The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
Quantitative proteomics for the analysis of spatio-temporal protein dynamics during autophagy
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
In the citing paper
“A modified version of this marker, GST-BHMT, can be expressed in other cell lines where it behaves similar to the wild-type protein [1028].”
From Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) 1 (2021) · cites this paper as [1028]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Mass spectrometry–based proteomics turns quantitative
Ong, S.-E., & Mann, M. (2005) · Nature Chemical Biology · doi:10.1038/nchembio736 · Cited by 1,572
Selective degradation of mitochondria by mitophagy
Kim, I., Rodriguez-Enriquez, S., & Lemasters, J. J. (2007) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2007.03.034 · Cited by 1,558
Network organization of the human autophagy system
Behrends, C., Sowa, M. E., Gygi, S. P., & Harper, J. W. (2010) · Nature · doi:10.1038/nature09204 · Cited by 1,554
Proteomic characterization of the human centrosome by protein correlation profiling
Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P., Nigg, E. A., & Mann, M. (2003) · Nature · doi:10.1038/nature02166 · Cited by 1,319
Kihara, A., Noda, T., Ishihara, N., & Ohsumi, Y. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.152.3.519 · Cited by 1,004
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., & Mann, M. (2008) · Nature · doi:10.1038/nature07341 · Cited by 873
Phosphotyrosine interactome of the ErbB‐receptor kinase family
Schulze, W. X., Deng, L., & Mann, M. (2005) · Molecular Systems Biology · doi:10.1038/msb4100012 · Cited by 753
Zalckvar, E., Berissi, H., Mizrachy, L., Idelchuk, Y., Koren, I., Eisenstein, M., Sabanay, H., Pinkas‐Kramarski, R., & Kimchi, A. (2009) · The EMBO Reports · doi:10.1038/embor.2008.246 · Cited by 592
Global analysis of cellular protein translation by pulsed SILAC
Schwanhäusser, B., Gossen, M., Dittmar, G., & Selbach, M. (2009) · PROTEOMICS · doi:10.1002/pmic.200800275 · Cited by 356
Turnover of the Human Proteome: Determination of Protein Intracellular Stability by Dynamic SILAC
Doherty, M. K., Hammond, D. E., Clague, M. J., Gaskell, S. J., & Beynon, R. J. (2009) · Journal of Proteome Research · doi:10.1021/pr800641v · Cited by 340
Prelysosomal convergence of autophagic and endocytic pathways
Gordon, P. B., & Seglen, P. O. (1988) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(88)90556-6 · Cited by 281
Fournier, M. L., Paulson, A., Pavelka, N., Mosley, A. L., Gaudenz, K., Bradford, W. D., Glynn, E., Li, H., Sardiu, M. E., Fleharty, B., et al. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900415-mcp200 · Cited by 161
Gao, W., Kang, J. H., Liao, Y., Ding, W.-X., Gambotto, A. A., Watkins, S. C., Liu, Y.-J., Stolz, D. B., & Yin, X.-M. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.054197 · Cited by 94
Mousson, F., Kolkman, A., Pijnappel, W. W. M. P., Timmers, H. T. M., & Heck, A. J. R. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700306-mcp200 · Cited by 67
Research works printed but not linked: 84
- Mizushima N, Levine B, Cuervo AM, Klionsky DJ. Autophagy fights disease through cellular self-digestion. Nature 2008; 451:1069-75.
- Kroemer G, Jäättelä M. Lysosomes and autophagy in cell death control. Nat Rev Cancer 2005; 5:886-97.
- Dice JF. Chaperone-mediated autophagy. Autophagy 2007; 3:295-9.
- Klionsky DJ, Cuervo AM, Seglen PO. Methods for monitoring autophagy from yeast to human. Autophagy 2007; 3:181-206.
- van der Vaart A, Mari M, Reggiori F. A picky eater: exploring the mechanisms of selective autophagy in human pathologies. Traffic 2008; 9:281-9.
- Bernales S, McDonald KL, Walter P. Autophagy coun- terbalances endoplasmic reticulum expansion dur- ing the unfolded protein response. PLoS Biol 2006; 4:e423.
- Tolkovsky AM. Mitophagy. Biochim Biophys Acta 2009; 1793:1508-15.
- Kraft C, Deplazes A, Sohrmann M, Peter M. Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nat Cell Biol 2008; 10:602-10.
- Beau I, Esclatine A, Codogno P. Lost to translation: when autophagy targets mature ribosomes. Trends Cell Biol 2008; 18:311-4.
- Dunn WA, Jr., Cregg JM, Kiel JAKW, van der Klei IJ, Oku M, Sakai Y, et al. Pexophagy: the selective autophagy of peroxisomes. Autophagy 2005; 1:75-83.
- Pohl C, Jentsch S. Midbody ring disposal by autophagy is a post-abscission event of cytokinesis. Nat Cell Biol 2009; 11:65-70.
- Kroemer G, White E. Autophagy for the avoidance of degenerative, inflammatory, infectious, and neoplastic disease. Curr Opin Cell Biol. 2010; 22:121-23
- Gannage M, Münz C. Macroautophagy in immunity and tolerance. Traffic 2009; 10:615-20.
- Kristensen AR, Schandorff S, Hoyer-Hansen M, Nielsen MO, Jäättelä M, Dengjel J, et al. Ordered Organelle Degradation during Starvation-induced Autophagy. Mol Cell Proteomics 2008; 7:2419-28.
- Pandey A, Mann M. Proteomics to study genes and genomes. Nature 2000; 405:837-46.
- Andersen JS, Mann M. Organellar proteomics: turning inventories into insights. EMBO Rep 2006; 7:874-9.
- Vermeulen M, Hubner NC, Mann M. High confi- dence determination of specific protein-protein interac- tions using quantitative mass spectrometry. Curr Opin Biotechnol 2008; 19:331-7.
- Macek B, Mann M, Olsen JV. Global and site-specific quantitative phosphoproteomics: Principles and applica- tions. Annu Rev Pharmacol Toxicol. 2009; 49:199-221.
- Cox J, Mann M. Is proteomics the new genomics? Cell 2007; 130:395-8.
- Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006; 127:635-48.
- Dengjel J, Kratchmarova I, Blagoev B. Receptor tyro- sine kinase signaling: a view from quantitative pro- teomics. Mol Biosyst 2009; 5:1112-21.
- Dengjel J, Akimov V, Olsen JV, Bunkenborg J, Mann M, Blagoev B, et al. Quantitative proteomic assessment of very early cellular signaling events. Nat Biotechnol 2007; 25:566-8.
- Steen H, Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 2004; 5:699-711.
- Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 2007; 389:1017-31.
- Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phospho- proteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 2003; 100:6940-5.
- Shiio Y, Donohoe S, Yi EC, Goodlett DR, Aebersold R, Eisenman RN. Quantitative proteomic analysis of Myc oncoprotein function. Embo J 2002; 21:5088-96.
- Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, et al. Multiplexed protein quanti- tation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004; 3:1154-69.
- Choe L, D'Ascenzo M, Relkin NR, Pappin D, Ross P, Williamson B, et al. 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics 2007; 7:3651-60.
- Miyagi M, Rao KC. Proteolytic 18O-labeling strategies for quantitative proteomics. Mass Spectrom Rev 2007; 26:121-36.
- Blagoev B, Mann M. Quantitative proteomics to study mitogen-activated protein kinases. Methods 2006; 40:243-50.
- Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002; 1:376-86.
- Sprenger A, Kuttner V, Biniossek ML, Gretzmeier C, Boerries M, Mack C, et al. Comparative quantitation of proteome alterations induced by aging or immortal- ization in primary human fibroblasts and keratinocytes for clinical applications. Mol Biosyst 2010; 6:1579-82.
- Griffin NM, Yu J, Long F, Oh P, Shore S, Li Y, et al. Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat Biotechnol; 28:83-9.
- Steen H, Jebanathirajah JA, Springer M, Kirschner MW. Stable isotope-free relative and absolute quantita- tion of protein phosphorylation stoichiometry by MS. Proc Natl Acad Sci U S A 2005; 102:3948-53.
- Wu SL, Kim J, Bandle RW, Liotta L, Petricoin E, Karger BL. Dynamic profiling of the post-translational modifications and interaction partners of epidermal growth factor receptor signaling after stimulation by epidermal growth factor using Extended Range Proteomic Analysis (ERPA). Mol Cell Proteomics 2006; 5:1610-27.
- Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005; 4:1265-72.
- Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008; 26:1367-72.
- Mortensen P, Gouw JW, Olsen JV, Ong SE, Rigbolt KT, Bunkenborg J, et al. MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res; 9:393-403.
- Sowa ME, Bennett EJ, Gygi SP, Harper JW. Defining the human deubiquitinating enzyme interaction land- scape. Cell 2009; 138:389-403.
- Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 2004; 22:1139-45.
- Selbach M, Mann M. Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat Methods 2006; 3:981-3.
- Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol 2003; 21:315-8.
- Chang NC, Nguyen M, Germain M, Shore GC. Antagonism of Beclin 1-dependent autophagy by BCL-2 at the endoplasmic reticulum requires NAF-1. Embo J; 29:606-18.
- Wang X, Huang L. Identifying dynamic interactors of protein complexes by quantitative mass spectrometry. Mol Cell Proteomics 2008; 7:46-57.
- Groen AJ, de Vries SC, Lilley KS. A proteomics approach to membrane trafficking. Plant Physiol 2008; 147:1584-9.
- Overbye A, Fengsrud M, Seglen PO. Proteomic analy- sis of membrane-associated proteins from rat liver autophagosomes. Autophagy 2007; 3:300-22.
- Shui W, Sheu L, Liu J, Smart B, Petzold CJ, Hsieh TY, et al. Membrane proteomics of phagosomes suggests a connection to autophagy. Proc Natl Acad Sci USA 2008; 105:16952-7.
- Desjardins M, Celis JE, van Meer G, Dieplinger H, Jahraus A, Griffiths G, et al. Molecular characterization of phagosomes. J Biol Chem 1994; 269:32194-200.
- Gannage M, Dormann D, Albrecht R, Dengjel J, Torossi T, Ramer PC, et al. Matrix protein 2 of influenza A virus blocks autophagosome fusion with lysosomes. Cell Host Microbe 2009; 6:367-80.
- Dunkley TP, Watson R, Griffin JL, Dupree P, Lilley KS. Localization of organelle proteins by isotope tagging (LOPIT). Mol Cell Proteomics 2004; 3:1128-34.
- Dunkley TP, Hester S, Shadforth IP, Runions J, Weimar T, Hanton SL, et al. Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci U S A 2006; 103:6518-23.
- Sadowski PG, Groen AJ, Dupree P, Lilley KS. Sub- cellular localization of membrane proteins. Proteomics 2008; 8:3991-4011.
- Hubbard MJ, Cohen P. On target with a new mecha- nism for the regulation of protein phosphorylation. Trends Biochem Sci 1993; 18:172-7.
- Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2002; 298:1912-34.
- Kalume DE, Molina H, Pandey A. Tackling the phos- phoproteome: tools and strategies. Curr Opin Chem Biol 2003; 7:64-9.
- de Graauw M, Hensbergen P, van de Water B. Phospho- proteomic analysis of cellular signaling. Electrophoresis 2006; 27:2676-86.
- Schreiber TB, Mausbacher N, Breitkopf SB, Grundner- Culemann K, Daub H. Quantitative phosphopro- teomics--an emerging key technology in signal-trans- duction research. Proteomics 2008; 8:4416-32.
- Yang Z, Klionsky DJ. An overview of the molecu- lar mechanism of autophagy. Curr Top Microbiol Immunol 2009; 335:1-32.
- Esclatine A, Chaumorcel M, Codogno P. Macroautophagy signaling and regulation. Curr Top Microbiol Immunol 2009; 335:33-70.
- He C, Klionsky DJ. Regulation mechanisms and sig- naling pathways of autophagy. Annu Rev Genet 2009; 43:67-93.
- Simonsen A, Tooze SA. Coordination of membrane events during autophagy by multiple class III PI3- kinase complexes. J Cell Biol 2009; 186:773-82.
- Diaz-Troya S, Perez-Perez ME, Florencio FJ, Crespo JL. The role of TOR in autophagy regulation from yeast to plants and mammals. Autophagy 2008; 4:851-65.
- Long X, Ortiz-Vega S, Lin Y, Avruch J. Rheb bind- ing to mammalian target of rapamycin (mTOR) is regulated by amino acid sufficiency. J Biol Chem 2005; 280:23433-6.
- Polak P, Hall MN. mTOR and the control of whole body metabolism. Curr Opin Cell Biol 2009; 21:209-18.
- Arico S, Petiot A, Bauvy C, Dubbelhuis PF, Meijer AJ, Codogno P, et al. The tumor suppressor PTEN positively regulates macroautophagy by inhibiting the phosphatidylinositol 3-kinase/protein kinase B path- way. J Biol Chem 2001; 276:35243-6.
- Inoki K, Zhu T, Guan K-L. TSC2 mediates cellular energy response to control cell growth and survival. Cell 2003; 115:577-90.
- Dorsey FC, Rose KL, Coenen S, Prater SM, Cavett V, Cleveland JL, et al. Mapping the phosphorylation sites of Ulk1. J Proteome Res 2009; 8:5253-63.
- Koren I, Reem E, Kimchi A. DAP1, a novel substrate of mTOR, negatively regulates autophagy. Curr Biol 2010; 20:1093-8.
- Mann M, Ong SE, Gronborg M, Steen H, Jensen ON, Pandey A. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol 2002; 20:261-8.
- Schmelzle K, Kane S, Gridley S, Lienhard GE, White FM. Temporal dynamics of tyrosine phosphorylation in insulin signaling. Diabetes 2006; 55:2171-9.
- Krüger M, Kratchmarova I, Blagoev B, Tseng YH, Kahn CR, Mann M. Dissection of the insulin signal- ing pathway via quantitative phosphoproteomics. Proc Natl Acad Sci USA 2008; 105:2451-6.
- Mizushima N, Yoshimori T, Levine B. Methods in mammalian autophagy research. Cell; 140:313-26.
- Martin DN, Balgley B, Dutta S, Chen J, Rudnick P, Cranford J, et al. Proteomic analysis of steroid-triggered autophagic programmed cell death during Drosophila development. Cell Death Differ 2007; 14:916-23.
- Köhler K, Brunner E, Guan XL, Boucke K, Greber UF, Mohanty S, et al. A combined proteomic and genetic analysis identifies a role for the lipid desaturase Desat1 in starvation-induced autophagy in Drosophila. Autophagy 2009; 5:980-90.
- Dengjel J, Kristensen AR, Andersen JS. Ordered bulk degradation via autophagy. Autophagy 2008; 4:1057-9.
- Cargile BJ, Bundy JL, Grunden AM, Stephenson JL, Jr. Synthesis/degradation ratio mass spectrometry for measuring relative dynamic protein turnover. Anal Chem 2004; 76:86-97.
- Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Widespread changes in pro- tein synthesis induced by microRNAs. Nature 2008; 455:58-63.
- Bauvy C, Meijer AJ, Codogno P. Assaying of autopha- gic protein degradation. Methods Enzymol 2009; 452:47-61.
- Kirkin V, McEwan DG, Novak I, Dikic I. A role for ubiquitin in selective autophagy. Mol Cell 2009; 34:259-69.
- Bjørkøy G, Lamark T, Brech A, Outzen H, Perander M, Øvervatn A, et al. p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death. J Cell Biol 2005; 171:603-14.
- Kirkin V, Lamark T, Sou YS, Bjorkoy G, Nunn JL, Bruun JA, et al. A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol Cell 2009; 33:505-16.
- Geisler S, Holmstrom KM, Skujat D, Fiesel FC, Rothfuss OC, Kahle PJ, et al. PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/ SQSTM1. Nat Cell Biol; 12:119-31.
- Meierhofer D, Wang X, Huang L, Kaiser P. Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. J Proteome Res 2008; 7:4566-76.
- Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, et al. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A 2004; 101:12130-5.
Cited by
Sorted by citations
Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
Klionsky, D. J., Abdelmohsen, K., Abe, A., Abedin, M. J., Abeliovich, H., Acevedo Arozena, A., Adachi, H., Adams, C. M., Adams, P. D., Adeli, K., et al. (2016) · Autophagy · doi:10.1080/15548627.2015.1100356 · Cited by 5,894
Self-citationGuidelines for the use and interpretation of assays for monitoring autophagy
Klionsky, D. J., Abdalla, F. C., Abeliovich, H., Abraham, R. T., Acevedo-Arozena, A., Adeli, K., Agholme, L., Agnello, M., Agostinis, P., Aguirre-Ghiso, J. A., et al. (2012) · Autophagy · doi:10.4161/auto.19496 · Cited by 3,996
Self-citationGuidelines for the use and interpretation of assays for monitoring autophagy (4th edition) 1
Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., Abeliovich, H., Abildgaard, M. H., Abudu, Y. P., Acevedo-Arozena, A., et al. (2021) · Autophagy · doi:10.1080/15548627.2020.1797280 · Cited by 2,897
Self-citationMolecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks
Boerries, M., Grahammer, F., Eiselein, S., Buck, M., Meyer, C., Goedel, M., Bechtel, W., Zschiedrich, S., Pfeifer, D., Laloë, D., et al. (2013) · Kidney International · doi:10.1038/ki.2012.487 · Cited by 141
Self-citation
Metadata
- Authors
- Zimmermann, A. C., Zarei, M., Eiselein, S., & Dengjel, J.
- Venue
- Autophagy
- Publisher
- Informa UK Limited
- Published
- 2010-11-16
- Volume
- 6
- Issue
- 8
- Pages
- 1009-1016
- ISSN
- 1554-8627
- 1554-8635
- Cited by
- 28
- References
- 14
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review