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Top Down proteomics: Facts and perspectives
Open accessAbstract
The rise of the "Top Down" method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious "inference" problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.
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“This approach is well-known for its high-throughput performance; however, critical information about PTMs and subunit protein assemblies (via non-covalent interactions) is generally lost after proteolysis14,31.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [31]
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A dual pressure linear ion trap orbitrap instrument with very high sequencing speed
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Detection of noncovalent receptor-ligand complexes by mass spectrometry
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Mass Spectrometry: Bottom-Up or Top-Down?
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Peer Reviewed: Top-Down Proteomics
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Self-citationJournal of The American Society for Mass Spectrometry
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“For intact proteins, RPLC is typically employed as a second dimension of separation, but it has often been successfully applied as the sole separation strategy [13,15,22,25].”
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“Additionally, many reports have been published using derivatized nonporous silica (NPS) particles, which offer increased speed and protein recovery, but suffer from limited loading capacity and high back pressure [15,16,17,18,19,20].”
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“5 T version of the LTQ-FT-ICR instrument has also been reported, featuring approximately 4-fold higher mass accuracy and twice the resolving power of the 7T instrument [99].”
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Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions
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“The potential for achieving full protein characterization has made the Top Down mass spectrometry approach extremely useful for analysis of single proteins or simple mixtures of significant biological interest [6,7,8,9,10,11].”
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BackgroundZhang, H., Cui, W., Wen, J., Blankenship, R. E., & Gross, M. L. (2011) · Analytical Chemistry · doi:10.1021/ac200695d · Cited by 163
Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures
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Analysis of Intact Monoclonal Antibody IgG1 by Electron Transfer Dissociation Orbitrap FTMS
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Wilcox, B., Hendrickson, C., & Marshall, A. (2002) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(02)00622-0 · Cited by 139 · cited 1×
“Significant advances to FT-ICR technology, often focused on improving the analysis of intact proteins, included increases in magnetic field [88,89], addition of a resolving quadrupole for mass selection [90], and an accumulation octupole for ion storage before transmission to the ICR cell [91,92].”
Hogan, C. J., Ruotolo, B., Robinson, C., & de la Mora, J. F. (2011) · Journal of Physical Chemistry B · doi:10.1021/jp109172k · Cited by 127
Cation-exchange chromatography of peptides on poly(2-sulfoethyl aspartamide)-silica.
Alpert, A. J., & Andrews, P. (1988) · Journal of Chromatography A · doi:10.1016/s0021-9673(00)94785-x · Cited by 127 · cited 1×
“In contrast with RPLC, HILIC utilizes a polar stationary phase and gradients of increasing water content, resulting in the elution of more hydrophobic species first [26,27].”
BackgroundParks, B. A., Jiang, L., Thomas, P. M., Wenger, C. D., Roth, M. J., Boyne, M. T., Burke, P. V., Kwast, K. E., & Kelleher, N. L. (2007) · Analytical Chemistry · doi:10.1021/ac070553t · Cited by 123 · cited 2×
“proteome [36] and a variety of membrane proteins [96,97].”
BackgroundMethodSelf-citationMultiplexed Size Separation of Intact Proteins in Solution Phase for Mass Spectrometry
Tran, J. C., & Doucette, A. A. (2009) · Analytical Chemistry · doi:10.1021/ac900729r · Cited by 122 · cited 1×
“It was shown that the device could be used as a first dimension of separation prior to a multiplexed version of GELFrEE, analogous to a twodimensional gel separation [55].”
MethodWeb and database software for identification of intact proteins using "top down" mass spectrometry.
Taylor, G. K., Kim, Y.-B., Forbes, A. J., Meng, F.-Y., McCarthy, R. T., & Kelleher, N. (2003) · Analytical Chemistry · doi:10.1021/ac0341721 · Cited by 119
Self-citationBalaguer, E., & Neusüß, C. (2006) · Analytical Chemistry · doi:10.1021/ac060376g · Cited by 117 · cited 1×
“Notable examples include the detection of the α and β subunits of hemoglobin from a single erythrocyte [60] and the detection of various protein glycoforms of erythropoietin, fetuin, and α1-acid glycoprotein [61].”
BackgroundGene-Specific Characterization of Human Histone H2B by Electron Capture Dissociation
Siuti, N., Roth, M. J., Mizzen, C. A., Kelleher, N. L., & Pesavento, J. J. (2006) · Journal of Proteome Research · doi:10.1021/pr050268v · Cited by 112 · cited 1×
“The potential for achieving full protein characterization has made the Top Down mass spectrometry approach extremely useful for analysis of single proteins or simple mixtures of significant biological interest [6,7,8,9,10,11].”
BackgroundSelf-citationA robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome
Lee, J. E., Kellie, J. F., Tran, J. C., Tipton, J. D., Catherman, A. D., Thomas, H. M., Ahlf, D. R., Durbin, K. R., Vellaichamy, A., Ntai, I., et al. (2009) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2009.08.001 · Cited by 108 · cited 3×
“Polymeric reversed-phase materials, offering increased mechanical strength, uniform hydrophobicity, and high recovery, have also been utilized for the separation of intact proteins [13,22,23,24].”
BackgroundMethodSelf-citationHigh-resolution tandem mass spectrometry of large biomolecules.
Loo, J., Quinn, J. P., Ryu, S. I., Henry, K. D., Senko, M., & McLafferty, F. (1992) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.89.1.286 · Cited by 105 · cited 1×
“The same instrument was also utilized to perform collision-induced dissociation (CID) and nozzle-skimmer dissociation (NSD) of ubiquitin, using the high resolving power of the instrument to determine charge state and identity of the fragment ions [83].”
MethodRoth, M. J., Forbes, A. J., Boyne, M. T., Kim, Y. B., Robinson, D. E., & Kelleher, N. L. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500064-mcp200 · Cited by 103 · cited 1×
“has been utilized for a variety of Top Down proteomic studies [16,38,45,94].”
MethodSelf-citationAnalysis of Intact Protein Isoforms by Mass Spectrometry
Tipton, J. D., Tran, J. C., Catherman, A. D., Ahlf, D. R., Durbin, K. R., & Kelleher, N. L. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.r111.239442 · Cited by 102 · cited 1×
“Extremely high resolution may be required to distinguish disulfide bridges (Δm = 2 Da), deamidation (Δm = 1 Da), trimethylation versus acetylation (Δm = 39 mDa), and phosphorylation versus sulfation (Δm = 10 mDa) [70].”
BackgroundSelf-citationZhang, D., Sweredoski, M. J., Graham, R. L. J., Hess, S. Y., & Shan, S. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.011585 · Cited by 101
Vellaichamy, A., Tran, J. C., Catherman, A. D., Lee, J. E., Kellie, J. F., Sweet, S. M. M., Zamdborg, L., Thomas, P. M., Ahlf, D. R., Durbin, K. R., et al. (2010) · Analytical Chemistry · doi:10.1021/ac9021083 · Cited by 100 · cited 2×
“Polymeric reversed-phase materials, offering increased mechanical strength, uniform hydrophobicity, and high recovery, have also been utilized for the separation of intact proteins [13,22,23,24].”
BackgroundSelf-citationKellie, J. F., Tran, J. C., Lee, J. E., Ahlf, D. R., Thomas, H. M., Ntai, I., Catherman, A. D., Durbin, K. R., Zamdborg, L., Vellaichamy, A., et al. (2010) · Molecular BioSystems · doi:10.1039/c000896f · Cited by 99 · cited 1×
“The great complexity within most proteomic samples requires that they be fractionated prior to introduction to the mass spectrometer [12].”
BackgroundSelf-citationCapriotti, A. L., Cavaliere, C., Foglia, P., Samperi, R., & Laganà, A. (2011) · Journal of Chromatography A · doi:10.1016/j.chroma.2011.05.094 · Cited by 95 · cited 6×
“While a variety of liquid chromatography methods have been developed, reversed-phase liquid chromatography (RPLC), hydrophobic interaction liquid chromatography (HILIC), and ion exchange chromatography (IEX) are three of the most common liquid chromatography approaches applied to intact proteins [13].”
BackgroundMethodInfluentialPatrie, S. M., Charlebois, J. P., Whipple, D., Kelleher, N., Hendrickson, C., Quinn, J. P., Marshall, A., & Mukhopadhyay, B. (2004) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2004.04.031 · Cited by 93
Self-citationDefinition of the mitochondrial proteome by measurement of molecular masses of membrane proteins
Carroll, J., Fearnley, I., & Walker, J. (2006) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0607719103 · Cited by 92 · cited 2×
“Membrane proteins extracted from bovine heart mitochondria have been fractionated using HILIC.”
MethodRyan, C., Souda, P., Bassilian, S., Ujwal, R., Zhang, J., Abramson, J., Ping, P., Durazo, A., Bowie, J., Hasan, S., et al. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900516-mcp200 · Cited by 91 · cited 1×
“proteome [36] and a variety of membrane proteins [96,97].”
BackgroundHenry, K. D., & McLafferty, F. (1990) · Organic Mass Spectrometry · doi:10.1002/oms.1210250912 · Cited by 91 · cited 1×
“8 Tesla (T) instrument, allowing for accurate mass determination [81,82].”
BackgroundEvaluation of the Compact High-Field Orbitrap for Top-Down Proteomics of Human Cells
Ahlf, D. R., Compton, P. D., Tran, J. C., Early, B. P., Thomas, P. M., & Kelleher, N. L. (2012) · Journal of Proteome Research · doi:10.1021/pr3004216 · Cited by 89 · cited 2×
“proteins from the H1299 human cancer cell line [51], followed by the identification of 1976 unique proteins from an H1299 cell line used to probe the proteome-wide difference in cellular senescence[118].”
BackgroundSelf-citationMazur, M. T., Cardasis, H. L., Spellman, D. S., Liaw, A., Yates, N. A., & Hendrickson, R. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910776107 · Cited by 87
Mass spectrometric studies on noncovalent dimers of leucine zipper peptides
Li, Y., Hsieh, Y.-L., Henion, J., Senko, M., McLafferty, F., & Ganem, B. (1993) · Journal of the American Chemical Society · doi:10.1021/ja00071a058 · Cited by 84
Improved fourier-transform ion-cyclotron-resonance mass spectrometry of large biomolecules
Beu, S. C., Senko, M. W., Quinn, J. P., & McLafferty, F. W. (1993) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(93)85077-b · Cited by 84
Symmetrical gas-phase dissociation of noncovalent protein complexes via surface collisions.
Jones, C. M., Beardsley, R. L., Galhena, A. S., Dagan, S., Cheng, G., & Wysocki, V. (2006) · Journal of the American Chemical Society · doi:10.1021/ja064586m · Cited by 81
Chong, B. E., Yan, F., Lubman, D., & Miller, F. (2001) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.227 · Cited by 81 · cited 2×
“variant of IEX which uses a change in pH rather than ionic strength to achieve elution, has been coupled to off-line RPLC for fractionation of intact proteins from breast cancer [17] and Methanosarcina acetivorans [38].”
BackgroundProteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry.
Sharma, S., Simpson, D., Toliċ, N., Jaitly, N., Mayampurath, A., Smith, R. D., & Paša-Tolić, L. (2007) · Journal of Proteome Research · doi:10.1021/pr060354a · Cited by 77 · cited 1×
“Anion exchange-RPLC has been utilized for the Top Down study of Shewanella oneidensis [35], yeast [36], and human leukocytes [37].”
MethodTop Down Proteomics of Human Membrane Proteins from Enriched Mitochondrial Fractions
Catherman, A. D., Li, M., Tran, J. C., Durbin, K. R., Compton, P. D., Early, B. P., Thomas, P. M., & Kelleher, N. L. (2013) · Analytical Chemistry · doi:10.1021/ac3031527 · Cited by 76 · cited 2×
“It should also be noted that the LTQ Velos has also been coupled to a 12 T FT-ICR mass spectrometer for Top Down analysis [52], however the instrument has not been commercialized and no other uses of such an instrument have been reported.”
BackgroundMethodSelf-citationEdwards, R., Griffiths, P., Bunch, J., & Cooper, H. (2012) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-012-0477-9 · Cited by 75
Resemann, A., Wunderlich, D., Rothbauer, U., Warscheid, B., Leonhardt, H., Fuchser, J., Kuhlmann, K., & Suckau, D. (2010) · Analytical Chemistry · doi:10.1021/ac1000515 · Cited by 68 · cited 1×
“The potential for achieving full protein characterization has made the Top Down mass spectrometry approach extremely useful for analysis of single proteins or simple mixtures of significant biological interest [6,7,8,9,10,11].”
BackgroundMillea, K. M., Krull, I. S., Cohen, S. A., Gebler, J. C., & Berger, S. J. (2005) · Journal of Proteome Research · doi:10.1021/pr050278w · Cited by 66
“Proteotyping”: Population Proteomics of Human Leukocytes Using Top Down Mass Spectrometry
Roth, M. J., Parks, B. A., Ferguson, J. T., Boyne, M. T., & Kelleher, N. L. (2008) · Analytical Chemistry · doi:10.1021/ac800141g · Cited by 65 · cited 2×
“A 12 T version of the instrument has been utilized for increased throughput studies using the automated on-line/offline RPLC-MS platform for the study of HeLa nuclei [22], human leukocytes [37], and M.”
MethodSelf-citationYang, L.-Y., Lee, C. S., Hofstadler, S., Paša-Tolić, L., & Smith, R. D. (1998) · Analytical Chemistry · doi:10.1021/ac980224o · Cited by 64
Kellie, J. F., Catherman, A. D., Durbin, K. R., Tran, J. C., Tipton, J. D., Norris, J. L., Witkowski, C. E., Thomas, P. M., & Kelleher, N. L. (2011) · Analytical Chemistry · doi:10.1021/ac202384v · Cited by 62 · cited 1×
“In the last few years, several papers have been published using GELFrEE for molecular-weight based fractionation for Top Down proteomics, allowing for increased throughput and number of identifications [24,49,50,51,52].”
BackgroundSelf-citationPatrie, S. M., Ferguson, J. T., Robinson, D. E., Whipple, D., Rother, M., Metcalf, W. W., & Kelleher, N. L. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500219-mcp200 · Cited by 62 · cited 2×
“variant of IEX which uses a change in pH rather than ionic strength to achieve elution, has been coupled to off-line RPLC for fractionation of intact proteins from breast cancer [17] and Methanosarcina acetivorans [38].”
BackgroundMethodSelf-citationWall, D. B., Berger, S. J., Finch, J. W., Cohen, S. A., Richardson, K., Chapman, R. L., Drabble, D., Brown, J. M., & Gostick, D. (2002) · Electrophoresis · doi:10.1002/1522-2683(200209)23:18 · Cited by 62
Self-citationPesavento, J. J., Garcia, B., Streeky, J. A., Kelleher, N., & Mizzen, C. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600404-mcp200 · Cited by 61 · cited 1×
“[28,29] HILIC has also been extensively applied for the separation of modified histone forms prior to Top Down mass spectrometry [30,31,32].”
MethodSelf-citationIdentification of membrane proteins by tandem mass spectrometry of protein ions
Carroll, J., Altman, M. C., Fearnley, I., & Walker, J. (2007) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0706817104 · Cited by 60 · cited 2×
“Membrane proteins extracted from bovine heart mitochondria have been fractionated using HILIC.”
MethodPrecursor ion independent algorithm for top-down shotgun proteomics
Tsai, Y. S., Scherl, A., Shaw, J. L., Mackay, C. L., Shaffer, S. A., Langridge‐Smith, P. R. R., & Goodlett, D. R. (2009) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2009.07.024 · Cited by 59
Wall, D., Kachman, M. T., Gong, S.-Y., Parus, S., Long, M. W., & Lubman, D. (2001) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.421 · Cited by 57 · cited 2×
“A preparative-scale Rotofor, capable of separating ~1 g of protein within 55 mL of buffer, and the mini-Rotofor, a smaller version of the device which can hold ~15 mL of solution, have been used for the fractionation of the human erythroleukemia cell line proteome prior to NPS-RPLC-MS [18,19,20].”
BackgroundMethodAnalysis of 953 Human Proteins from a Mitochondrial HEK293 Fraction by Complexome Profiling
Wessels, H. J. C. T., Vogel, R. O., Lightowlers, R. N., Spelbrink, J. N., Rodenburg, R. J., van den Heuvel, L. P., van Gool, A. J., Gloerich, J., Smeitink, J. A. M., & Nijtmans, L. G. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068340 · Cited by 55
Zhou, F., & Johnston, M. (2004) · Analytical Chemistry · doi:10.1021/ac035446n · Cited by 54 · cited 1×
“cIEF has also been coupled to RPLC-MS, which allowed for a second dimension of separation and the removal of ampholytes which can cause significant ionization suppression [68].”
MethodBereszczak, J. Z., Barbu, I., Tan, M., Xia, M., Jiang, X., van Duijn, E., & Heck, A. J. R. (2012) · Journal of Structural Biology · doi:10.1016/j.jsb.2012.01.005 · Cited by 53
Théberge, R., Infusini, G., Tong, W., McComb, M. E., & Costello, C. E. (2010) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2010.08.012 · Cited by 44
Moini, M., & Huang, H.-Y. (2004) · Electrophoresis · doi:10.1002/elps.200305906 · Cited by 42
Tipton, J. D., Tran, J. C., Catherman, A. D., Ahlf, D. R., Durbin, K. R., Lee, J. E., Kellie, J. F., Kelleher, N. L., Hendrickson, C. L., & Marshall, A. G. (2012) · Analytical Chemistry · doi:10.1021/ac202651v · Cited by 42 · cited 1×
“This instrument was also utilized for analysis of GELFrEE fractions, using the improvement in sensitivity and resolution for the detection and identification of higher molecular weight proteins [23,100].”
MethodSelf-citationRoth, M. J., Plymire, D. A., Chang, A. N., Kim, J., Maresh, E. M., Larson, S. E., & Patrie, S. M. (2011) · Analytical Chemistry · doi:10.1021/ac202339x · Cited by 42 · cited 1×
“Use of superficially porous particles, which contain a nonporous silica core and a porous shell, has been reported for protein separations, offering similar efficiency to that of nonporous columns but with reduced back pressure and improved loading capacity [21].”
BackgroundThangaraj, B., Ryan, C., Souda, P., Krause, K., Faull, K. F., Weber, A. P. M., Fromme, P., & Whitelegge, J. P. (2010) · Proteomics · doi:10.1002/pmic.201000190 · Cited by 41 · cited 1×
“proteome [36] and a variety of membrane proteins [96,97].”
BackgroundTop-down proteomics reveals novel protein forms expressed in methanosarcina acetivorans
Ferguson, J. T., Wenger, C. D., Metcalf, W. W., & Kelleher, N. L. (2009) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2009.05.014 · Cited by 41 · cited 1×
“acetivorans [98] as well as the GELFrEE platform for the analysis of S.”
MethodSelf-citationZhou, F., Hanson, T. E., & Johnston, M. (2007) · Analytical Chemistry · doi:10.1021/ac071147c · Cited by 40 · cited 1×
“Using this platform, 1200 polypeptides/proteins from Chlorobium tepidum were detected over an eight hour separation [69].”
MethodDoerr, A. (2008) · Nature Methods · doi:10.1038/nmeth1162 · Cited by 40
Belov, M. E., Nikolaev, E. N., Anderson, G., Auberry, K., Harkewicz, R., & Smith, R. D. (2001) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(00)00198-7 · Cited by 40 · cited 1×
“Significant advances to FT-ICR technology, often focused on improving the analysis of intact proteins, included increases in magnetic field [88,89], addition of a resolving quadrupole for mass selection [90], and an accumulation octupole for ion storage before transmission to the ICR cell [91,92].”
Structural characterization of intact antibodies by high‐resolution LTQ Orbitrap mass spectrometry
Zhang, J., Liu, H., & Katta, V. (2009) · Journal of Mass Spectrometry · doi:10.1002/jms.1700 · Cited by 40
Tran, J. C., & Doucette, A. (2008) · Journal of Proteome Research · doi:10.1021/pr700677u · Cited by 37 · cited 1×
“Another variant of solution isoelectric focusing (sIEF) for protein fractionation was reported in 2008 [54].”
BackgroundErales, J., Gontero, B., Whitelegge, J. P., & Halgand, F. (2008) · Biochemical Journal · doi:10.1042/bj20082004 · Cited by 36 · cited 1×
“The potential for achieving full protein characterization has made the Top Down mass spectrometry approach extremely useful for analysis of single proteins or simple mixtures of significant biological interest [6,7,8,9,10,11].”
BackgroundAlpert, A. J. (1988) · Journal of Chromatography A · doi:10.1016/s0021-9673(01)94030-0 · Cited by 35 · cited 1×
“In contrast with RPLC, HILIC utilizes a polar stationary phase and gradients of increasing water content, resulting in the elution of more hydrophobic species first [26,27].”
BackgroundDurbin, K. R., Fellers, R. T., Ntai, I., Kelleher, N. L., & Compton, P. D. (2014) · Analytical Chemistry · doi:10.1021/ac402904h · Cited by 34
Self-citationVersatile Online−Offline Engine for Automated Acquisition of High-Resolution Tandem Mass Spectra
Wenger, C. D., Boyne, M. T., Ferguson, J. T., Robinson, D. E., & Kelleher, N. L. (2008) · Analytical Chemistry · doi:10.1021/ac8010704 · Cited by 33 · cited 4×
“Polymeric reversed-phase materials, offering increased mechanical strength, uniform hydrophobicity, and high recovery, have also been utilized for the separation of intact proteins [13,22,23,24].”
BackgroundMethodInfluentialSelf-citationDavidsson, P., & Nilsson, C. L. (1999) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/s0304-4165(99)00197-x · Cited by 32 · cited 1×
“Proteins can be electroeluted from SDS-PAGE gels using an orthogonally applied electric field to the gel; however few studies have been reported, likely due to poor recovery [44].”
BackgroundDu, Y., Meng, F.-Y., Patrie, S. M., Miller, L. M., & Kelleher, N. (2004) · Journal of Proteome Research · doi:10.1021/pr0499489 · Cited by 27 · cited 2×
“An improvement to this original separation used a mini prep-cell, featuring a 7 mm gel column, rather than a 37 mm column, coupled to a 320 μm C4 column allowing for 15 to 300-fold less sample loading as well some on-line analysis [45].”
MethodSelf-citationUse of rotofor preparative isoelectrofocusing cell in protein purification procedure
Ayala, A., Parrado, J., & Machado, A. (1998) · Applied Biochemistry and Biotechnology · doi:10.1007/bf02786017 · Cited by 26 · cited 1×
“The Rotofor device uses an IEF separation but within an open channel, where the pH gradient is formed through the use of carrier ampholytes in solution between an acidic anode and a basic cathode [53].”
MethodWu, S., Brown, R. N., Payne, S., Meng, D., Zhao, R., Tolić, N., Cao, L., Shukla, A. K., Monroe, M. E., Moore, R. J., et al. (2013) · International Journal of Proteomics · doi:10.1155/2013/279590 · Cited by 22
Global histone profiling by LC–FTMS after inhibition and knockdown of deacetylases in human cells
Li, M., Jiang, L., & Kelleher, N. L. (2009) · Journal of Chromatography B · doi:10.1016/j.jchromb.2009.09.042 · Cited by 21 · cited 1×
“The potential for achieving full protein characterization has made the Top Down mass spectrometry approach extremely useful for analysis of single proteins or simple mixtures of significant biological interest [6,7,8,9,10,11].”
BackgroundSelf-citationHofstadler, S., Severs, J., Smith, R. D., Swanek, F., & Ewing, A. (1996) · doi:10.1002/jhrc.1240191105 · Cited by 17 · cited 1×
“Notable examples include the detection of the α and β subunits of hemoglobin from a single erythrocyte [60] and the detection of various protein glycoforms of erythropoietin, fetuin, and α1-acid glycoprotein [61].”
BackgroundWall, D., Parus, S., & Lubman, D. (2001) · Journal of Chromatography B: Biomedical Sciences and Applications · doi:10.1016/s0378-4347(01)00382-6 · Cited by 12 · cited 2×
“A preparative-scale Rotofor, capable of separating ~1 g of protein within 55 mL of buffer, and the mini-Rotofor, a smaller version of the device which can hold ~15 mL of solution, have been used for the fractionation of the human erythroleukemia cell line proteome prior to NPS-RPLC-MS [18,19,20].”
BackgroundMethodSeparation of polymerase chain reaction amplified bird genes by capillary electrophoresis
Lesaicherre, M.-L., Li, S. F. Y., & Lee, H. K. (2000) · Electrophoresis · doi:10.1002/(sici)1522-2683(20000401)21:7 · Cited by 1
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Metadata
- Authors
- Catherman, A. D., Skinner, O. S., & Kelleher, N. L.
- Affiliations
- Northwestern University (US)
- Corresponding author
- Kelleher, Neil L.
- Venue
- Biochemical and Biophysical Research Communications
- Publisher
- Elsevier BV
- Published
- 2014-03
- Volume
- 445
- Issue
- 4
- Pages
- 683-693
- ISSN
- 0006-291X (ISSN-L)
- PMC
- PMC4103433
- OpenAlex
- W2070948666
- Cited by
- 507
- References
- 143
- Citations by year
- 2026: 21 · 2025: 32 · 2024: 31 · 2023: 37 · 2022: 48 · 2021: 49 · 2020: 49 · 2019: 46 · 2018: 41 · 2017: 59 · 2016: 38 · 2015: 42 · 2014: 14
- FWCI
- 5.00
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Biochemical and Biophysical Research Communications (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM067193)
- 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 › Metabolomics and Mass Spectrometry Studies
- Keywords
- top-down proteomics, post-translational modification, protein characterization, protein separation, protein complex identification
- MeSH terms
- Amino Acid Sequence, Animals, Chromatography, Liquid, Electrophoresis, Equipment Design, Humans, Molecular Sequence Data, Proteins, Mass Spectrometry, Proteomics
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 ›
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