1932

Abstract

Mass spectrometry (MS)–based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-anchem-071213-020216
2014-06-12
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/anchem/7/1/annurev-anchem-071213-020216.html?itemId=/content/journals/10.1146/annurev-anchem-071213-020216&mimeType=html&fmt=ahah

Literature Cited

  1. Smith LM, Kelleher NL. 1. Consort. Top Down Proteomics 2013. Proteoform: a single term describing protein complexity. Nat. Methods 10:3186–87 [Google Scholar]
  2. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R. 2.  2000. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97:9390–95 [Google Scholar]
  3. Monteoliva L, Albar JP. 3.  2004. Differential proteomics: an overview of gel and non-gel based approaches. Brief. Funct. Genomics Proteomics 3:220–39 [Google Scholar]
  4. Yates JR, Ruse CI, Nakorchevsky A. 4.  2009. Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 11:49–79 [Google Scholar]
  5. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. 5.  1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71 [Google Scholar]
  6. Karas M, Hillenkamp F. 6.  1988. Laser desorption ionization of proteins with molecular masses exceeding 10000 daltons. Anal. Chem. 60:2299–301 [Google Scholar]
  7. Eng JK, Mccormack AL, Yates JR. 7.  1994. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J. Am. Soc. Mass Spectr. 5:976–89 [Google Scholar]
  8. Perkins DN, Pappin DJC, Creasy DM, Cottrell JS. 8.  1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551–67 [Google Scholar]
  9. Zhou F, Hanson TE, Johnston MV. 9.  2007. Intact protein profiling of Chlorobium tepidum by capillary isoelectric focusing, reversed-phase liquid chromatography, and mass spectrometry. Anal. Chem. 79:7145–53 [Google Scholar]
  10. Meng F, Cargile BJ, Patrie SM, Johnson JR, McLoughlin SM, Kelleher NL. 10.  2002. Processing complex mixtures of intact proteins for direct analysis by mass spectrometry. Anal Chem 74:2923–29 [Google Scholar]
  11. Tran JC, Zamdborg L, Ahlf DR, Lee JE, Catherman AD. 11.  et al. 2011. Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 480:254–58 [Google Scholar]
  12. McDonald WH, Yates JR. 12.  2003. Shotgun proteomics: integrating technologies to answer biological questions. Curr. Opin. Mol. Ther. 5:302–9 [Google Scholar]
  13. Kocher T, Swart R, Mechtler K. 13.  2011. Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides. Anal. Chem. 83:2699–704 [Google Scholar]
  14. Shen Y, Zhao R, Belov ME, Conrads TP, Anderson GA. 14.  et al. 2001. Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. Anal. Chem. 73:1766–75 [Google Scholar]
  15. Shen YF, Moore RJ, Zhao R, Blonder J, Auberry DL. 15.  et al. 2003. High-efficiency on-line solid-phase extraction coupling to 15–150-μm i.d. column liquid chromatography for proteomic analysis. Anal. Chem. 75:3596–605 [Google Scholar]
  16. Shen YF, Zhang R, Moore RJ, Kim J, Metz TO. 16.  et al. 2005. Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000–1500 and capabilities in proteomics and metabolomics. Anal. Chem. 77:3090–100 [Google Scholar]
  17. Sandra K, Moshir M, D'hondt F, Verleysen K, Kas K, Sandra P. 17.  2008. Highly efficient peptide separations in proteomics: Part 1. Unidimensional high performance liquid chromatography. J. Chromatogr. B 866:48–63 [Google Scholar]
  18. Liu H, Finch JW, Lavallee MJ, Collamati RA, Benevides CC, Gebler JC. 18.  2007. Effects of column length, particle size, gradient length and flow rate on peak capacity of nano-scale liquid chromatography for peptide separations. J. Chromatogr. A114730–36
  19. Luo QZ, Shen YF, Hixson KK, Zhao R, Yang F. 19.  et al. 2005. Preparation of 20-μm i.d. silica-based monolithic columns and their performance for proteomics analyses. Anal. Chem. 77:5028–35 [Google Scholar]
  20. Iwasaki M, Miwa S, Ikegami T, Tomita M, Tanaka N, Ishihama Y. 20.  2010. One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. Anal. Chem. 82:2616–20 [Google Scholar]
  21. Iwasaki M, Sugiyama N, Tanaka N, Ishihama Y. 21.  2012. Human proteome analysis by using reversed phase monolithic silica capillary columns with enhanced sensitivity. J. Chromatogr. A 1228:292–97 [Google Scholar]
  22. Min H-K, Hyung S-W, Shin J-W, Nam H-S, Ahn S-H. 22.  et al. 2007. Ultrahigh-pressure dual online solid phase extraction/capillary reverse-phase liquid chromatography/tandem mass spectrometry (DO-SPE/cRPLC/MS/MS): a versatile separation platform for high-throughput and highly sensitive proteomic analyses. Electrophoresis 28:1012–21 [Google Scholar]
  23. Motoyama A, Venable JD, Ruse CI, Yates JR. 23.  2006. Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. Anal. Chem. 78:5109–18 [Google Scholar]
  24. Thakur SS, Geiger T, Chatterjee B, Bandilla P, Frohlich F. 24.  et al. 2011. Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell. Proteomics 10:M110.003699 [Google Scholar]
  25. Zhou F, Lu Y, Ficarro SB, Webber JT, Marto JA. 25.  2012. Nanoflow low pressure high peak capacity single dimension LC-MS/MS platform for high-throughput, in-depth analysis of mammalian proteomes. Anal. Chem. 84:5133–39 [Google Scholar]
  26. Motoyama A, Yates JR. 26.  2008. Multidimensional LC separations in shotgun proteomics. Anal. Chem. 80:7187–93 [Google Scholar]
  27. Xie F, Smith RD, Shen YF. 27.  2012. Advanced proteomic liquid chromatography. J. Chromatogr. A 1261:78–90 [Google Scholar]
  28. Sandra K, Moshir M, D'hondt F, Tuytten R, Verleysen K. 28.  et al. 2009. Highly efficient peptide separations in proteomics. Part 2: bi- and multidimensional liquid-based separation techniques. J. Chromatogr. B 877:1019–39 [Google Scholar]
  29. Pinkse MWH, Mohammed S, Gouw JW, van Breukelen B, Vos HR, Heck AJR. 29.  2007. Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster. J. Proteome Res. 7:687–97 [Google Scholar]
  30. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ. 30.  et al. 1999. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17:676–82 [Google Scholar]
  31. Washburn MP, Wolters D, Yates JR. 31.  2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19:242–47 [Google Scholar]
  32. Siu SO, Lam MPY, Lau E, Kong RPW, Lee SMY, Chu IK. 32.  2011. Fully automatable two-dimensional reversed-phase capillary liquid chromatography with online tandem mass spectrometry for shotgun proteomics. Proteomics 11:2308–19 [Google Scholar]
  33. Wilson SR, Jankowski M, Pepaj M, Mihailova A, Boix F. 33.  et al. 2007. 2D LC separation and determination of bradykinin in rat muscle tissue dialysate with on-line SPE-HILIC-SPE-RP-MS. Chromatographia 66:469–74 [Google Scholar]
  34. Nagano K, Taoka M, Yamauchi Y, Itagaki C, Shinkawa T. 34.  et al. 2005. Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics 5:1346–61 [Google Scholar]
  35. Simpson DC, Ahn S, Paša-Tolić L, Bogdanov B, Mottaz HM. 35.  et al. 2006. Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling. Electrophoresis 27:2722–33 [Google Scholar]
  36. Chen JZ, Balgley BM, DeVoe DL, Lee CS. 36.  2003. Capillary isoelectric focusing-based multidimensional concentration/separation platform for proteome analysis. Anal. Chem. 75:3145–52 [Google Scholar]
  37. Guo T, Rudnick PA, Wang WJ, Lee CS, Devoe DL, Balgley BM. 37.  2006. Characterization of the human salivary proteome by capillary isoelectric focusing/nanoreversed-phase liquid chromatography coupled with ESI-tandem MS. J. Proteome Res. 5:1469–78 [Google Scholar]
  38. Yang Z, Hancock WS, Chew TR, Bonilla L. 38.  2005. A study of glycoproteins in human serum and plasma reference standards (HUPO) using multilectin affinity chromatography coupled with RPLC-MS/MS. Proteomics 5:3353–66 [Google Scholar]
  39. Lee JH, Hyung S-W, Mun D-G, Jung H-J, Kim H. 39.  et al. 2012. Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses. J. Proteome Res. 11:4373–81 [Google Scholar]
  40. Murphy J, Stapels M, Fadgen K, Geromanos S. 40.  2008. A reproducible method for online RP/RP 2D nanoLC/MS for the analysis of proteomic samples. Proceedings of the 56th ASMS Conference on Mass Spectrometry and Allied Topics Santa Fe, NM: ASMS
  41. Zhou F, Sikorski TW, Ficarro SB, Webber JT, Marto JA. 41.  2011. Online nanoflow reversed phase-strong anion exchange-reversed phase liquid chromatography-tandem mass spectrometry platform for efficient and in-depth proteome sequence analysis of complex organisms. Anal. Chem. 83:6996–7005 [Google Scholar]
  42. Chen JZ, Lee CS, Shen YF, Smith RD, Baehrecke EH. 42.  2002. Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation. Electrophoresis 23:3143–48 [Google Scholar]
  43. Xie HW, Rhodus NL, Griffin RJ, Carlis JV, Griffin TJ. 43.  2005. A catalogue of human saliva proteins identified by free flow electrophoresis-based peptide separation and tandem mass spectrometry. Mol. Cell. Proteomics 4:1826–30 [Google Scholar]
  44. Li YH, Champion MM, Sun LL, Champion PAD, Wojcik R, Dovichi NJ. 44.  2012. Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry as an alternative proteomics platform to ultraperformance liquid chromatography-electrospray ionization-tandem mass spectrometry for samples of intermediate complexity. Anal. Chem. 84:1617–22 [Google Scholar]
  45. Yan X, Essaka DC, Sun L, Zhu G, Dovichi NJ. 45.  2013. Bottom-up proteome analysis of E. coli using capillary zone electrophoresis-tandem mass spectrometry with an electrokinetic sheath-flow electrospray interface. Proteomics 13:172546–51 [Google Scholar]
  46. Liu HB, Sadygov RG, Yates JR. 46.  2004. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76:4193–201 [Google Scholar]
  47. Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JR. 47.  2003. Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal. Chem. 75:2470–77 [Google Scholar]
  48. Xie F, Liu T, Qian WJ, Petyuk VA, Smith RD. 48.  2011. Liquid chromatography-mass spectrometry-based quantitative proteomics. J. Biol. Chem. 286:25443–49 [Google Scholar]
  49. Smith RD, Anderson GA, Lipton MS, Paša-Tolić L, Shen YF. 49.  et al. 2002. An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2:513–23 [Google Scholar]
  50. Andreev VP, Li L, Cao L, Gu Y, Rejtar T. 50.  et al. 2007. A new algorithm using cross-assignment for label-free quantitation with LC/LTQ-FT MS. J. Proteome Res. 6:2186–94 [Google Scholar]
  51. Duan X, Young R, Straubinger RM, Page B, Cao J. 51.  et al. 2009. A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome. J. Proteome Res. 8:2838–50 [Google Scholar]
  52. Luber CA, Cox J, Lauterbach H, Fancke B, Selbach M. 52.  et al. 2010. Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 32:279–89 [Google Scholar]
  53. Monroe ME, Tolić N, Jaitly N, Shaw JL, Adkins JN, Smith RD. 53.  2007. VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics 23:2021–23 [Google Scholar]
  54. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H. 54.  et al. 2002. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1:376–86 [Google Scholar]
  55. Ong SE, Mann M. 55.  2005. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1:252–62 [Google Scholar]
  56. Tzouros M, Golling S, Avila D, Lamerz J, Berrera M. 56.  et al. 2013. Development of a 5-plex SILAC method tuned for the quantitation of tyrosine phosphorylation dynamics. Mol. Cell. Proteomics 12:3339–49 [Google Scholar]
  57. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. 57.  1999. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:994–99 [Google Scholar]
  58. Yi EC, Li XJ, Cooke K, Lee H, Raught B. 58.  et al. 2005. Increased quantitative proteome coverage with C-13/C-12-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics 5:380–87 [Google Scholar]
  59. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K. 59.  et al. 2004. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3:1154–69 [Google Scholar]
  60. Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J. 60.  et al. 2003. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75:1895–904 [Google Scholar]
  61. Angel TE, Aryal UK, Hengel SM, Baker ES, Kelly RT. 61.  et al. 2012. Mass spectrometry-based proteomics: existing capabilities and future directions. Chem. Soc. Rev. 41:3912–28 [Google Scholar]
  62. Christoforou AL, Lilley KS. 62.  2012. Isobaric tagging approaches in quantitative proteomics: the ups and downs. Anal. Bioanal. Chem. 404:1029–37 [Google Scholar]
  63. Ting L, Rad R, Gygi SP, Haas W. 63.  2011. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods 8:937–40 [Google Scholar]
  64. Wenger CD, Lee MV, Hebert AS, McAlister GC, Phanstiel DH. 64.  et al. 2011. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat. Methods 8:933–35 [Google Scholar]
  65. Jenuwein T, Allis CD. 65.  2001. Translating the histone code. Science 293:1074–80 [Google Scholar]
  66. Capriotti AL, Cavaliere C, Foglia P, Samperi R, Lagana A. 66.  2011. Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics. J. Chromatogr. A12188760–76
  67. Wu SL, Jardine I, Hancock WS, Karger BL. 67.  2004. A new and sensitive on-line liquid chromatography/mass spectrometric approach for top-down protein analysis: the comprehensive analysis of human growth hormone in an E. coli lysate using a hybrid linear ion trap/Fourier transform ion cyclotron resonance mass spectrometer. Rapid Commun. Mass Sp. 18:2201–7 [Google Scholar]
  68. Roth MJ, Plymire DA, Chang AN, Kim J, Maresh EM. 68.  et al. 2011. Sensitive and reproducible intact mass analysis of complex protein mixtures with superficially porous capillary reversed-phase liquid chromatography mass spectrometry. Anal. Chem. 83:9586–92 [Google Scholar]
  69. Ansong C, Wu S, Meng D, Liu X, Brewer HM. 69.  et al. 2013. Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions. Proc. Natl. Acad. Sci. USA 110:10153–58 [Google Scholar]
  70. Sharma S, Simpson DC, Tolić N, Jaitly N, Mayampurath AM. 70.  et al. 2007. Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry. J. Proteome Res. 6:602–10 [Google Scholar]
  71. Tian Z, Zhao R, Tolić N, Moore RJ, Stenoien DL. 71.  et al. 2010. Two-dimensional liquid chromatography system for online top-down mass spectrometry. Proteomics 10:3610–20 [Google Scholar]
  72. Tran JC, Doucette AA. 72.  2009. Multiplexed size separation of intact proteins in solution phase for mass spectrometry. Anal. Chem. 81:6201–9 [Google Scholar]
  73. Tran JC, Doucette AA. 73.  2008. Gel-eluted liquid fraction entrapment electrophoresis: an electrophoretic method for broad molecular weight range proteome separation. Anal. Chem. 80:1568–73 [Google Scholar]
  74. Catherman AD, Durbin KR, Ahlf DR, Early BP, Fellers RT. 74.  et al. 2013. Large-scale top down proteomics of the human proteome: membrane proteins, mitochondria, and senescence. Mol. Cell. Proteomics 12:3465–73 [Google Scholar]
  75. Zabrouskov V, Giacomelli L, van Wijk KJ, McLafferty FW. 75.  2003. New approach for plant proteomics: characterization of chloroplast proteins of Arabidopsis thaliana by top-down mass spectrometry. Mol. Cell. Proteomics 2:1253–60 [Google Scholar]
  76. VerBerkmoes NC, Bundy JL, Hauser L, Asano KG, Razumovskaya J. 76.  et al. 2002. Integrating “top-down” and “bottom-up” mass spectrometric approaches for proteomic analysis of Shewanella oneidensis. J. Proteome Res. 1:239–52 [Google Scholar]
  77. Millea KM, Krull IS, Cohen SA, Gebler JC, Berger SJ. 77.  2006. Integration of multidimensional chromatographic protein separations with a combined “top-down” and “bottom-up” proteomic strategy. J. Proteome Res. 5:135–46 [Google Scholar]
  78. Wu S, Lourette NM, Tolić N, Zhao R, Robinson EW. 78.  et al. 2009. An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications. J. Proteome Res. 8:1347–57 [Google Scholar]
  79. López-Ferrer D, Petritis K, Robinson EW, Hixson KK, Tian Z. 79.  et al. 2011. Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics. Mol. Cell. Proteomics 10:M110.001479 [Google Scholar]
  80. Castagnola M, Messana I, Inzitari R, Fanali C, Cabras T. 80.  et al. 2008. Hypo-phosphorylation of salivary peptidome as a clue to the molecular pathogenesis of autism spectrum disorders. J. Proteome Res. 7:5327–32 [Google Scholar]
  81. Cabras T, Pisano E, Montaldo C, Giuca MR, Iavarone F. 81.  et al. 2013. Significant modifications of the salivary proteome potentially associated with complications of Down syndrome revealed by top-down proteomics. Mol. Cell. Proteomics 12:1844–52 [Google Scholar]
  82. Cabras T, Pisano E, Mastinu A, Denotti G, Pusceddu PP. 82.  et al. 2010. Alterations of the salivary secretory peptidome profile in children affected by type 1 diabetes. Mol. Cell. Proteomics 9:2099–108 [Google Scholar]
  83. Wang WX, Zhou HH, Lin H, Roy S, Shaler TA. 83.  et al. 2003. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75:4818–26 [Google Scholar]
  84. Wiener MC, Sachs JR, Deyanova EG, Yates NA. 84.  2004. Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal. Chem. 76:6085–96 [Google Scholar]
  85. Meng FY, Wiener MC, Sachs JR, Burns C, Verma P. 85.  et al. 2007. Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry. J. Am. Soc. Mass Spectr. 18:226–33 [Google Scholar]
  86. Mazur MT, Cardasis HL, Spellman DS, Liaw A, Yates NA, Hendrickson RC. 86.  2010. Quantitative analysis of intact apolipoproteins in human HDL by top-down differential mass spectrometry. Proc. Natl. Acad. Sci. USA 107:7728–33 [Google Scholar]
  87. Johnson KL, Mason CJ, Muddiman DC, Eckel JE. 87.  2004. Analysis of the low molecular weight fraction of serum by LC-dual ESI-FT-ICR mass spectrometry: precision of retention time, mass, and ion abundance. Anal. Chem. 76:5097–103 [Google Scholar]
  88. Paša-Tolić L, Jensen PK, Anderson GA, Lipton MS, Peden KK. 88.  et al. 1999. High throughput proteome-wide precision measurements of protein expression using mass spectrometry. J. Am. Chem. Soc. 121:7949–50 [Google Scholar]
  89. Veenstra TD, Martinovic S, Anderson GA, Paša-Tolić L, Smith RD. 89.  2000. Proteome analysis using selective incorporation of isotopically labeled amino acids. J. Am. Soc. Mass Spectr. 11:78–82 [Google Scholar]
  90. Martinovic S, Veenstra TD, Anderson GA, Paša-Tolić L, Smith RD. 90.  2002. Selective incorporation acids for identification proteome-wide level. J. Mass Spectrom. 37:99–107 [Google Scholar]
  91. Parks BA, Jiang L, Thomas PM, Wenger CD, Roth MJ. 91.  et al. 2007. Top-down proteomics on a chromatographic time scale using linear ion trap Fourier transform hybrid mass spectrometers. Anal. Chem. 79:7984–91 [Google Scholar]
  92. Waanders LF, Hanke S, Mann M. 92.  2007. Top-down quantitation and characterization of SILAC-labeled proteins. J. Am. Soc. Mass. Spectrom. 18:2058–64 [Google Scholar]
  93. Collier TS, Hawkridge AM, Georgianna DR, Payne GA, Muddiman DC. 93.  2008. Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer. Anal. Chem. 80:4994–5001 [Google Scholar]
  94. Collier TS, Muddiman DC. 94.  2012. Analytical strategies for the global quantification of intact proteins. Amino Acids 43:1109–17 [Google Scholar]
  95. Hung CW, Tholey A. 95.  2012. Tandem mass tag protein labeling for top-down identification and quantification. Anal. Chem. 84:161–70 [Google Scholar]
  96. Garcia BA, Pesavento JJ, Mizzen CA, Kelleher NL. 96.  2007. Pervasive combinatorial modification of histone H3 in human cells. Nat. Methods 4:487–89 [Google Scholar]
  97. Pesavento JJ, Bullock CR, LeDuc RD, Mizzen CA, Kelleher NL. 97.  2008. Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry. J. Biol. Chem. 283:14927–37 [Google Scholar]
  98. Tian Z, Tolić N, Zhao R, Moore RJ, Hengel SM. 98.  et al. 2012. Enhanced top-down characterization of histone post-translational modifications. Genome Biol. 13:R86 [Google Scholar]
  99. Young NL, DiMaggio PA, Plazas-Mayorca MD, Baliban RC, Floudas CA, Garcia BA. 99.  2009. High throughput characterization of combinatorial histone codes. Mol. Cell. Proteomics 8:2266–84 [Google Scholar]
  100. Lanucara F, Eyers CE. 100.  2013. Top-down mass spectrometry for the analysis of combinatorial post-translational modifications. Mass Spectrom. Rev. 32:27–42 [Google Scholar]
  101. Horn DM, Zubarev RA, McLafferty FW. 101.  2000. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 11:320–32 [Google Scholar]
  102. Zabrouskov V, Senko MW, Du Y, Leduc RD, Kelleher NL. 102.  2005. New and automated MSn approaches for top-down identification of modified proteins. J. Am. Soc. Mass Spectrom. 16:2027–38 [Google Scholar]
  103. Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N. 103.  et al. 2010. Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol. Cell. Proteomics 9:2772–82 [Google Scholar]
  104. LeDuc RD, Taylor GK, Kim Y-B, Januszyk TE, Bynum LH. 104.  et al. 2004. ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Res. 32:W340–45 [Google Scholar]
  105. Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS. 105.  et al. 2011. Protein identification using top-down spectra. Mol. Cell. Proteomics 11:M111.008524 [Google Scholar]
  106. Karabacak NM, Li L, Tiwari A, Hayward LJ, Hong P. 106.  et al. 2009. Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry. Mol. Cell. Proteomics 8:846–56 [Google Scholar]
  107. Tsai Y, Scherl A, Shaw J, MacKay CL, Shaffer S. 107.  et al. 2009. Precursor ion independent algorithm for top-down shotgun proteomics. J. Am. Soc. Mass Spectr. 20:2154–66 [Google Scholar]
  108. Liu X, Hengel S, Wu S, Tolić N, Paša-Tolić L, Pevzner PA. 108.  2013. Identification of ultramodified proteins using top-down spectra. J. Proteome Res. 12:125830–38 [Google Scholar]
  109. Schwartz JC, Senko MW, Syka JEP. 109.  2002. A two-dimensional quadrupole ion trap mass spectrometer. J. Am. Soc. Mass Spectr. 13:659–69 [Google Scholar]
  110. Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ. 110.  et al. 2009. Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal. Chem. 81:7757–65 [Google Scholar]
  111. Weisbrod CR, Hoopmann MR, Senko MW, Bruce JE. 111.  2013. Performance evaluation of a dual linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer for proteomics research. J. Proteomics 88:109–19 [Google Scholar]
  112. Syka JEP, Marto JA, Bai DL, Horning S, Senko MW. 112.  et al. 2004. Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 3:621–26 [Google Scholar]
  113. Olsen JV, de Godoy LMF, Li G, Macek B, Mortensen P. 113.  et al. 2005. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 4:2010–21 [Google Scholar]
  114. Olsen JV, Schwartz JC, Griep-Raming J, Nielsen ML, Damoc E. 114.  et al. 2009. A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol. Cell. Proteomics 8:2759–69 [Google Scholar]
  115. Hardman M, Makarov AA. 115.  2003. Interfacing the Orbitrap mass analyzer to an electrospray ion source. Anal. Chem. 75:1699–705 [Google Scholar]
  116. Senko MW, Hendrickson CL, Paša-Tolić L, Marto JA, White FM. 116.  et al. 1996. Electrospray ionization Fourier transform ion cyclotron resonance at 9.4 T. Rapid Commun. Mass Sp. 10:1824–28 [Google Scholar]
  117. Xian F, Hendrickson CL, Blakney GT, Beu SC, Marshall AG. 117.  2010. Automated broadband phase correction of Fourier transform ion cyclotron resonance mass spectra. Anal. Chem. 82:8807–12 [Google Scholar]
  118. Qi Y, Barrow MP, Li H, Meier JE, Van Orden SL. 118.  et al. 2012. Absorption-mode: the next generation of Fourier transform mass spectra. Anal. Chem. 84:2923–29 [Google Scholar]
  119. Qi Y, Thompson C, Orden S, O'Connor P. 119.  2011. Phase correction of Fourier transform ion cyclotron resonance mass spectra using MatLab. J. Am. Soc. Mass Spectr. 22:138–47 [Google Scholar]
  120. Lange O, Damoc E, Wieghaus A, Makarov A. 120.  2011. Enhanced FT for Orbitrap mass spectrometry. Proceedings of the 59th ASMS Conference on Mass Spectrometry & Allied Topics Santa Fe, NM: ASMS
  121. Patrie SM, Charlebois JP, Whipple D, Kelleher NL, Hendrickson CL. 121.  et al. 2004. Construction of a hybrid quadrupole/Fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa. J. Am. Soc. Mass Spectr. 15:1099–108 [Google Scholar]
  122. Michalski A, Damoc E, Hauschild JP, Lange O, Wieghaus A. 122.  et al. 2011. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell. Proteomics 10:M111.011015 [Google Scholar]
  123. Steen H, Kuster B, Mann M. 123.  2001. Quadrupole time-of-flight versus triple-quadrupole mass spectrometry for the determination of phosphopeptides by precursor ion scanning. J. Mass Spectrom. 36:782–90 [Google Scholar]
  124. Andrews GL, Simons BL, Young JB, Hawkridge AM, Muddiman DC. 124.  2011. Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal. Chem. 83:5442–46 [Google Scholar]
  125. Zubarev RA, Kelleher NL, McLafferty FW. 125.  1998. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 120:3265–66 [Google Scholar]
  126. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. 126.  2004. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 101:9528–33 [Google Scholar]
  127. Little DP, Speir JP, Senko MW, O'Connor PB, Mclafferty FW. 127.  1994. Infrared multiphoton dissociation of large multiply-charged ions for biomolecule sequencing. Anal. Chem. 66:2809–15 [Google Scholar]
  128. Guan ZQ, Kelleher NL, O'Connor PB, Aaserud DJ, Little DP, McLafferty FW. 128.  1996. 193 nm photodissociation of larger multiply-charged biomolecules. Int. J. Mass Spectrom. Ion Process. 157:357–64 [Google Scholar]
  129. Jones AW, Cooper HJ. 129.  2011. Dissociation techniques in mass spectrometry-based proteomics. Analyst 136:3419–29 [Google Scholar]
  130. Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M. 130.  2007. Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods 4:709–12 [Google Scholar]
  131. Shaw JB, Li W, Holden DD, Zhang Y, Griep-Raming J. 131.  et al. 2013. Complete protein characterization using top-down mass spectrometry and ultraviolet photodissociation. J. Am. Chem. Soc. 135:12646–51 [Google Scholar]
  132. Boldin IA, Nikolaev EN. 132.  2011. Fourier transform ion cyclotron resonance cell with dynamic harmonization of the electric field in the whole volume by shaping of the excitation and detection electrode assembly. Rapid Commun. Mass Sp. 25:122–26 [Google Scholar]
  133. Xian F, Hendrickson CL, Marshall AG. 133.  2012. High resolution mass spectrometry. Anal. Chem. 84:708–19 [Google Scholar]
  134. Michalski A, Damoc E, Lange O, Denisov E, Nolting D. 134.  et al. 2012. Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol. Cell. Proteomics 11:3O111.013698 [Google Scholar]
  135. Valeja SG, Kaiser NK, Xian F, Hendrickson CL, Rouse JC, Marshall AG. 135.  2011. Unit mass baseline resolution for an intact 148 kDa therapeutic monoclonal antibody by Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 83:8391–95 [Google Scholar]
  136. Shaw JB, Brodbelt JS. 136.  2013. Extending the isotopically resolved mass range of Orbitrap mass spectrometers. Anal. Chem. 85:8313–18 [Google Scholar]
  137. van den Heuvel RHH, van Duijn E, Mazon H, Synowsky SA, Lorenzen K. 137.  et al. 2006. Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry. Anal. Chem. 78:7473–83 [Google Scholar]
  138. Chernushevich IV, Thomson BA. 138.  2004. Collisional cooling of large ions in electrospray mass spectrometry. Anal. Chem. 76:1754–60 [Google Scholar]
  139. Sobott F, Hernandez H, McCammon MG, Tito MA, Robinson CV. 139.  2002. A tandem mass spectrometer for improved transmission and analysis of large macromolecular assemblies. Anal. Chem. 74:1402–7 [Google Scholar]
  140. Rose RJ, Damoc E, Denisov E, Makarov A, Heck AJ. 140.  2012. High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies. Nat. Methods 9:1084–86 [Google Scholar]
  141. Horn DM, Ge Y, McLafferty FW. 141.  2000. Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Anal. Chem. 72:4778–84 [Google Scholar]
  142. Hakansson K, Chalmers MJ, Quinn JP, McFarland MA, Hendrickson CL, Marshall AG. 142.  2003. Combined electron capture and infrared multiphoton dissociation for multistage MS/MS in a Fourier transform ion cyclotron resonance mass spectrometer. Anal. Chem. 75:3256–62 [Google Scholar]
  143. Ledvina AR, Beauchene NA, McAlister GC, Syka JEP, Schwartz JC. 143.  et al. 2010. Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture. Anal. Chem. 82:10068–74 [Google Scholar]
  144. Wei BC, Rogers BJ, Wirth MJ. 144.  2012. Slip flow in colloidal crystals for ultraefficient chromatography. J. Am. Chem. Soc. 134:10780–82 [Google Scholar]
  145. Rogers BJ, Birdsall RE, Wu Z, Wirth MJ. 145.  2013. RPLC of intact proteins using sub-0.5-μm particles and commercial instrumentation. Anal. Chem. 85:6820–25 [Google Scholar]
  146. Wu Z, Rogers BJ, Wei BC, Wirth MJ. 146.  2013. Insights from theory and experiments on slip flow in chromatography. J. Sep. Sci. 36:1871–76 [Google Scholar]
  147. Kanu AB, Dwivedi P, Tam M, Matz L, Hill HH. 147.  2008. Ion mobility-mass spectrometry. J. Mass Spectrom. 43:1–22 [Google Scholar]
  148. Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL. 148.  2012. Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Mol. Cell. Proteomics 11:M111.014985 [Google Scholar]
  149. Creese AJ, Shimwell NJ, Larkins KPB, Heath JK, Cooper HJ. 149.  2013. Probing the complementarity of FAIMS and strong cation exchange chromatography in shotgun proteomics. J. Am. Soc. Mass Spectrom. 24:431–43 [Google Scholar]
  150. Canterbury JD, Yi XH, Hoopmann MR, MacCoss MJ. 150.  2008. Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics. Anal. Chem. 80:6888–97 [Google Scholar]
  151. Creese AJ, Smart J, Cooper HJ. 151.  2013. Large-scale analysis of peptide sequence variants: the case for high-field asymmetric waveform ion mobility spectrometry. Anal. Chem. 85:4836–43 [Google Scholar]
  152. Zinnel NF, Pai PJ, Russell DH. 152.  2012. Ion mobility-mass spectrometry (IM-MS) for top-down proteomics: increased dynamic range affords increased sequence coverage. Anal. Chem. 84:3390–97 [Google Scholar]
  153. Tang KQ, Li FM, Shvartsburg AA, Strittmatter EF, Smith RD. 153.  2005. Two-dimensional gas-phase separations coupled to mass spectrometry for analysis of complex mixtures. Anal. Chem. 77:6381–88 [Google Scholar]
  154. Merenbloom SI, Koeniger SL, Valentine SJ, Plasencia MD, Clemmer DE. 154.  2006. IMS−IMS and IMS−IMS−IMS/MS for separating peptide and protein fragment ions. Anal. Chem. 78:2802–9 [Google Scholar]
  155. Bohrer BC, Clemmer DE. 155.  2011. Shift reagents for multidimensional ion mobility spectrometry-mass spectrometry analysis of complex peptide mixtures: evaluation of 18-crown-6 ether complexes. Anal. Chem. 83:5377–85 [Google Scholar]
  156. Merenbloom SI, Glaskin RS, Henson ZB, Clemmer DE. 156.  2009. High-resolution ion cyclotron mobility spectrometry. Anal. Chem. 81:1482–87 [Google Scholar]
  157. Glaskin RS, Valentine SJ, Clemmer DE. 157.  2010. A scanning frequency mode for ion cyclotron mobility spectrometry. Anal. Chem. 82:8266–71 [Google Scholar]
  158. Dephoure N, Gygi SP. 158.  2012. Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast. Sci. Signal. 5:rs2 [Google Scholar]
  159. Hebert AS, Merrill AE, Bailey DJ, Still AJ, Westphall MS. 159.  et al. 2013. Neutron-encoded mass signatures for multiplexed proteome quantification. Nat. Methods 10:332–34 [Google Scholar]
  160. Ficarro SB, Biagi JM, Wang J, Scotcher J, Koleva RI. 160.  et al. 2014. Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents. J. Am. Soc. Mass Spectrom. 25:4636–50 [Google Scholar]
  161. Rose CM, Merrill AE, Bailey DJ, Hebert AS, Westphall MS, Coon JJ. 161.  2013. Neutron encoded labeling for peptide identification. Anal. Chem. 85:5129–37 [Google Scholar]
  162. Hebert AS, Merrill AE, Stefely JA, Bailey DJ, Wenger CD. 162.  et al. 2013. Amine-reactive neutron-encoded labels for highly-plexed proteomic quantitation. Mol. Cell. Proteomics 12:P3360–69 [Google Scholar]
  163. Weerapana E, Speers AE, Cravatt BF. 163.  2007. Tandem orthogonal proteolysis-activity-based protein profiling (TOP-ABPP)—a general method for mapping sites of probe modification in proteomes. Nat. Protoc. 2:1414–25 [Google Scholar]
  164. Bachovchin DA, Ji T, Li W, Simon GM, Blankman JL. 164.  et al. 2010. Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening. Proc. Natl. Acad. Sci. USA 107:4920941–46 [Google Scholar]
  165. Chang JW, Nomura D K, Cravatt B F. 165.  2011. A potent and selective inhibitor of KIAA1363/AADACL1 that impairs prostate cancer pathogenesis. Chem. Biol. 18:476–84 [Google Scholar]
  166. Li N, Overkleeft HS, Florea BI. 166.  2012. Activity-based protein profiling: an enabling technology in chemical biology research. Curr. Opin. Chem. Biol. 16:227–33 [Google Scholar]
  167. Garcia BA.167.  2010. What does the future hold for top down mass spectrometry?. J. Am. Soc. Mass Spectr. 21:193–202 [Google Scholar]
  168. Phanstiel D, Brumbaugh J, Berggren WT, Conard K, Feng X. 168.  et al. 2008. Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells. Proc. Natl. Acad. Sci. USA 105:4093–98 [Google Scholar]
  169. Kalli A, Sweredoski MJ, Hess S. 169.  2013. Data-dependent middle-down nano-liquid chromatography-electron capture dissociation-tandem mass spectrometry: an application for the analysis of unfractionated histones. Anal. Chem. 85:3501–7 [Google Scholar]
  170. Coon JJ, Ueberheide B, Syka JEP, Dryhurst DD, Ausio J. 170.  et al. 2005. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 102:9463–68 [Google Scholar]
  171. Good DM, Wirtala M, McAlister GC, Coon JJ. 171.  2007. Performance characteristics of electron transfer dissociation mass spectrometry. Mol. Cell. Proteomics 6:1942–51 [Google Scholar]
  172. McAlister GC, Berggren WT, Griep-Raming J, Horning S, Makarov A. 172.  et al. 2008. A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-Orbitrap mass spectrometer. J. Proteome Res. 7:3127–36 [Google Scholar]
  173. McAlister GC, Phanstiel D, Good DM, Berggren WT, Coon JJ. 173.  2007. Implementation of electron-transfer dissociation on a hybrid linear ion trap-Orbitrap mass spectrometer. Anal. Chem. 79:3525–34 [Google Scholar]
  174. Wu C, Tran JC, Zamdborg L, Durbin KR, Li MX. 174.  et al. 2012. A protease for “middle-down” proteomics. Nat. Methods 9:822–24 [Google Scholar]
  175. Hebert AS, Richards AL, Bailey DJ, Ulbrich A, Coughlin EE. 175.  et al. 2013. The one hour yeast proteome. Mol. Cell. Proteomics 13:339–47 [Google Scholar]
  176. Gillet LC, Navarro P, Tate S, Röst H, Selevsek N. 176.  et al. 2012. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11:O111.016717 [Google Scholar]
  177. Curran TG, Bryson BD, Reigelhaupt M, Johnson H, White FM. 177.  2013. Computer aided manual validation of mass spectrometry-based proteomic data. Methods 61:219–26 [Google Scholar]
  178. Anderson NL, Anderson NG. 178.  2002. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1:845–67 [Google Scholar]
  179. Baker ES, Livesay EA, Orton DJ, Moore RJ, Danielson WF III. 179.  et al. 2010. An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J. Proteome Res. 9:997–1006 [Google Scholar]
/content/journals/10.1146/annurev-anchem-071213-020216
Loading
/content/journals/10.1146/annurev-anchem-071213-020216
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error