and viral processes.
“These enrichment strategies confer increased sensitivity, providing greater molecular details of host and viral processes.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
PremisecitationPM enrichment by chemical derivatization and affinity purification lowers organelle contamination and improves detection of low-abundance membrane receptors.
“To profile cell surface proteins by MS, PM enrichment by chemical derivatization–affinity purification confers reduced organelle contamination and improved detection of low-abundance membrane receptors (107, 108).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [107] Peirce MJ, Wait R, Begum S, Saklatvala J, Cope AP. 2004 Expression profiling of lymphocyte plasma membrane proteins. Mol. Cell. Proteomics 3: 56– 65 14573526 source
- cites [108] Wollscheid B, Bausch-Fluck D, Henderson C, O’Brien R, Bibel M, 2009 Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat. Biotechnol 27: 378– 86 19349973 PMC2829300 source
Probably not a substantial claim.
PremisecitationLRP1 negatively regulates cholesterol influx into cells.
“The low-density lipoprotein receptor LRP1, which negatively regulates cholesterol influx into cells (15), was strongly upregulated early in infection.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [15] Terrand J, Bruban V, Zhou L, Gong W, El Asmar Z, 2009 LRP1 controls intracellular cholesterol storage and fatty acid synthesis through modulation of Wnt signaling. J. Biol. Chem 284: 381– 88 18990694 PMC2610522 source
It may state two separate claims as one.
InterpretationreasoningLRP1 recruitment to the PM may be a general antiviral response that starves infected cells of cholesterol and promotes infection-incompetent virions.
“Thus, the LRP1 PM recruitment could reflect a general antiviral response that starves the infected cell of cholesterol, promoting the production of infection-incompetent virions.”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationAbout 10% of human genome open reading frames encode secreted proteins.
“Importantly, approximately 10% of the human genome open reading frames encode proteins that are secreted (117).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [117] Pavlou MP, Diamandis EP. 2010 The cancer cell secretome: a good source for discovering biomarkers? J. Proteomics 73: 1896– 906 20394844 source
It may state two separate claims as one.
InterpretationreasoningQuantitative MS can complement traditional antibody array-based secretome analyses and reveal details of cellular immune responses to viral infection.
“These studies illustrate the ability of quantitative MS to complement traditional antibody array–based analyses of secretomes and reveal details of cellular immune responses to viral infection.”
Quote in the paperSubstantial claim- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
Probably not a substantial claim.
PremisecitationInterleukin-1β secretion depends on the inflammasome, a caspase-1-containing complex.
“Finally, the authors found no secretion of the proinflammatory cytokine interleukin-1β, a process known to depend on the inflammasome—a caspase-1-containing complex (122).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [122] Rathinam VA, Jiang Z, Waggoner SN, Sharma S, Cole LE, 2010 The AIM2 inflammasome is essential for host defense against cytosolic bacteria and DNA viruses. Nat. Immunol 11: 395– 402 20351692 PMC2887480 source
It may state two separate claims as one.
PremisecitationSecreted cathepsin protease activity is required for both inflammasome stimulation and apoptosis in response to influenza.
“Secreted cathepsin protease activity was shown to be required for both inflammasome stimulation and apoptosis in response to influenza (120).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [120] Lietzén N, Ohman T, Rintahaka J, Julkunen I, Aittokallio T, 2011 Quantitative subcellular proteome and secretome profiling of influenza A virus–infected human primary macrophages. PLoS Pathog. 7: e1001340 PMC3093355 21589892 source
It may state two separate claims as one.
PremisecitationThe HSV-1-induced secretome contains known secreted danger signals and immunomodulators, plus interferon-inducible proteins not previously known to be secreted, including IFIT1, STAT1, and MxA.
“Furthermore, though the HSV-1-induced secretome was composed of known secreted danger signals and immunomodulators, interferon-inducible proteins not known to be secreted were also detected, including IFIT1, STAT1, and MxA.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [121] Miettinen JJ, Matikainen S, Nyman TA. 2012 Global secretome characterization of herpes simplex virus 1–infected human primary macrophages. J. Virol 86: 12770– 78 22973042 PMC3497699 Multiplexed, quantitative MS analysis of the HSV-1-stimulated macrophage secretome identifies interferon-inducible proteins. source
- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
It may state two separate claims as one.
PremisecitationIFI16 is a DNA sensor and effector of innate immune responses during viral infection, detecting viral DNA in both nucleus and cytoplasm.
“For instance, the DNA sensor IFI16 is an effector of innate immune responses during viral infection, detecting viral DNA in both the nucleus and the cytoplasm (71–73, 136, 137).”
Quote in the paperSubstantial claim0 of 5 sources checked- cites [71] Li T, Diner BA, Chen J, Cristea IM. 2012 Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16. Proc. Natl. Acad. Sci. USA 109: 10558– 63 22691496 PMC3387042 Acetylation modulates the localization of the first viral DNA sensor that functions in the nucleus. source
- cites [72] Orzalli MH, DeLuca NA, Knipe DM. 2012 Nuclear IFI16 induction of IRF-3 signaling during herpesviral infection and degradation of IFI16 by the viral ICP0 protein. Proc. Natl. Acad. Sci. USA 109: E3008–17 PMC3497734 23027953 source
- cites [73] Li T, Chen J, Cristea IM. 2013 Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion. Cell Host Microbe 14: 591– 99 Host-mediated phosphorylation of a viral protein during infection inhibits its function in viral immune evasion. 24237704 PMC3876934 source
- cites [136] Jakobsen MR, Bak RO, Andersen A, Berg RK, Jensen SB, 2013 IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication. Proc. Natl. Acad. Sci. USA 110: E4571–80 PMC3845190 24154727 source
- cites [137] Unterholzner L, Keating SE, Baran M, Horan KA, Jensen SB, 2010 IFI16 is an innate immune sensor for intracellular DNA. Nat. Immunol 11: 997– 1004 20890285 PMC3142795 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
It may state two separate claims as one.
InterpretationreasoningThe kinases mediating HSV-1 phosphorylation events either have altered behavior during infection or have not yet been characterized.
“Analysis of these phosphorylation sites revealed great sequence degeneracy, suggesting that the kinases mediating these phosphorylation events either have altered behavior during infection or have not yet been characterized.”
Quote in the paperSubstantial claim- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
It may state two separate claims as one.
PremisecitationSupernatants from HCMV-infected cells induce angiogenesis and wound healing responses in primary human endothelial cells.
“Indeed, supernatants from HCMV-infected cells induced angiogenesis and wound healing responses in primary human endothelial cells.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [124] Dumortier J, Streblow DN, Moses AV, Jacobs JM, Kreklywich CN, 2008 Human cytomegalovirus secretome contains factors that induce angiogenesis and wound healing. J. Virol 82: 6524– 35 18448536 PMC2447085 source
- Rests on an assumption: Viral infection significantly alters the proteome within the extracellular space.
It may state two separate claims as one.
PremisecitationTwo acetylations within the nuclear localization signal of IFI16 modulate its nuclear-cytoplasmic distribution, expanding its immunosurveillance to both subcellular compartments.
“Using AP-MS, we identified two acetylations within its nuclear localization signal that modulate IFI16 nuclear-cytoplasmic distribution, effectively expanding its range of immunosurveillance to both subcellular compartments (71).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [71] Li T, Diner BA, Chen J, Cristea IM. 2012 Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16. Proc. Natl. Acad. Sci. USA 109: 10558– 63 22691496 PMC3387042 Acetylation modulates the localization of the first viral DNA sensor that functions in the nucleus. source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
It may state two separate claims as one.
PremisecitationUnique DUB activity is identified following EBV establishment of latency and correlates with changes in cell proliferation rates.
“Unique DUB activity was additionally identified following EBV establishment of latency and correlated with changes in cell proliferation rates.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [145] Ovaa H, Kessler BM, Rolén U, Galardy PJ, Ploegh HL, Masucci MG. 2004 Activity-based ubiquitin-specific protease (USP) profiling of virus-infected and malignant human cells. Proc. Natl. Acad. Sci. USA 101: 2253– 58 14982996 PMC356937 source
- Rests on an assumption: PTMs regulate protein stability, localization, activity, and interactions.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
Premisenone givenNuclear-replicating DNA viral genomes associate with core histones, implicating cellular effectors of chromatinization as important regulators of viral gene expression.
“Furthermore, the discovery that nuclear-replicating DNA viral genomes associate with core histones implicates cellular effectors of chromatinization as important regulators of viral gene expression.”
Quote in the paperNot a substantial claim- Rests on an assumption: Viral infection modulates the epigenetic landscape of the cell.
It may state two separate claims as one.
Interpretationnone givenParallel genomic and bioinformatic analyses have enabled functional categorization of host response pathways and identification of previously uncharacterized viral gene products.
“Paired with MS detection, parallel genomic and bioinformatic analyses have enabled functional categorization of host response pathways and identification of previously uncharacterized viral gene products.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper may give no reason why it holds.
Interpretationnone givenMS-based proteomics has significantly contributed to multifaceted discoveries in virology.
“In summary, MS-based proteomics has already significantly contributed to multifaceted discoveries in virology.”
Quote in the paperNot a substantial claim- Rests on an assumption: Intimate virus-host coevolution has shaped viruses in every facet.
- Rests on an assumption: Viruses must induce complex alterations in intracellular protein abundance and activity to dismantle host functions and promote propagation.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
Premisenone givenViral proteins interact with chromatin-remodeling enzymes and virus-induced changes in histone PTMs and DNA methylation profiles accomplish epigenetic modulation.
“This is accomplished via interactions of viral proteins with chromatin-remodeling enzymes and virus-induced changes in histone PTMs and DNA methylation profiles.”
Quote in the paperNot a substantial claim- Rests on an assumption: Viral infection modulates the epigenetic landscape of the cell.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Study design and conductnone givenMS-based analyses of protein complexes have challenges, including distinguishing specific from nonspecific associations.
“These MS-based analyses come with their own challenges, including distinguishing specific from nonspecific associations.”
Quote in the paperNot a substantial claim
The paper relies on this without support.
The progression of viral infection depends on the establishment of numerous finely tuned virus-host and virus-virus protein interactions.
“The progression of viral infection depends on the establishment of numerous finely tuned virus-host and virus-virus protein interactions.”
The paper relies on this without support.
Through dynamic protein-protein interactions, complex cellular pathways are modulated to promote viral replication or host defense.
“Through these dynamic protein-protein interactions, complex cellular pathways are modulated to promote viral replication or act in host defense.”
The paper relies on this without support.
Genome replication mechanisms vary widely across virus families, yet all viruses leverage host protein functions.
“Genome replication mechanisms vary widely across virus families, yet all viruses leverage host protein functions.”
The paper relies on this without support.
Many viruses do not encode their own transcription machinery, and regulation of viral gene transcription is achieved via recruitment of host polymerases and host factors.
“As many viruses do not encode their own transcription machinery, regulation of viral gene transcription is achieved via recruitment of host polymerases and host factors.”
The paper relies on this without support.
Most cellular pathways are modulated at the proteome level, and viral or host genes exert most of their functions during infection at the protein level.
“In fact, it is at the proteome level that most cellular pathways are modulated; viral or host genes exert most of their functions during infection at the protein level.”
The paper relies on this without support.
Viral infection significantly alters the proteome within the extracellular space.
“Viral infection also significantly alters the proteome within the extracellular space.”
The paper relies on this without support.
PTMs regulate protein stability, localization, activity, and interactions.
“PTMs have been recognized to regulate an expanding array of protein properties, for example, stability, localizations, activities, and interactions.”
The paper relies on this without support.
Viral infection modulates the epigenetic landscape of the cell.
“In recent years, it has become increasingly evident that viral infection modulates the epigenetic landscape of the cell.”
The paper relies on this without support.
Intimate virus-host coevolution has shaped viruses in every facet.
“Intimate virus-host coevolution has shaped viruses in their every facet.”
The paper relies on this without support.
Viruses must induce complex alterations in intracellular protein abundance and activity to dismantle host functions and promote propagation.
“As a consequence, viruses must induce complex alterations in intracellular protein abundance and activity to dismantle inhibitory host functions and promote their own propagation.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Proteomics and the HPP have made fundamental contributions to understanding pathogenic infection, providing diagnostics and developing therapies.
“Proteomics and the HPP have made fundamental contributions to understanding pathogenic infection, providing diagnostics and developing therapies132.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [132]
Studies using tagged proteins in AP-MS workflows are susceptible to the co-isolation of non-specific associations.
“studies using tagged proteins in AP-MS workflows are susceptible to the co-isolation of non-specific associations.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [85]
AP-MS analyses frequently lead to the identification of hundreds of proteins that can represent strong and weak, and direct and indirect associations.
“AP-MS analyses frequently lead to the identification of hundreds of proteins that can represent strong and weak, and direct and indirect associations.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [85]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
A herpes simplex citation points to a cholesterol study
MinorThe text cites reference 15 for proteomic analyses of herpes simplex viruses, but reference 15 is a study of LRP1 and cholesterol regulation, not herpes simplex virus.
“herpes simplex viruses (7, 9, 15)”
“15. Terrand J, Bruban V, Zhou L, Gong W, El Asmar Z, 2009 LRP1 controls intracellular cholesterol storage and fatty acid synthesis through modulation of Wnt signaling.”
Citations
Cites
The Reactome pathway Knowledgebase
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 5,605
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398 · cited 1×
“Bioinformatic network tools, including STRING and GeneMania (93, 94), can score direct and indirect protein functional relationships using public database repositories, such as IntAct and Reactome (95, 96).”
MethodLysine acetylation targets protein complexes and co-regulates major cellular functions
Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., & Mann, M. (2009) · Science · doi:10.1126/science.1175371 · Cited by 4,040 · cited 1×
“Interestingly, multiple acetylations within other innate immunity signaling components—OAS2, TRIM25, IRAK4, and RIG-I—were identified using anti-acetyllysine antibody enrichment and MS (138).”
BackgroundA generic protein purification method for protein complex characterization and proteome exploration
Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., & Séraphin, B. (1999) · Nature Biotechnology · doi:10.1038/13732 · Cited by 2,707 · cited 1×
“Another significant advancement to increase AP specificity was the development of the tandem affinity purification (TAP) tag system, originally applied to characterizing multiprotein complexes in yeast (49) and subsequently extended to mammalian systems (50).”
MethodThe Reactome pathway knowledgebase
Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1102 · Cited by 1,889 · cited 2×
“Bioinformatic network tools, including STRING and GeneMania (93, 94), can score direct and indirect protein functional relationships using public database repositories, such as IntAct and Reactome (95, 96).”
MethodIFI16 is an innate immune sensor for intracellular DNA
Unterholzner, L., Keating, S. E., Baran, M., Horan, K. A., Jensen, S. B., Sharma, S., Sirois, C. M., Jin, T., Latz, E., Xiao, T. S., et al. (2010) · Nature Immunology · doi:10.1038/ni.1932 · Cited by 1,643
Defining the Human Deubiquitinating Enzyme Interaction Landscape
Sowa, M. E., Bennett, E. J., Gygi, S. P., & Harper, J. W. (2009) · Cell · doi:10.1016/j.cell.2009.04.042 · Cited by 1,523
The AIM2 inflammasome is essential for host defense against cytosolic bacteria and DNA viruses
Rathinam, V. A. K., Jiang, Z., Waggoner, S. N., Sharma, S., Cole, L. E., Waggoner, L., Vanaja, S. K., Monks, B. G., Ganesan, S., Latz, E., et al. (2010) · Nature Immunology · doi:10.1038/ni.1864 · Cited by 1,331
Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions
Picotti, P., & Aebersold, R. (2012) · Nature Methods · doi:10.1038/nmeth.2015 · Cited by 1,302 · cited 16×
“Altogether, these studies provide just a glimpse of the value that defining PTMs in the context of infection can provide for understanding the molecular details of viral infection.”
InfluentialInvolvement of the TIP60 Histone Acetylase Complex in DNA Repair and Apoptosis
Ikura, T., Ogryzko, V. V., Grigoriev, M., Groisman, R., Wang, J., Horikoshi, M., Scully, R., Qin, J., & Nakatani, Y. (2000) · Cell · doi:10.1016/s0092-8674(00)00051-9 · Cited by 1,029 · cited 1×
“Another significant advancement to increase AP specificity was the development of the tandem affinity purification (TAP) tag system, originally applied to characterizing multiprotein complexes in yeast (49) and subsequently extended to mammalian systems (50).”
SAINT: probabilistic scoring of affinity purification–mass spectrometry data
Choi, H., Larsen, B., Lin, Z.-Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z. S., Tyers, M., Gingras, A.-C., & Nesvizhskii, A. I. (2011) · Nature Methods · doi:10.1038/nmeth.1541 · Cited by 800 · cited 1×
“Although these tools have yet to be used routinely for virus-host AP-MS data sets, we have used the Significance Analysis of INTeractome (SAINT) scoring algorithm (90), which models protein spectral counts between experimental and control affinity purifications (Figure 2), in our study of HSV-1 pUL46 tegument protein…”
MethodProteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus.
Yao, X.-D., Freas, A., Ramirez, J., Demirev, P., & Fenselau, C. (2001) · Analytical Chemistry · doi:10.1021/ac001404c · Cited by 787 · cited 1×
“A noteworthy exception was the comparison of adenovirus subtypes using isotope-labeled (18O) water by the Fenselau laboratory (13), an early application of 18O for comparative quantitative proteomics of complex biological samples.”
BackgroundGlobal landscape of HIV–human protein complexes
Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J. R., McGovern, K. E., Clarke, S. C., Shales, M., Mercenne, G., Pache, L., Li, K., et al. (2012) · Nature · doi:10.1038/nature10719 · Cited by 731
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The IntAct molecular interaction database in 2010
Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A. T., Kerrien, S., Khadake, J., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp878 · Cited by 620 · cited 2×
“Bioinformatic network tools, including STRING and GeneMania (93, 94), can score direct and indirect protein functional relationships using public database repositories, such as IntAct and Reactome (95, 96).”
MethodMilo, R. (2013) · BioEssays · doi:10.1002/bies.201300066 · Cited by 614
Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome
Varnum, S. M., Streblow, D. N., Monroe, M. E., Smith, P., Auberry, K. J., Paša-Tolić, L., Wang, D., Camp, D. G., Rodland, K., Wiley, S., et al. (2004) · Journal of Virology · doi:10.1128/jvi.78.20.10960-10966.2004 · Cited by 598 · cited 1×
“analyses have been conducted on mammalian herpesviruses, such as human (8) and murine (5) cytomegaloviruses, herpes simplex viruses (7, 9, 15), Epstein–Barr virus (EBV) (4), and pseudorabies virus (PRV) (6).”
MethodDecoding Human Cytomegalovirus
Stern-Ginossar, N., Weisburd, B., Michalski, A., Le, V. T. K., Hein, M. Y., Huang, S.-X., Ma, M., Shen, B., Qian, S.-B., Hengel, H., et al. (2012) · Science · doi:10.1126/science.1227919 · Cited by 589
Chemistry-Based Functional Proteomics Reveals Novel Members of the Deubiquitinating Enzyme Family
Borodovsky, A., Ovaa, H., Kolli, N., Gan-Erdene, T., Wilkinson, K. D., Ploegh, H. L., & Kessler, B. M. (2002) · Chemistry & Biology · doi:10.1016/s1074-5521(02)00248-x · Cited by 588 · cited 1×
“For instance, hemagglutinin-affinity-tagged ubiquitin derivatives were developed as active site–directed probes for deubiquitinating enzymes (DUBs) (144).”
BackgroundMass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins
Wollscheid, B., Bausch-Fluck, D., Henderson, C., O'Brien, R., Bibel, M., Schiess, R., Aebersold, R., & Watts, J. D. (2009) · Nature Biotechnology · doi:10.1038/nbt.1532 · Cited by 547 · cited 1×
“To profile cell surface proteins by MS, PM enrichment by chemical derivatization–affinity purification confers reduced organelle contamination and improved detection of low-abundance membrane receptors (107, 108).”
BackgroundChertova, E., Chertov, O., Coren, L. V., Roser, J. D., Trubey, C. M., Bess, J. W., Sowder, R. C., Barsov, E., Hood, B. L., Fisher, R. J., et al. (2006) · Journal of Virology · doi:10.1128/jvi.01013-06 · Cited by 462
ViralZone: a knowledge resource to understand virus diversity
Hulo, C., de Castro, E., Masson, P., Bougueleret, L., Bairoch, A., Xenarios, I., & Le Mercier, P. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq901 · Cited by 452 · cited 2×
“ViralZone: a knowledge resource to understand virus diversity.”
MethodProteins of purified Epstein-Barr virus
Johannsen, E., Luftig, M., Chase, M. R., Weicksel, S., Cahir-McFarland, E., Illanes, D., Sarracino, D., & Kieff, E. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407320101 · Cited by 450
Orzalli, M. H., DeLuca, N. A., & Knipe, D. M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211302109 · Cited by 422
GeneMANIA Prediction Server 2013 Update
Zuberi, K., Franz, M., Rodriguez, H., Montojo, J., Lopes, C. T., Bader, G. D., & Morris, Q. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt533 · Cited by 396 · cited 1×
“Bioinformatic network tools, including STRING and GeneMania (93, 94), can score direct and indirect protein functional relationships using public database repositories, such as IntAct and Reactome (95, 96).”
MethodZhao, Y., & Jensen, O. N. (2009) · PROTEOMICS · doi:10.1002/pmic.200900398 · Cited by 384
Ebola Virus VP40 Drives the Formation of Virus-Like Filamentous Particles Along with GP
Noda, T., Sagara, H., Suzuki, E., Takada, A., Kida, H., & Kawaoka, Y. (2002) · Journal of Virology · doi:10.1128/jvi.76.10.4855-4865.2002 · Cited by 381 · cited 1×
“In Ebola virus infection, because VP40 expression alone and its transport to the plasma membrane (PM) lead to release of filamentous virus-like particles (77), Yamayoshi et al.”
BackgroundA Controlled Trial of Ganciclovir to Prevent Cytomegalovirus Disease after Heart Transplantation
Merigan, T. C., Renlund, D. G., Keay, S., Bristow, M. R., Starnes, V., O'Connell, J. B., Resta, S., Dunn, D., Gamberg, P., Ratkovec, R. M., et al. (1992) · New England Journal of Medicine · doi:10.1056/nejm199204303261803 · Cited by 376
Comprehensive Characterization of Extracellular Herpes Simplex Virus Type 1 Virions
Loret, S., Guay, G., & Lippé, R. (2008) · Journal of Virology · doi:10.1128/jvi.00904-08 · Cited by 365
Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection
Jäger, S., Kim, D. Y., Hultquist, J. F., Shindo, K., LaRue, R. S., Kwon, E., Li, M., Anderson, B. D., Yen, L., Stanley, D., et al. (2012) · Nature · doi:10.1038/nature10693 · Cited by 352
IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication
Jakobsen, M. R., Bak, R. O., Andersen, A., Berg, R. K., Jensen, S. B., Jin, T., Laustsen, A., Hansen, K., Østergaard, L., Fitzgerald, K. A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1311669110 · Cited by 344
Roger, T., Lugrin, J., Le Roy, D., Goy, G., Mombelli, M., Koessler, T., Ding, X. C., Chanson, A.-L., Reymond, M. K., Miconnet, I., et al. (2011) · Blood · doi:10.1182/blood-2010-05-284711 · Cited by 341
Cellular Proteins in Influenza Virus Particles
Shaw, M. L., Stone, K. L., Colangelo, C. M., Gulcicek, E. E., & Palese, P. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.1000085 · Cited by 324
Build, Compute, Critique, Repeat: Data Analysis with Latent Variable Models
Blei, D. (2014) · Annual Review of Statistics and Its Application · doi:10.1146/annurev-statistics-022513-115657 · Cited by 311
Li, T., Diner, B. A., Chen, J., & Cristea, I. M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1203447109 · Cited by 297
Self-citationThe functional interactome landscape of the human histone deacetylase family
Joshi, P., Greco, T. M., Guise, A. J., Luo, Y., Yu, F., Nesvizhskii, A. I., & Cristea, I. M. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.26 · Cited by 289
Self-citationJohnson, K. E., Chikoti, L., & Chandran, B. (2013) · Journal of Virology · doi:10.1128/jvi.00082-13 · Cited by 271 · cited 1×
“These results implicated an HSV-1 mechanism for antagonizing inflammasome activity, which was subsequently demonstrated (123).”
BackgroundInterrogating viral capsid assembly with ion mobility–mass spectrometry
Uetrecht, C., Barbu, I. M., Shoemaker, G. K., van Duijn, E., & Heck, A. J. R. (2011) · Nature Chemistry · doi:10.1038/nchem.947 · Cited by 267 · cited 1×
“An emerging biomolecular technique, termed native MS, enables the detection of complexes of several million daltons (23, 24).”
MethodChung, C.-S., Chen, C.-H., Ho, M.-Y., Huang, C.-Y., Liao, C.-L., & Chang, W. (2006) · Journal of Virology · doi:10.1128/jvi.80.5.2127-2140.2006 · Cited by 253
Fluorescent Proteins as Proteomic Probes
Cristea, I. M., Williams, R., Chait, B. T., & Rout, M. P. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500227-mcp200 · Cited by 251 · cited 2×
“The GFP tag afforded the temporal examination of protein localization and interactions (37) at a given moment in infected cells (38, 39).”
BackgroundSelf-citationTaylor, T. J., & Knipe, D. M. (2004) · Journal of Virology · doi:10.1128/jvi.78.11.5856-5866.2004 · Cited by 229 · cited 1×
“For example, the Knipe laboratory (34, 35) used AP-MS to study virus-host protein complexes containing the immediate-early proteins ICP27 or ICP8 at an early stage of herpes simplex virus 1 (HSV-1) infection in human Hep2 cells.”
MethodHuman Cytomegalovirus Tegument Protein pUL83 Inhibits IFI16-Mediated DNA Sensing for Immune Evasion
Li, T., Chen, J., & Cristea, I. M. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.10.007 · Cited by 226
Self-citationProbabilistic assembly of human protein interaction networks from label-free quantitative proteomics
Sardiu, M. E., Cai, Y., Jin, J., Swanson, S. K., Conaway, R. C., Conaway, J. W., Florens, L., & Washburn, M. P. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706983105 · Cited by 226
Role for Influenza Virus Envelope Cholesterol in Virus Entry and Infection
Sun, X., & Whittaker, G. R. (2003) · Journal of Virology · doi:10.1128/jvi.77.23.12543-12551.2003 · Cited by 224
Analyzing Protein–Protein Interaction Networks
Koh, G. C. K. W., Porras, P., Aranda, B., Hermjakob, H., & Orchard, S. E. (2012) · Journal of Proteome Research · doi:10.1021/pr201211w · Cited by 221
Mayer, D., Molawi, K., Martínez-Sobrido, L., Ghanem, A., Thomas, S., Baginsky, S., Grossmann, J., García-Sastre, A., & Schwemmle, M. (2007) · Journal of Proteome Research · doi:10.1021/pr060432u · Cited by 216 · cited 1×
“AP-MS has been employed to determine the identity of such host proteins, for instance, proteins in replication complexes at viral promoters in herpesviruses (67–69), viral polymerases of influenza virus (53), and preintegration complexes in HIV-1 (70).”
MethodVirusMINT: a viral protein interaction database
Chatr-aryamontri, A., Ceol, A., Peluso, D., Nardozza, A., Panni, S., Sacco, F., Tinti, M., Smolyar, A., Castagnoli, L., Vidal, M., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn739 · Cited by 213 · cited 2×
“VirusMINT: a viral protein interaction database.”
MethodThe cancer cell secretome: A good source for discovering biomarkers?
Pavlou, M. P., & Diamandis, E. P. (2010) · Journal of Proteomics · doi:10.1016/j.jprot.2010.04.003 · Cited by 200 · cited 1×
“Importantly, approximately 10% of the human genome open reading frames encode proteins that are secreted (117).”
BackgroundInterferons: Signaling, antiviral and viral evasion
Bonjardim, C. A., Ferreira, P. C. P., & Kroon, E. G. (2009) · Immunology Letters · doi:10.1016/j.imlet.2008.11.002 · Cited by 196 · cited 1×
“This is critical from the host perspective, as the virus-induced secretion of signaling factors mediates the onset of innate and adaptive immunity (116).”
BackgroundYoun, S., Li, T., McCune, B. T., Edeling, M. A., Fremont, D. H., Cristea, I. M., & Diamond, M. (2012) · Journal of Virology · doi:10.1128/jvi.00157-12 · Cited by 196 · cited 1×
“The power of these approaches for the discovery and functional characterization of various virus-host interactions (33) was demonstrated in our studies of diverse viruses, including Sindbis virus (38, 40), human cytomegalovirus (HCMV) (41–44), HSV-1 (45), PRV (46, 47), and West Nile virus (48).”
BackgroundSelf-citationMoorman, N. J., Cristea, I. M., Terhune, S. S., Rout, M. P., Chait, B. T., & Shenk, T. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.03.002 · Cited by 194
Self-citationTracking and Elucidating Alphavirus-Host Protein Interactions
Cristea, I. M., Carroll, J.-W. N., Rout, M. P., Rice, C. M., Chait, B. T., & MacDonald, M. R. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m603980200 · Cited by 192
Self-citationOvaa, H., Kessler, B. M., Rolén, U., Galardy, P. J., Ploegh, H. L., & Masucci, M. G. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308411100 · Cited by 190 · cited 1×
“By using AP of active DUBs and MS analysis, the activities of several DUBs were found to be strongly upregulated in EBV-infected lymphocytes (145).”
MethodHalili, M. A., Andrews, M. R., Labzin, L. I., Schroder, K., Matthias, G., Cao, C., Lovelace, E., Reid, R. C., Le, G. T., Hume, D. A., et al. (2010) · Journal of Leukocyte Biology · doi:10.1189/jlb.0509363 · Cited by 186
Greninger, A., Knudsen, G., Betegon, M., Burlingame, A., & Derisi, J. (2012) · Journal of Virology · doi:10.1128/jvi.06778-11 · Cited by 180
Role for Human Immunodeficiency Virus Type 1 Membrane Cholesterol in Viral Internalization
Guyader, M., Kiyokawa, E., Abrami, L., Turelli, P., & Trono, D. (2002) · Journal of Virology · doi:10.1128/jvi.76.20.10356-10364.2002 · Cited by 170
Formation of nsP3-Specific Protein Complexes during Sindbis Virus Replication
Frolova, E., Gorchakov, R., Garmashova, N., Atasheva, S., Vergara, L., & Frolov, I. (2006) · Journal of Virology · doi:10.1128/jvi.80.8.4122-4134.2006 · Cited by 160 · cited 1×
“The GFP tag afforded the temporal examination of protein localization and interactions (37) at a given moment in infected cells (38, 39).”
BackgroundCristea, I. M., Moorman, N. J., Terhune, S. S., Cuevas, C. D., O'Keefe, E. S., Rout, M. P., Chait, B. T., & Shenk, T. (2010) · Journal of Virology · doi:10.1128/jvi.00139-10 · Cited by 155 · cited 14×
“IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication.”
BackgroundInfluentialSelf-citationMapping the Phosphoproteome of Influenza A and B Viruses by Mass Spectrometry
Hutchinson, E. C., Denham, E. M., Thomas, B., Trudgian, D. C., Hester, S. S., Ridlova, G., York, A., Turrell, L., & Fodor, E. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002993 · Cited by 151 · cited 2×
“Recently, TiO2 phospho-enrichment was successfully applied for mapping the phosphoproteome of influenza A–infected human cell lines (131).”
BackgroundRaghu, H., Sharma-Walia, N., Veettil, M. V., Sadagopan, S., & Chandran, B. (2009) · Journal of Virology · doi:10.1128/jvi.02498-08 · Cited by 149 · cited 1×
“For example, after initial binding to cell surface receptors, Kaposi sarcoma–associated herpesvirus (KSHV) is rapidly translocated in a c-Cbldependent manner to lipid rafts and internalized into macropinosomes (65).”
BackgroundIdentification of Proteins Associated with Murine Cytomegalovirus Virions
Kattenhorn, L. M., Mills, R., Wagner, M., Lomsadze, A., Makeev, V., Borodovsky, M., Ploegh, H. L., & Kessler, B. M. (2004) · Journal of Virology · doi:10.1128/jvi.78.20.11187-11197.2004 · Cited by 147
Terrand, J., Bruban, V., Zhou, L., Gong, W., El Asmar, Z., May, P., Zurhove, K., Haffner, P., Philippe, C., Woldt, E., et al. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m806538200 · Cited by 143 · cited 2×
“analyses have been conducted on mammalian herpesviruses, such as human (8) and murine (5) cytomegaloviruses, herpes simplex viruses (7, 9, 15), Epstein–Barr virus (EBV) (4), and pseudorabies virus (PRV) (6).”
BackgroundMethodNorwalk Virus Assembly and Stability Monitored by Mass Spectrometry
Shoemaker, G. K., van Duijn, E., Crawford, S. E., Uetrecht, C., Baclayon, M., Roos, W. H., Wuite, G. J. L., Estes, M. K., Prasad, B. V. V., & Heck, A. J. R. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900620-mcp200 · Cited by 140 · cited 1×
“As many capsid proteins self-assemble in vitro, native ion mobility MS can monitor the dynamics of capsid morphology and stability as a function of pH and ionic strength (28, 29).”
BackgroundVirion-associated cholesterol is critical for the maintenance of HIV-1 structure and infectivity
Campbell, S. M., Crowe, S. M., & Mak, J. (2002) · AIDS · doi:10.1097/00002030-200211220-00004 · Cited by 139
Lietzén, N., Öhman, T., Rintahaka, J., Julkunen, I., Aittokallio, T., Matikainen, S., & Nyman, T. A. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1001340 · Cited by 137 · cited 2×
“Secreted cathepsin protease activity was shown to be required for both inflammasome stimulation and apoptosis in response to influenza (120).”
BackgroundWeekes, M. P., Tan, S. Y. L., Poole, E., Talbot, S., Antrobus, R., Smith, D. L., Montag, C., Gygi, S. P., Sinclair, J. H., & Lehner, P. J. (2013) · Science · doi:10.1126/science.1235047 · Cited by 131 · cited 1×
“More recently, during latent HCMV infection, the degradation of the PM drug transporter MRP1 by the viral protein pUL138 was discovered by SILAC-MS after PM enrichment (110).”
MethodI-DIRT, A General Method for Distinguishing between Specific and Nonspecific Protein Interactions
Tackett, A. J., DeGrasse, J. A., Sekedat, M. D., Oeffinger, M., Rout, M. P., & Chait, B. T. (2005) · Journal of Proteome Research · doi:10.1021/pr050225e · Cited by 131 · cited 1×
“To address this issue, an approach using metabolic labeling with stable isotopes was developed (I-DIRT; see Figure 2) (91, 92).”
MethodProbing the biophysical interplay between a viral genome and its capsid
Snijder, J., Uetrecht, C., Rose, R. J., Sanchez-Eugenia, R., Marti, G. A., Agirre, J., Guérin, D. M. A., Wuite, G. J. L., Heck, A. J. R., & Roos, W. H. (2013) · Nature Chemistry · doi:10.1038/nchem.1627 · Cited by 127
Proteomics Analysis of the Nucleolus in Adenovirus-infected Cells
Lam, Y.-W., Evans, V. C., Heesom, K., Lamond, A., & Matthews, D. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900338-mcp200 · Cited by 127 · cited 1×
“Other noteworthy studies have coupled nuclear-cytoplasmic biochemical fractionation with quantitative MS to delineate modulation of compartment-specific pathway functions during HSV-1 (103), influenza A (104), adenovirus (105), and respiratory syncytial virus (106) infection.”
BackgroundStreblow, D. N., Dumortier, J., Moses, A. V., Orloff, S. L., & Nelson, J. A. (2008) · Current Topics in Microbiology and Immunology · doi:10.1007/978-3-540-77349-8_22 · Cited by 125 · cited 1×
“Considering recent evidence implicating angiogenesis in HCMV-associated vasculopathies (128), Dumortier et al.”
BackgroundNaji, S., Ambrus, G., Cimermancic, P., Reyes, J. R., Johnson, J. R., Filbrandt, R., Huber, M. D., Vesely, P., Krogan, N., Yates, J., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.015313 · Cited by 124
Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing
Dumortier, J., Streblow, D. N., Moses, A. V., Jacobs, J. M., Kreklywich, C. N., Camp, D., Smith, R. D., Orloff, S. L., & Nelson, J. A. (2008) · Journal of Virology · doi:10.1128/jvi.00502-08 · Cited by 123 · cited 23×
“Recently, MS and ribosome occupancy profiling were used to identify and temporally resolve unique, previously unreported HCMV polypeptides (>50) and transcripts (>550) during infection (101).”
BackgroundInfluentialRoby, C., & Gibson, W. (1986) · Journal of Virology · doi:10.1128/jvi.59.3.714-727.1986 · Cited by 119 · cited 1×
“For instance, the HCMV immunosuppressant protein pUL83 (73) was known for several decades to be heavily phosphorylated (132); however, the sites and functions of these phosphorylations remained unclear.”
BackgroundCristea, I., Rozjabek, H., Molloy, K., Karki, S., White, L. L., Rice, C., Rout, M., Chait, B., & MacDonald, M. (2010) · Journal of Virology · doi:10.1128/jvi.01983-09 · Cited by 119 · cited 1×
“The power of these approaches for the discovery and functional characterization of various virus-host interactions (33) was demonstrated in our studies of diverse viruses, including Sindbis virus (38, 40), human cytomegalovirus (HCMV) (41–44), HSV-1 (45), PRV (46, 47), and West Nile virus (48).”
BackgroundSelf-citationAtomic Force Microscopy in Imaging of Viruses and Virus-Infected Cells
Kuznetsov, Y., & McPherson, A. (2011) · Microbiology and Molecular Reviews · doi:10.1128/mmbr.00041-10 · Cited by 117
Radhakrishnan, A., Yeo, D., Brown, G., Myaing, M. Z., Iyer, L. R., Fleck, R., Tan, B.-H., Aitken, J., Sanmun, D., Tang, K., et al. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.001651 · Cited by 114
Chakraborty, S., Veettil, M. V., Bottero, V., & Chandran, B. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1119592109 · Cited by 105
Miteva, Y. V., Budayeva, H. G., & Cristea, I. M. (2013) · Analytical Chemistry · doi:10.1021/ac3033257 · Cited by 105
Self-citationPox proteomics: mass spectrometry analysis and identification of Vaccinia virion proteins
Yoder, J. D., Chen, T. S., Gagnier, C. R., Vemulapalli, S., Maier, C. S., & Hruby, D. E. (2006) · Virology Journal · doi:10.1186/1743-422x-3-10 · Cited by 104
Manes, N. P., Estep, R. D., Mottaz, H. M., Moore, R. J., Clauss, T. R. W., Monroe, M. E., Du, X., Adkins, J. N., Wong, S. W., & Smith, R. D. (2008) · Journal of Proteome Research · doi:10.1021/pr070432+ · Cited by 103
Kinesin-3 Mediates Axonal Sorting and Directional Transport of Alphaherpesvirus Particles in Neurons
Kramer, T., Greco, T. M., Taylor, M. P., Ambrosini, A. E., Cristea, I. M., & Enquist, L. W. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.10.013 · Cited by 102 · cited 2×
“F or p er so na l u se o nl y. VI01CH28-Cristea ARI 20 August 2014 13:53 analyses have been conducted on mammalian herpesviruses, such as human (8) and murine (5) cytomegaloviruses, herpes simplex viruses (7, 9, 15), Epstein–Barr virus (EBV) (4), and pseudorabies virus (PRV) (6).”
BackgroundSelf-citationEbola Virus Matrix Protein VP40 Uses the COPII Transport System for Its Intracellular Transport
Yamayoshi, S., Noda, T., Ebihara, H., Goto, H., Morikawa, Y., Lukashevich, I. S., Neumann, G., Feldmann, H., & Kawaoka, Y. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.02.001 · Cited by 100 · cited 2×
“The COPII complex component Sec24C was identified and validated by colocalization and reciprocal isolations, and its contribution to virus-like particle formation was demonstrated by knockdown studies (54).”
BackgroundMoorman, N. J., Sharon-Friling, R., Shenk, T., & Cristea, I. M. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900485-mcp200 · Cited by 97 · cited 2×
“To investigate the spatial-temporal relationship of virion components during HCMV virion assembly, we combined AP-MS, molecular virology, and confocal microscopy (42).”
BackgroundMethodSelf-citationMukerji, J., Olivieri, K. C., Misra, V., Agopian, K. A., & Gabuzda, D. H. (2012) · Retrovirology · doi:10.1186/1742-4690-9-33 · Cited by 97
Proteomic Characterization of Pseudorabies Virus Extracellular Virions
Kramer, T., Greco, T. M., Enquist, L. W., & Cristea, I. M. (2011) · Journal of Virology · doi:10.1128/jvi.02253-10 · Cited by 96
Self-citationKratchmarov, R., Kramer, T., Greco, T., Taylor, M. P., Ch'ng, T. H., Cristea, I., & Enquist, L. (2013) · Journal of Virology · doi:10.1128/jvi.01317-13 · Cited by 96 · cited 2×
“F or p er so na l u se o nl y. VI01CH28-Cristea ARI 20 August 2014 13:53 analyses have been conducted on mammalian herpesviruses, such as human (8) and murine (5) cytomegaloviruses, herpes simplex viruses (7, 9, 15), Epstein–Barr virus (EBV) (4), and pseudorabies virus (PRV) (6).”
BackgroundSelf-citationNesvizhskii, A. I. (2012) · PROTEOMICS · doi:10.1002/pmic.201100537 · Cited by 95
Emmott, E., Munday, D., Bickerton, E., Britton, P., Rodgers, M. A., Whitehouse, A., Zhou, E.-M., & Hiscox, J. A. (2013) · Journal of Virology · doi:10.1128/jvi.00321-13 · Cited by 93
Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus
Munday, D. C., Emmott, E., Surtees, R., Lardeau, C.-H., Wu, W., Duprex, W. P., Dove, B. K., Barr, J. N., & Hiscox, J. A. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.001859 · Cited by 92 · cited 1×
“Other noteworthy studies have coupled nuclear-cytoplasmic biochemical fractionation with quantitative MS to delineate modulation of compartment-specific pathway functions during HSV-1 (103), influenza A (104), adenovirus (105), and respiratory syncytial virus (106) infection.”
BackgroundExpression Profiling of Lymphocyte Plasma Membrane Proteins
Peirce, M. J., Wait, R., Begum, S., Saklatvala, J., & Cope, A. P. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m300064-mcp200 · Cited by 92 · cited 1×
“To profile cell surface proteins by MS, PM enrichment by chemical derivatization–affinity purification confers reduced organelle contamination and improved detection of low-abundance membrane receptors (107, 108).”
BackgroundHistone Deacetylase Inhibitors Impair Antibacterial Defenses of Macrophages
Mombelli, M., Lugrin, J., Rubino, I., Chanson, A.-L., Giddey, M., Calandra, T., & Roger, T. (2011) · The Journal of Infectious Diseases · doi:10.1093/infdis/jir553 · Cited by 89
Investigating the human immunodeficiency virus type 1-infected monocyte-derived macrophage secretome
Ciborowski, P., Kadiu, I., Rozek, W., Smith, L., Bernhardt, K., Fladseth, M., Ricardo-Dukelow, M., & Gendelman, H. E. (2007) · Virology · doi:10.1016/j.virol.2007.01.013 · Cited by 87 · cited 1×
“Additionally, other MS-based studies have investigated the mechanisms of HIV-associated neurodegeneration through secretome profiling of HIV-infected phagocytes (118, 119).”
BackgroundGPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data
Fahey, M. E., Bennett, M. J., Mahon, C., Jäger, S., Pache, L., Kumar, D., Shapiro, A., Rao, K., Chanda, S. K., Craik, C. S., et al. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-298 · Cited by 87 · cited 1×
“Virus-centric repositories have also been established, including ViralZone (97) and VirusMINT (98), as well as GPS-Prot, which focuses on HIV-host interactions (99).”
MethodHarris, D., Zhang, Z., Chaubey, B., & Pandey, V. N. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500429-mcp200 · Cited by 87 · cited 1×
“For example, the first RNA-based AP-MS studies investigated cellular factors associated with the 3′ untranslated region of hepatitis C virus RNA using biotinylated oligonucleotides complementary to the vRNA (81, 82).”
MethodTerry, L. J., Vastag, L., Rabinowitz, J. D., & Shenk, T. (2012) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1200494109 · Cited by 87 · cited 1×
“The authors demonstrated that drug inhibition of AMPK, a kinase found to be upregulated during infection, decreased virus growth, in agreement with a previous RNA interference screen of kinases during HCMV infection (143).”
ResultAlexander, C. G., Jürgens, M. C., Shepherd, D. A., Freund, S. M. V., Ashcroft, A. E., & Ferguson, N. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1308846110 · Cited by 85
Gudleski-O'Regan, N., Greco, T. M., Cristea, I. M., & Shenk, T. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.05.012 · Cited by 84 · cited 1×
“Our lab used affinity isolation and label-free MS quantification (Figure 2) to investigate HCMV-induced PM changes across productive immediate-early, early, and late stages of infection (111).”
MethodSelf-citationEmmott, E., Wise, H., Loucaides, E. M., Matthews, D., Digard, P., & Hiscox, J. (2010) · Journal of Proteome Research · doi:10.1021/pr100593g · Cited by 84 · cited 1×
“Other noteworthy studies have coupled nuclear-cytoplasmic biochemical fractionation with quantitative MS to delineate modulation of compartment-specific pathway functions during HSV-1 (103), influenza A (104), adenovirus (105), and respiratory syncytial virus (106) infection.”
BackgroundFontaine-Rodriguez, E. C., Taylor, T. J., Olesky, M., & Knipe, D. M. (2004) · Virology · doi:10.1016/j.virol.2004.10.002 · Cited by 83 · cited 1×
“For example, the Knipe laboratory (34, 35) used AP-MS to study virus-host protein complexes containing the immediate-early proteins ICP27 or ICP8 at an early stage of herpes simplex virus 1 (HSV-1) infection in human Hep2 cells.”
MethodVliegen, I., Duijvestijn, A., Grauls, G., Herngreen, S., Bruggeman, C., & Stassen, F. (2004) · Microbes and Infection · doi:10.1016/j.micinf.2003.09.024 · Cited by 80
Identification of RNA-Protein Interaction Networks Involved in the Norovirus Life Cycle
Vashist, S., Urena, L., Chaudhry, Y., & Goodfellow, I. (2012) · Journal of Virology · doi:10.1128/jvi.00432-12 · Cited by 78 · cited 1×
“Although protein AP can target host proteins to identify unknown effectors of viral transcription, an alternative approach is to target the viral genome itself (78, 79).”
BackgroundSaphire, A. C. S., Gallay, P. A., & Bark, S. J. (2006) · Journal of Proteome Research · doi:10.1021/pr050276b · Cited by 77
Pollock, S., Nichita, N. B., Böhmer, A., Radulescu, C., Dwek, R. A., & Zitzmann, N. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1009445107 · Cited by 76
Galán, C., Sola, I., Nogales, A., Thomas, B., Akoulitchev, A., Enjuanes, L., & Almazán, F. (2009) · Virology · doi:10.1016/j.virol.2009.06.006 · Cited by 76 · cited 1×
“AP-MS approaches have been adapted to identify proteins that bind viral RNA (vRNA), most often to the 5′ or 3′ untranslated regions thought to function in the initial stages of vRNA replication and translation (80).”
MethodHerpes Simplex Virus 1 ICP4 Forms Complexes with TFIID and Mediator in Virus-Infected Cells
Lester, J. T., & DeLuca, N. A. (2011) · Journal of Virology · doi:10.1128/jvi.00385-11 · Cited by 74
Identification of Structural Proteins of Channel Catfish Virus by Mass Spectrometry
Davison, A. J., & Davison, M. D. (1995) · Virology · doi:10.1006/viro.1995.1026 · Cited by 73 · cited 1×
“In a pioneering study, MS analysis of purified channel catfish virus virions provided amino acid sequence data to support the common evolutionary origin of this virus with other herpesviruses (14), a hypothesis previously based only on capsid and virion morphology.”
MethodIdentifying the Membrane Proteome of HIV-1 Latently Infected Cells
Berro, R., de la Fuente, C., Klase, Z., Kehn, K., Parvin, L., Pumfery, A., Agbottah, E., Vertes, A., Nekhai, S., & Kashanchi, F. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m606324200 · Cited by 72 · cited 1×
“(109) used cell surface biotinylation coupled with streptavidin affinity chromatography to investigate PM changes in HIV-1 latently infected lymphocytes.”
MethodSpurgers, K. B., Alefantis, T., Peyser, B. D., Ruthel, G. T., Bergeron, A. A., Costantino, J. A., Enterlein, S., Kota, K. P., Boltz, R. C. D., Aman, M. J., et al. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.003418 · Cited by 71 · cited 2×
“Technological advances in MS instrumentation have improved the sensitivity of detection, providing near-complete proteome coverage and access to low-abundance virion components (6, 7, 16).”
BackgroundTerhune, S. S., Moorman, N. J., Cristea, I. M., Savaryn, J. P., Cuevas-Bennett, C., Rout, M. P., Chait, B. T., & Shenk, T. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000965 · Cited by 70
Self-citationChavez, J. D., Cilia, M., Weisbrod, C. R., Ju, H.-J., Eng, J. K., Gray, S. M., & Bruce, J. E. (2012) · Journal of Proteome Research · doi:10.1021/pr300041t · Cited by 69
Tingting, P., Caiyun, F., Zhigang, Y., Pengyuan, Y., & Zhenghong, Y. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.06.144 · Cited by 68 · cited 1×
“For example, the first RNA-based AP-MS studies investigated cellular factors associated with the 3′ untranslated region of hepatitis C virus RNA using biotinylated oligonucleotides complementary to the vRNA (81, 82).”
MethodStegen, C., Yakova, Y., Henaff, D., Nadjar, J., Duron, J., & Lippé, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053276 · Cited by 66 · cited 1×
“Current approaches involve determining proteinase sensitivity (6, 9) and/or performing functional RNA interference–based virus propagation assays (16, 22).”
BackgroundBuilding Protein-Protein Interaction Networks with Proteomics and Informatics Tools
Sardiu, M. E., & Washburn, M. P. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.r110.174052 · Cited by 64
Structure of complex viruses and virus-infected cells by electron cryo tomography.
Grünewald, K., & Cyrklaff, M. (2006) · Current Opinion in Microbiology · doi:10.1016/j.mib.2006.06.016 · Cited by 64
Linde, M. E., Colquhoun, D. R., Ubaida Mohien, C., Kole, T., Aquino, V., Cotter, R., Edwards, N., Hildreth, J. E. K., & Graham, D. R. (2013) · Journal of Proteome Research · doi:10.1021/pr300918r · Cited by 60
Gao, Y., Colletti, K., & Pari, G. S. (2008) · Journal of Virology · doi:10.1128/jvi.01559-07 · Cited by 58
Gabaev, I., Steinbrück, L., Pokoyski, C., Pich, A., Stanton, R. J., Schwinzer, R., Schulz, T. F., Jacobs, R., Messerle, M., & Kay-Fedorov, P. C. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002432 · Cited by 58 · cited 2×
“(66) identified the HCMV pUL11—a glycoprotein expressed at the cell surface—as an interaction partner and ligand of the receptor tyrosine phosphatase CD45.”
BackgroundWagenaar, T. R., & Moss, B. (2007) · Journal of Virology · doi:10.1128/jvi.00274-07 · Cited by 56 · cited 1×
“For example, a streptavidin- and calmodulin-binding TAP system was used to isolate the vaccinia virus A56 and K2 proteins, which localize to the cell surface and are required for interaction with the entry fusion complex (51).”
MethodRaghavendra, N. K., Shkriabai, N., Graham, R. L., Hess, S., Kvaratskhelia, M., & Wu, L. (2010) · Retrovirology · doi:10.1186/1742-4690-7-66 · Cited by 56 · cited 12×
“IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication.”
MethodInfluentialTuma, R., Coward, L. U., Kirk, M. C., Barnes, S., & Prevelige, P. E. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4383 · Cited by 53 · cited 1×
“In addition to native ion mobility MS, hydrogen/deuterium (H/D) exchange MS has been used as a complementary strategy for characterizing the assembly of viral capsids (30).”
MethodEWI-2 Association with α-Actinin Regulates T Cell Immune Synapses and HIV Viral Infection
Gordón‐Alonso, M., Sala-Valdés, M., Rocha‐Perugini, V., et al. (2012) · The Journal of Immunology · doi:10.4049/jimmunol.1103708 · Cited by 51
Hydrogen/Deuterium Exchange Analysis of HIV-1 Capsid Assembly and Maturation
Monroe, E. B., Kang, S., Kyere, S. K., Li, R., & Prevelige, P. E. (2010) · Structure · doi:10.1016/j.str.2010.08.016 · Cited by 49 · cited 1×
“For example, the Prevelige laboratory (31) compared H/D exchange rates for immature, mature, and Gag/CA5 mutant capsids.”
BackgroundPhosphorylation Site Mutations Affect Herpes Simplex Virus Type 1 ICP0 Function
Davido, D. J., von Zagorski, W. F., Lane, W. S., & Schaffer, P. A. (2005) · Journal of Virology · doi:10.1128/jvi.79.2.1232-1243.2005 · Cited by 49 · cited 1×
“Similarly, several identified phosphorylations within the multifunctional HSV-1 protein ICP0 were found to modulate its ubiquitin ligase, transactivation, and localization activities using an AP-MS/mutagenesis approach (133).”
MethodGlobal Secretome Characterization of Herpes Simplex Virus 1-Infected Human Primary Macrophages
Miettinen, J. J., Matikainen, S., & Nyman, T. A. (2012) · Journal of Virology · doi:10.1128/jvi.01545-12 · Cited by 48
Vliegen, I., Herngreen, S. B., Grauls, G. E. L. M., Bruggeman, C. A., & Stassen, F. R. M. (2005) · Atherosclerosis · doi:10.1016/j.atherosclerosis.2004.12.035 · Cited by 46
Lenarcic, E. M., Landry, D. M., Greco, T., Cristea, I., & Thompson, S. (2013) · Journal of Virology · doi:10.1128/jvi.00950-13 · Cited by 45 · cited 1×
“I-DIRT: a metabolic labeling AP-MS method for distinguishing specific from nonspecific interactions and relative interaction stability which is ideal for studying vRNA-protein associations directly from infected cells (84).”
MethodSelf-citationPhysical analysis of virus particles using electrospray differential mobility analysis
Pease, L. F. (2012) · Trends in Biotechnology · doi:10.1016/j.tibtech.2011.11.004 · Cited by 43 · cited 1×
“An emerging biomolecular technique, termed native MS, enables the detection of complexes of several million daltons (23, 24).”
MethodHistone Deacetylases in Herpesvirus Replication and Virus-Stimulated Host Defense
Guise, A., Budayeva, H., Diner, B., & Cristea, I. (2013) · Viruses · doi:10.3390/v5071607 · Cited by 43
Self-citationHutterer, C., Wandinger, S. K., Wagner, S., Müller, R., Stamminger, T., Zeitträger, I., Godl, K., Baumgartner, R., Strobl, S., & Marschall, M. (2013) · Antiviral Research · doi:10.1016/j.antiviral.2013.04.017 · Cited by 43 · cited 1×
“Taking advantage of this concept, metabolic labeling was effectively coupled with AP of cellular kinases via immobilized inhibitors to quantify cellular kinome changes during HCMV infection (142).”
MethodVogels, M. W., van Balkom, B. V., Kaloyanova, D., Batenburg, J. J., Heck, A. J., Helms, J. B., Rottier, P. J. M., & de Haan, C. D. (2011) · doi:10.1002/prca.201190043 · Cited by 43 · cited 1×
“For instance, metabolic labeling using stable isotope labeling in cell culture (SILAC; see Figure 2) was employed to quantify virus-induced expression changes in Golgi-enriched fractions from mouse hepatitis virus (MHV)infected hepatocytes (102).”
MethodBell, C., Desjardins, M., Thibault, P., & Radtke, K. (2013) · Journal of Proteome Research · doi:10.1021/pr301157j · Cited by 42 · cited 1×
“(129) discovered 95 phosphorylations and 10 ubiquitinations within HSV-1 proteins enriched for cellular trafficking and immune evasion functions.”
BackgroundVogels, M. W., van Balkom, B. W. M., Kaloyanova, D. V., Batenburg, J. J., Heck, A. J., Helms, J. B., Rottier, P. J. M., & de Haan, C. A. M. (2011) · PROTEOMICS · doi:10.1002/pmic.201000309 · Cited by 40
Global analysis of modifications of the human BK virus structural proteins by LC-MS/MS.
Fang, C.-Y., Chen, H.-Y., Wang, M.-L., Chen, P.-L., Chang, C.-F., Chen, L.-S., Shen, C.-H., Ou, W.-C., Tsai, M., Hsu, P.-H., et al. (2010) · Virology · doi:10.1016/j.virol.2010.03.029 · Cited by 40 · cited 1×
“In addition to studying intracellular viral PTMs, several studies have profiled modifications within purified mature virions (6, 131, 134, 135).”
BackgroundTanaka, M., Sata, T., & Kawaguchi, Y. (2008) · Virology Journal · doi:10.1186/1743-422x-5-125 · Cited by 39
Tran, K., Kamil, J. P., Coen, D., & Spector, D. (2010) · Journal of Virology · doi:10.1128/jvi.01260-10 · Cited by 39
Lin, A. E., Greco, T. M., Döhner, K., Sodeik, B., & Cristea, I. M. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.030866 · Cited by 38 · cited 14×
“For example, Bell et al. (129) discovered 95 phosphorylations and 10 ubiquitinations within HSV-1 proteins enriched for cellular trafficking and immune evasion functions.”
BackgroundMethodInfluentialSelf-citationVirus-host protein interactions in RNA viruses.
Vidalain, P.-O., & Tangy, F. (2010) · Microbes and infection · doi:10.1016/j.micinf.2010.09.001 · Cited by 37 · cited 1×
“Although protein AP can target host proteins to identify unknown effectors of viral transcription, an alternative approach is to target the viral genome itself (78, 79).”
BackgroundCiborowski, P., Enose, Y., Mack, A., Fladseth, M., & Gendelman, H. (2004) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2004.08.033 · Cited by 36 · cited 1×
“Additionally, other MS-based studies have investigated the mechanisms of HIV-associated neurodegeneration through secretome profiling of HIV-infected phagocytes (118, 119).”
BackgroundUpadhyay, A., Dixit, U., Manvar, D., Chaturvedi, N., & Pandey, V. N. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.017020 · Cited by 36
Gingras, A.-C., & Raught, B. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.03.065 · Cited by 34 · cited 1×
“Future AP-MS studies will benefit from increased use of quantitative MS (100), particularly for determining complex stability and absolute abundances within viral complexes.”
BackgroundKagele, D., Rossetto, C. C., Tarrant, M. T., & Pari, G. S. (2012) · Virology · doi:10.1016/j.virol.2011.12.010 · Cited by 32
Mouse cytomegalovirus egress protein pM50 interacts with cellular endophilin‐A2
Lemnitzer, F., Raschbichler, V., Kolodziejczak, D., Israel, L., Imhof, A., Bailer, S., Koszinowski, U., & Ruzsics, Z. (2013) · Cellular Microbiology · doi:10.1111/cmi.12080 · Cited by 29
Vörös, J., Urbanek, A., Rautureau, G. J. P., O'Connor, M., Fisher, H. C., Ashcroft, A. E., & Ferguson, N. (2014) · Journal of Virology · doi:10.1128/jvi.02575-13 · Cited by 27
Post translational modifications in adenovirus type 2
Bergström Lind, S., Artemenko, K. A., Elfineh, L., Zhao, Y., Bergquist, J., & Pettersson, U. (2013) · Virology · doi:10.1016/j.virol.2013.08.033 · Cited by 26
Smirnova, E., Collingwood, T., Bisbal, C., Tsygankova, O., Bogush, M., Meinkoth, J., Henderson, E., Annan, R., & Tsygankov, A. (2008) · Virology · doi:10.1016/j.virol.2007.10.012 · Cited by 26
A proteomic study of TAR-RNA binding protein (TRBP)-associated factors
Chi, Y., Semmes, O., & Jeang, K. (2011) · Cell & Bioscience · doi:10.1186/2045-3701-1-9 · Cited by 26
Shepherd, D. A., Holmes, K., Rowlands, D. J., Stonehouse, N. J., & Ashcroft, A. E. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2013.07.028 · Cited by 25
Proteomic Characterization of Murid Herpesvirus 4 Extracellular Virions
Vidick, S., Leroy, B., Palmeira, L., Machiels, B., Mast, J., François, S., Wattiez, R., Vanderplasschen, A., & Gillet, L. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083842 · Cited by 24 · cited 2×
“analyses have been conducted on mammalian herpesviruses, such as human (8) and murine (5) cytomegaloviruses, herpes simplex viruses (7, 9, 15), Epstein–Barr virus (EBV) (4), and pseudorabies virus (PRV) (6).”
BackgroundMethodHepatitis B virus core interacts with the host cell nucleolar protein, nucleophosmin 1
Lee, S.-J., Shim, H., Hsieh, A., Min, J.-Y., & Jung, G. (2009) · Journal of Microbiology · doi:10.1007/s12275-009-2720-z · Cited by 21
Santamaría, E., Mora, M. I., Potel, C., Fernández‐Irigoyen, J., Carro-Roldán, E., Hernández-Alcoceba, R., Prìeto, J., Epstein, A. L., & Corrales, F. J. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800202-mcp200 · Cited by 21 · cited 14×
“For example, Bell et al. (129) discovered 95 phosphorylations and 10 ubiquitinations within HSV-1 proteins enriched for cellular trafficking and immune evasion functions.”
BackgroundInfluentialDiscovery of Host–Viral Protein Complexes During Infection
Rowles, D. L., Terhune, S. S., & Cristea, I. M. (2013) · Methods in Molecular Biology · doi:10.1007/978-1-62703-601-6_4 · Cited by 15 · cited 2×
“The power of these approaches for the discovery and functional characterization of various virus-host interactions (33) was demonstrated in our studies of diverse viruses, including Sindbis virus (38, 40), human cytomegalovirus (HCMV) (41–44), HSV-1 (45), PRV (46, 47), and West Nile virus (48).”
BackgroundSelf-citation
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AAV-Mediated Gene Therapy for Research and Therapeutic Purposes
Samulski, R. J., & Muzyczka, N. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085355 · Cited by 606
Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry
Verbeeck, N., Caprioli, R. M., & de Plas, R. V. (2019) · Mass Spectrometry Reviews · doi:10.1002/mas.21602 · Cited by 297
“Although there are some reviews on this subject (Cobo, 2013; Greco et al., 2014), the area is developing rapidly, and any attempt to summarize the latest achievements may be helpful.”
A high-stringency blueprint of the human proteome
Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19045-9 · Cited by 210
Self-citationBeltran, P. M. J., Federspiel, J. D., Sheng, X., & Cristea, I. M. (2017) · Molecular Systems Biology · doi:10.15252/msb.20167062 · Cited by 218
“When studying host – pathogen associations, advantages of IP-MS are that experiments can be performed in relevant cellular model systems and in the context of viral infection to enable unbiased detection of PPIs, as reviewed in Greco et al (2014).”
Self-citationMass spectrometry-based proteomics as an emerging tool in clinical laboratories
Birhanu, A. G. (2023) · Clinical Proteomics · doi:10.1186/s12014-023-09424-x · Cited by 236
Lum, K. K., & Cristea, I. M. (2016) · Expert Review of Proteomics · doi:10.1586/14789450.2016.1147353 · Cited by 113
Self-citationHerpesvirus Genome Integration into Telomeric Repeats of Host Cell Chromosomes.
Osterrieder, N., Wallaschek, N., & Kaufer, B. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085422 · Cited by 99
Hashimoto, Y., Sheng, X., Murray‐Nerger, L. A., & Cristea, I. M. (2020) · Nature Communications · doi:10.1038/s41467-020-14586-5 · Cited by 101
Self-citationSuvarna, K., Biswas, D., Pai, M. G. J., Acharjee, A., Bankar, R., Palanivel, V., Salkar, A., Verma, A., Mukherjee, A., Choudhury, M., et al. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.652799 · Cited by 74
“The sensitive and high-throughput mass spectrometers have allowed scientists to detect even the faintest of changes in host physiology (Greco et al., 2014).”
BackgroundSöderholm, S., Kainov, D. E., Öhman, T., Denisova, O. V., Schepens, B., Kulesskiy, E., Imanishi, S. Y., Corthals, G. L., Hintsanen, P., Aittokallio, T. A., et al. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m116.057984 · Cited by 64
“detailed understanding of disease mechanisms (4, 5).”
Cypryk, W., Lorey, M. B., Puustinen, A., Nyman, T. A., & Matikainen, S. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00596 · Cited by 64
Three-Dimensional Imaging of Viral Infections
Risco, C., de Castro, I. F., Sanz-Sánchez, L., Narayan, K., Grandinetti, G., & Subramaniam, S. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085351 · Cited by 64
Justice, J. L., Kennedy, M. A., Hutton, J. E., Liu, D., Song, B., Phelan, B., & Cristea, I. M. (2021) · Science Advances · doi:10.1126/sciadv.abg6680 · Cited by 53
“3 of 19 Immuno affinity purification (IP) mass spectrometry (MS) and proximity labeling approaches ascorbic acid peroxidase (APEX) or biotin identification (BioID) have been proven valuable for uncovering virus–host protein interactions (2, 17).”
BackgroundSelf-citationVirus-Host Interactions: From Unbiased Genetic Screens to Function
Ramage, H. R., & Cherry, S. R. (2015) · Annual Review of Virology · doi:10.1146/annurev-virology-100114-055238 · Cited by 55
“A recent review detailed the contributions of proteomics studies to our understanding of virus-host interactions and highlighted the research potential in continuing to employ these techniques (153).”
BackgroundZhuang, S., & Torbett, B. E. (2021) · Viruses · doi:10.3390/v13030417 · Cited by 53
Proteomics Tracing the Footsteps of Infectious Disease
Greco, T. M., & Cristea, I. M. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o116.066001 · Cited by 54
“tion, and (3) what are the mechanisms of pathogen replication”
BackgroundSelf-citationInvestigating the biology of alpha herpesviruses with mass spectrometry-based proteomics
Engel, E., Song, R., Koyuncu, O. O., & Enquist, L. (2015) · Proteomics · doi:10.1002/pmic.201400604 · Cited by 38
“In this review, we focus on four -HV species (see Table 1) where innovative MS-based proteomics (MSBP) methods have contributed toward understanding basic and clinical aspects of these pathogens [10].”
BackgroundBalance and Stealth: The Role of Noncoding RNAs in the Regulation of Virus Gene Expression
Cox, J. E., & Sullivan, C. S. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085439 · Cited by 34
Exploring and Exploiting Proteome Organization during Viral Infection
Beltran, P. M. J., Cook, K. C., & Cristea, I. (2017) · Journal of Virology · doi:10.1128/jvi.00268-17 · Cited by 32
“Mass spectrometry (MS)-based proteomics has become established as an important tool for sensitive detection and quantification of thousands of proteins in biological samples and has been successfully applied to diverse viral infection studies (15).”
BackgroundSelf-citationBadia, R., Garcia-Vidal, E., & Ballana, E. (2022) · Frontiers in Virology · doi:10.3389/fviro.2022.935933 · Cited by 29
“Indeed, AP-MS also has been shown to be informative about viral RNA-host protein interaction, changes in virus-host protein abundance and post-translational modifications as a result of a viral infection (7, 26, 54).”
BackgroundNew Methods in Tissue Engineering: Improved Models for Viral Infection
Ramanan, V., Scull, M. A., Sheahan, T. P., Rice, C. M., & Bhatia, S. N. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085437 · Cited by 28
Teo, C. S. H., Serwa, R. A., & O'Hare, P. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005927 · Cited by 25
Investigation of the HIV-1 Matrix interactome during virus replication
Li, Y., Frederick, K. M., Haverland, N. A., Ciborowski, P., & Belshan, M. (2015) · PROTEOMICS - Clinical Applications · doi:10.1002/prca.201400189 · Cited by 25
“Second, certain virus–host interactions may involve multiple viral components and will be missed if only a single protein is expressed [47].”
BackgroundFederspiel, J. D., Cook, K. C., Kennedy, M. A., Venkatesh, S. S., Otter, C. J., Hofstadter, W. A., Beltran, P. M. J., & Cristea, I. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107943 · Cited by 24
“All viruses, despite differences in viral structure, tropism, and replication strategies, rely on protein interactions to infect host cells, produce infectious particles, and spread between organisms (Greco et al., 2014).”
BackgroundSelf-citationHVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1
Ashford, P., Durán, A. H., Greco, T. M., Buch, A., Sodeik, B., Cristea, I. M., Grünewald, K., Shepherd, A. J., & Topf, M. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m116.058552 · Cited by 17
Self-citationStructural Proteomics of Herpesviruses
Leroy, B., Gillet, L., Vanderplasschen, A. F. C., & Wattiez, R. (2016) · Viruses · doi:10.3390/v8020050 · Cited by 23
“Frequently, the cellular response to virus infection is analyzed by looking at changes in cellular protein abundances and post-translational modifications but also viral-host protein interactions (for a global review see [3,4]).”
BackgroundSchuchman, R. M., Kilianski, A., Piper, A., Vancini, R. G., Ribeiro, J. M. C., Sprague, T. R., Nasar, F., Boyd, G., Hernandez, R. G., & Glaros, T. (2018) · Journal of Virology · doi:10.1128/jvi.00694-18 · Cited by 24
Posttranscriptional Regulation in Adenovirus Infected Cells.
Zhao, H.-X., Konzer, A., Mi, J., Chen, M., Pettersson, U., & Lind, S. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00834 · Cited by 20
MASS SPECTROMETRY IN VIROLOGICAL SCIENCES
Milewska, A., Ner‐Kluza, J., Dąbrowska, A., Bodzoń‐Kułakowska, A., Pyrć, K., & Suder, P. (2019) · Mass Spectrometry Reviews · doi:10.1002/mas.21617 · Cited by 33
“Although there are some reviews on this subject (Cobo, 2013; Greco et al., 2014), the area is developing rapidly, and any attempt to summarize the latest achievements may be helpful.”
BackgroundAbraham, R., Singh, S., Nair, S., Hulyalkar, N., Surendran, A., Jaleel, A., & Sreekumar, E. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00513 · Cited by 19
Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein
Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., Kosack, L., Bhattacharya, A., Májek, P., Stukalov, A., et al. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006758 · Cited by 20
Post-translational modification control of viral DNA sensors and innate immune signaling
Song, B., Liu, D., Greco, T. M., & Cristea, I. M. (2021) · Advances in virus research · doi:10.1016/bs.aivir.2021.03.001 · Cited by 20
Self-citationThe art of hijacking: how Nsp1 impacts host gene expression during coronaviral infections
Karousis, E. (2024) · Biochemical Society Transactions · doi:10.1042/bst20231119 · Cited by 13
Mathias, R. A., Greco, T., & Cristea, I. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3667-0_15 · Cited by 13
“Different bioinformatics platforms can be used for this purpose and, while the description of these computational approaches is outside the scope of this chapter, we point the reader to data workflows used in several protein interaction studies [15, 22, 23, 26, 27].”
MethodSelf-citationZhu, H., You, Z.-H., Shi, W.-L., Xu, S.-J., Jiang, T., & Zhuang, L.-H. (2019) · IEEE Access · doi:10.1109/access.2019.2907132 · Cited by 12
“Owing to the development of large-scale experimental technologies such as yeast two hybrid (Y2H) screens [11], tandem affinity purification (TAP) [12], mass spectrometricbased protein complex identification approaches (MS-PCI), as well as other high-throughput biotechnologies for PPI prediction [13].”
BackgroundMass spectrometry-based investigation of measles and mumps virus proteome
Sviben, D., Forčić, D., Halassy, B., Allmaier, G., Marchetti-Deschmann, M., & Brgles, M. (2018) · Virology Journal · doi:10.1186/s12985-018-1073-9 · Cited by 12
Bioinformatics and HIV Latency
Ciuffi, A., Mohammadi, P., Golumbeanu, M., di Iulio, J., & Telenti, A. (2015) · Current HIV/AIDS Reports · doi:10.1007/s11904-014-0240-x · Cited by 13
“Recent technological advances and the advent of mass spectrometry (MS)-based proteomics have made a strong positive impact on virology and have helped uncover and characterize many proteomic responses triggered by viral infection [89, 90].”
BackgroundIdentification of mumps virus protein and lipid composition by mass spectrometry
Brgles, M., Bonta, M., Šantak, M., Jagušić, M., Forčić, D., Halassy, B., Allmaier, G., & Marchetti-Deschmann, M. (2016) · Virology Journal · doi:10.1186/s12985-016-0463-0 · Cited by 10
“Mass spectrometry (MS) is a powerful tool in the field of biochemistry and is emerging as a core component of fundamental discoveries also in the field of virology [33].”
BackgroundA Proteomics Perspective on Viral DNA Sensors in Host Defense and Viral Immune Evasion Mechanisms
Crow, M. S., Javitt, A., & Cristea, I. M. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.02.016 · Cited by 9
Self-citationApplications of mass spectrometry imaging in virus research.
Bertzbach, L. D., Kaufer, B., & Karger, A. (2021) · Advances in Virus Research · doi:10.1016/bs.aivir.2020.10.002 · Cited by 10
A TRUSTED targeted mass spectrometry assay for pan-herpesvirus protein detection
Kennedy, M. A., Tyl, M. D., Betsinger, C. N., Federspiel, J. D., Sheng, X., Arbuckle, J. H., Kristie, T. M., & Cristea, I. M. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110810 · Cited by 9
“An indicator of the presence of a viral infection and the stage of a replication cycle is the expression and abundance of viral proteins (Greco et al., 2014; Gruffat et al., 2016).”
BackgroundSelf-citationSystem-Based Approaches to Delineate the Antiviral Innate Immune Landscape
Krey, K., Babnis, A. W., & Pichlmair, A. (2020) · Viruses · doi:10.3390/v12101196 · Cited by 10
Chatterjee, S., & Zaia, J. (2022) · Mass spectrometry reviews (Print) · doi:10.1002/mas.21813 · Cited by 7
“Proteomics‐based MS, in the past decade, has renewed the growing interest in structural virology (Greco et al., 2014; Grenga & Armengaud, 2021; Grossegesse et al., 2020; Terracciano et al., 2021).”
BackgroundProtein composition of the occlusion bodies of Epinotia aporema granulovirus
Masson, T., Fabre, M. L., Ferrelli, M. L., Pidre, M. L., & Romanowski, V. (2019) · PLoS ONE · doi:10.1371/journal.pone.0207735 · Cited by 9
“Mass spectrometry-based (MS) proteomics represents a powerful technique to interrogate the structural landscape of viral particles [8].”
BackgroundTeo, C. S. H., & O'Hare, P. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1007196 · Cited by 7
Virus systems biology: Proteomics profiling of dynamic protein networks during infection
Klann, K., Tascher, G., & Münch, C. (2021) · Advances in virus research · doi:10.1016/bs.aivir.2020.12.001 · Cited by 7
Aguirre, J., & Guantes, R. (2023) · bioRxiv · doi:10.1016/j.isci.2023.108475 · Cited by 5
“19 With few exceptions, 20–22 most virus-host PINs provide only a static picture of the molecular interactome.”
BackgroundComprehensive interactome analysis of the spike protein of swine acute diarrhea syndrome coronavirus
Wang, Q., Luo, Y., Shang, W., Shi, Z.-L., Xiao, G.-F., & Zhang, L.-K. (2021) · Biosafety and Health · doi:10.1016/j.bsheal.2021.05.002 · Cited by 5
“The identification of virus‐host interactions has benefited greatly from the use of affinity purification (AP)‐coupled mass spectrum (MS)‐based proteomic analysis [11].”
Källsten, M., Bergquist, J., Zhao, H.-X., Konzer, A., & Lind, S. (2016) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-016-9333-2 · Cited by 5
“Currently, the importance of mass spectrometry-based proteomics is increasing in the field of virology [18].”
BackgroundWu, S.-T., Zhu, Z., Lin, Y.-J., Xu, Q.-Y., Lei, X., Wei, J.-G., & Qin, Q.-W. (2025) · Fish and Shellfish Immunology · doi:10.1016/j.fsi.2025.110887 · Cited by 4
Wang, R., Cao, X.-H., Lu, K.-J., Chang, Z.-W., Dong, X., Guo, H., Wei, X., Dang, R.-Y., Wang, J., Wang, X.-L., et al. (2024) · Frontiers in Veterinary Science · doi:10.3389/fvets.2024.1418760 · Cited by 2
Hodgkins, C., Buckton, L. K., Walker, G., Crossett, B., Cordwell, S., Horvath, A., & Rawlinson, W. (2022) · Scientific Reports · doi:10.1038/s41598-022-16250-y · Cited by 2
The Host-Pathogen Ecosystem Viewed Through the Prism of Proteomics*
Cristea, I. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.e117.068270 · Cited by 2
“To the already proven value of proteomics in making discoveries in infectious disease research (21) can be added the ongoing developments of sensitive, accurate, and robust proteomic approaches.”
BackgroundSelf-citationImproved in Silico Identification of Protein‐Protein Interactions Using Deep Learning Approach
Khan, I., Arif, M., Ghulam, A., Albaradei, S., Thafar, M. A., & Worachartcheewan, A. (2025) · IET Systems Biology · doi:10.1049/syb2.70008 · Cited by 1
“…for example, mass spectrometry [10], mass spectrometry‐based (MS) screening and analysis of PPI [11], yeast to hybrid (Y2H) screen [12], tandem affinity purification (TAP) [13], protein chip technology [14], and other reliable biological methods [15] are successfully applied to investigate PPIs.”
COVID-19 plasma deep proteome reveals distinct signatures in severe patients
Suvarna, K., Biswas, D., Pai, M. G., Acharjee, A., Bankar, R., Viswanthram, P., Salkar, A., Verma, A., Mukherjee, A., Choudhury, M., et al. (2020) · doi:10.21203/rs.3.rs-120570/v2
Lessons for SARS-CoV-2 Study (COVID-19 Disease) From Its Exosome RelativesPreprint
Arsène, P. (2020) · Preprints.org · doi:10.20944/preprints202006.0145.v1
“This could be very valuable (Schoeman & Fielding, 2019) in designing more sustainable SARS-CoV-2 vaccines.”
BackgroundWorkflows and considerations for investigating protein interactions of viral DNA sensors
Howard, T. R., Song, B., & Cristea, I. M. (2019) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2019.04.026
Self-citationOmics Approaches in Viral Biotechnology
Waqar, K., Irfan, R., & Gul, A. (2018) · Omics Technologies and Bio-Engineering · doi:10.1016/b978-0-12-815870-8.00002-4
Metadata
- Authors
- Greco, T. M., Diner, B. A., & Cristea, I. M.
- Affiliations
- Princeton University (US)
- Venue
- Annual Review of Virology
- Publisher
- Annual Reviews
- Published
- 2014-11-03
- Volume
- 1
- Issue
- 1
- Pages
- 581-604
- ISSN
- 2327-056X (ISSN-L)
- 2327-0578
- PMC
- PMC6889812
- OpenAlex
- W2115120876
- Cited by
- 67
- References
- 160
- Citations by year
- 2025: 3 · 2024: 5 · 2023: 4 · 2022: 4 · 2021: 8 · 2020: 6 · 2019: 4 · 2018: 6 · 2017: 7 · 2016: 10 · 2015: 5 · 2014: 5
- FWCI
- 0.88
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Annual Review of Virology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- American Heart Association
- National Institutes of Health (NIAID R21AI102187)
- National Institute on Drug Abuse (DP1DA026192)
- National Institute of Allergy and Infectious Diseases (R21AI102187)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- mass spectrometry-based proteomics, viral infection, host-virus interaction, host defense, viral pathogenesis, viral morphogenesis, viral replication, viral assembly, host response to infection, post-translational modification, protein-protein interaction, subcellular localization, protein secretion
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