Abstract
Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.
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Abbreviations
- AP:
-
Affinity purification
- DDA:
-
Data-dependent acquisition
- ESI:
-
Electrospray ionization
- HCD:
-
Higher-energy collision-induced dissociation
- HDAC:
-
Histone deacetylase
- HPLC:
-
High-pressure liquid chromatography
- ICP:
-
Inductively coupled plasma
- IMAC:
-
Immobilized metal affinity chromatography
- iTRAQ:
-
Isobaric tags for absolute and relative quantification
- LC:
-
Liquid chromatography
- MRM:
-
Multiple reaction monitoring
- MS:
-
Mass spectrometry
- MS/MS:
-
Tandem mass spectrometry
- PAI:
-
Protein abundance index
- PrEST:
-
Protein epitope signature tag
- PSAQ:
-
Protein standard absolute quantification
- PSM:
-
Peptide-to-spectrum match
- PTM:
-
Post-translational modification
- QTOF:
-
Quadrupole time of flight
- SILAC:
-
Stable isotope labeling with amino acids in cell culture
- SRM:
-
Selected reaction monitoring
- TMT:
-
Tandem mass tag
- UPLC:
-
Ultra-high-pressure liquid chromatography
- XIC:
-
Extracted ion chromatogram
References
Aebersold R, Mann M (2003) Nature 422(6928):198–207. doi:10.1038/nature01511nature01511
Mallick P, Kuster B (2010) Nat Biotechnol 28(7):695–709. doi:10.1038/nbt.1658
Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B (2007) Anal Bioanal Chem 389(4):1017–1031. doi:10.1007/s00216-007-1486-6
Gao M, Qi D, Zhang P, Deng C, Zhang X (2011) Expert Rev Proteomics 7(5):665–678. doi:10.1586/epr.10.49
Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, Aebersold R (2011) Mol Syst Biol 7:549. doi:10.1038/msb.2011.82
Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Paabo S, Mann M (2011) Mol Syst Biol 7:548. doi:10.1038/msb.2011.81
Cox J, Mann M (2008) Nat Biotechnol 26(12):1367–1372. doi:10.1038/nbt.1511
Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R (2010) Proteomics 10(6):1150–1159. doi:10.1002/pmic.200900375
Jung K (2011) Methods Mol Biol 696:259–272. doi:10.1007/978-1-60761-987-1_16
Lemeer S, Heck AJ (2009) Curr Opin Chem Biol 13(4):414–420. doi:10.1016/j.cbpa.2009.06.022
Norris KL, Lee JY, Yao TP (2009) Sci Signal 2(97):pe76. doi:10.1126/scisignal.297pe76
Whiteaker JR, Zhao L, Abbatiello SE, Burgess M, Kuhn E, Lin C, Pope ME, Razavi M, Anderson NL, Pearson TW, Carr SA, Paulovich AG (2011) Mol Cell Proteomics 10(4):M110.005645. doi:10.1074/mcp.M110.005645
Schirle M, Bantscheff M, Kuster B (2012) Chem Biol 19(1):72–84. doi:10.1016/j.chembiol.2012.01.002
Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Mol Cell Proteomics 1(5):376–386
Zhang R, Sioma CS, Wang S, Regnier FE (2001) Anal Chem 73(21):5142–5149
Lam YW, Lamond AI, Mann M, Andersen JS (2007) Curr Biol 17(9):749–760. doi:10.1016/j.cub.2007.03.064
Milner E, Barnea E, Beer I, Admon A (2006) Mol Cell Proteomics 5(2):357–365. doi:10.1074/mcp.M500241-MCP200
Schwanhausser B, Gossen M, Dittmar G, Selbach M (2009) Proteomics 9(1):205–209. doi:10.1002/pmic.200800275
Cambridge SB, Gnad F, Nguyen C, Bermejo JL, Kruger M, Mann M (2011) J Proteome Res 10(12):5275–5284. doi:10.1021/pr101183k
Looso M, Borchardt T, Kruger M, Braun T (2010) Mol Cell Proteomics 9(6):1157–1166. doi:10.1074/mcp.M900426-MCP200
Ebner OA, Selbach M (2011) Methods Mol Biol 725:315–331. doi:10.1007/978-1-61779-046-1_20
Wu Z, Moghaddas Gholami A, Kuster B (2012) Mol Cell Proteomics 11:M111.016675. doi:10.1074/mcp.M111.016675
Geiger T, Cox J, Ostasiewicz P, Wisniewski JR, Mann M (2010) Nat Methods 7(5):383–385. doi:10.1038/nmeth.1446
Geiger T, Wisniewski JR, Cox J, Zanivan S, Kruger M, Ishihama Y, Mann M (2011) Nat Protoc 6(2):147–157. doi:10.1038/nprot.2010.192
Kruger M, Moser M, Ussar S, Thievessen I, Luber CA, Forner F, Schmidt S, Zanivan S, Fassler R, Mann M (2008) Cell 134(2):353–364. doi:10.1016/j.cell.2008.05.033
Gouw JW, Krijgsveld J, Heck AJ (2010) Mol Cell Proteomics 9(1):11–24. doi:10.1074/mcp.R900001-MCP200
Hanke S, Besir H, Oesterhelt D, Mann M (2008) J Proteome Res 7(3):1118–1130. doi:10.1021/pr7007175
Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C (2003) Anal Chem 75(8):1895–1904
Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ (2004) Mol Cell Proteomics 3(12):1154–1169. doi:10.1074/mcp.M400129-MCP200
Wiese S, Reidegeld KA, Meyer HE, Warscheid B (2007) Proteomics 7(3):340–350. doi:10.1002/pmic.200600422
Bantscheff M, Boesche M, Eberhard D, Matthieson T, Sweetman G, Kuster B (2008) Mol Cell Proteomics 7(9):1702–1713. doi:10.1074/mcp.M800029-MCP200
Griffin TJ, Xie H, Bandhakavi S, Popko J, Mohan A, Carlis JV, Higgins L (2007) J Proteome Res 6(11):4200–4209. doi:10.1021/pr070291b
Meany DL, Xie H, Thompson LV, Arriaga EA, Griffin TJ (2007) Proteomics 7(7):1150–1163. doi:10.1002/pmic.200600450
Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M (2007) Nat Methods 4(9):709–712. doi:10.1038/nmeth1060
McAlister GC, Phanstiel DH, Brumbaugh J, Westphall MS, Coon JJ (2011) Mol Cell Proteomics 10(5):O111 009456. doi:10.1074/mcp.O111.009456
Han H, Pappin DJ, Ross PL, McLuckey SA (2008) J Proteome Res 7(9):3643–3648. doi:10.1021/pr8001113
Phanstiel D, Unwin R, McAlister GC, Coon JJ (2009) Anal Chem 81(4):1693–1698. doi:10.1021/ac8019202
Phanstiel D, Zhang Y, Marto JA, Coon JJ (2008) J Am Soc Mass Spectrom 19(9):1255–1262. doi:10.1016/j.jasms.2008.05.023
Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV, Lilley KS (2010) Mol Cell Proteomics 9(9):1885–1897. doi:10.1074/mcp.M900628-MCP200
Ting L, Rad R, Gygi SP, Haas W (2011) Nat Methods 8(11):937–940. doi:10.1038/nmeth.1714
Wenger CD, Lee MV, Hebert AS, McAlister GC, Phanstiel DH, Westphall MS, Coon JJ (2011) Nat Methods 8(11):933–935. doi:10.1038/nmeth.1716
DeSouza LV, Taylor AM, Li W, Minkoff MS, Romaschin AD, Colgan TJ, Siu KW (2008) J Proteome Res 7(8):3525–3534. doi:10.1021/pr800312m
Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE, Jaffe JD, Carr SA (2012) Mol Cell. Proteomics. doi:10.1074/mcp.M111.014423
Hsu JL, Huang SY, Chow NH, Chen SH (2003) Anal Chem 75(24):6843–6852. doi:10.1021/ac0348625
Huang SY, Tsai ML, Wu CJ, Hsu JL, Ho SH, Chen SH (2006) Proteomics 6(6):1722–1734. doi:10.1002/pmic.200500507
Boersema PJ, Aye TT, van Veen TA, Heck AJ, Mohammed S (2008) Proteomics 8(22):4624–4632. doi:10.1002/pmic.200800297
Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ (2009) Nat Protoc 4(4):484–494. doi:10.1038/nprot.2009.21
Prudova A, auf dem Keller U, Butler GS, Overall CM (2010) Mol Cell Proteomics 9(5):894–911. doi:10.1074/mcp.M000050-MCP201
Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP (2008) Proc Natl Acad Sci USA 105(31):10762–10767. doi:10.1073/pnas.0805139105
Taouatas N, Altelaar AF, Drugan MM, Helbig AO, Mohammed S, Heck AJ (2009) Mol Cell Proteomics 8(1):190–200. doi:10.1074/mcp.M800285-MCP200
Wisniewski JR, Nagaraj N, Zougman A, Gnad F, Mann M (2010) J Proteome Res 9(6):3280–3289. doi:10.1021/pr1002214
Delmotte N, Lasaosa M, Tholey A, Heinzle E, Huber CG (2007) J Proteome Res 6(11):4363–4373. doi:10.1021/pr070424t
Pinkse MW, Mohammed S, Gouw JW, van Breukelen B, Vos HR, Heck AJ (2008) J Proteome Res 7(2):687–697. doi:10.1021/pr700605z
Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP (2004) Proc Natl Acad Sci USA 101(33):12130–12135. doi:10.1073/pnas.0404720101
Di Palma S, Boersema PJ, Heck AJ, Mohammed S (2011) Anal Chem 83(9):3440–3447. doi:10.1021/ac103312e
McNulty DE, Annan RS (2008) Mol Cell Proteomics 7(5):971–980. doi:10.1074/mcp.M700543-MCP200
Ow SY, Salim M, Noirel J, Evans C, Wright PC (2011) Proteomics 11(11):2341–2346. doi:10.1002/pmic.201000752
Eeltink S, Dolman S, Swart R, Ursem M, Schoenmakers PJ (2009) J Chromatogr A 1216(44):7368–7374. doi:10.1016/j.chroma.2009.02.075
Hyung SW, Kim MS, Mun DG, Lee H, Lee SW (2011) Analyst 136(10):2100–2105. doi:10.1039/c0an00724b
Motoyama A, Venable JD, Ruse CI, Yates JR 3rd (2006) Anal Chem 78(14):5109–5118. doi:10.1021/ac060354u
Nagaraj N, Alexander Kulak N, Cox J, Neuhauser N, Mayr K, Hoerning O, Vorm O, Mann M (2012) Mol Cell Proteomics 11(3):M111 013722. doi:10.1074/mcp.M111.013722
Kocher T, Swart R, Mechtler K (2011) Anal Chem 83(7):2699–2704. doi:10.1021/ac103243t
Lee J, Soper SA, Murray KK (2009) J Mass Spectrom 44(5):579–593. doi:10.1002/jms.1585
Mohammed S, Kraiczek K, Pinkse MW, Lemeer S, Benschop JJ, Heck AJ (2008) J Proteome Res 7(4):1565–1571. doi:10.1021/pr700635a
Vollmer M, Horth P, Rozing G, Coute Y, Grimm R, Hochstrasser D, Sanchez JC (2006) J Sep Sci 29(4):499–509
Kim MS, Pandey A (2012) Proteomics 12(4–5):530–542. doi:10.1002/pmic.201100517
Domon B, Aebersold R (2010) Nat Biotechnol 28(7):710–721. doi:10.1038/nbt.1661
Michalski A, Cox J, Mann M (2011) J Proteome Res 10(4):1785–1793. doi:10.1021/pr101060v
Gillet LC, Navarro P, Tate S, Roest H, Selevsek N, Reiter L, Bonner R, Aebersold R (2012) Mol Cell Proteomics 11:O111.016717. doi:10.1074/mcp.O111.016717
Pelander A, Decker P, Baessmann C, Ojanpera I (2011) J Am Soc Mass Spectrom 22(2):379–385. doi:10.1007/s13361-010-0046-z
Swaney DL, McAlister GC, Coon JJ (2008) Nat Methods 5(11):959–964. doi:10.1038/nmeth.1260
Kuster B, Schirle M, Mallick P, Aebersold R (2005) Nat Rev Mol Cell Biol 6(7):577–583. doi:10.1038/nrm1683
Panchaud A, Affolter M, Moreillon P, Kussmann M (2008) J Proteomics 71(1):19–33. doi:10.1016/j.jprot.2007.12.001
Panchaud A, Scherl A, Shaffer SA, von Haller PD, Kulasekara HD, Miller SI, Goodlett DR (2009) Anal Chem 81(15):6481–6488. doi:10.1021/ac900888s
Geiger T, Cox J, Mann M (2010) Mol Cell Proteomics 9(10):2252–2261. doi:10.1074/mcp.M110.001537
Plumb RS, Johnson KA, Rainville P, Smith BW, Wilson ID, Castro-Perez JM, Nicholson JK (2006) Rapid Commun Mass Spectrom 20(13):1989–1994. doi:10.1002/rcm.2550
Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ (2010) Anal Chem 82(3):833–841. doi:10.1021/ac901801b
Carvalho PC, Han X, Xu T, Cociorva D, da Gloria Carvalho M, Barbosa VC, Yates JR 3rd (2010) Bioinformatics 26(6):847–848. doi:10.1093/bioinformatics/btq031
Geromanos SJ, Vissers JP, Silva JC, Dorschel CA, Li GZ, Gorenstein MV, Bateman RH, Langridge JI (2009) Proteomics 9(6):1683–1695. doi:10.1002/pmic.200800562
Washburn MP, Wolters D, Yates JR 3rd (2001) Nat Biotechnol 19(3):242–247. doi:10.1038/85686
Liu H, Sadygov RG, Yates JR 3rd (2004) Anal Chem 76(14):4193–4201. doi:10.1021/ac0498563
Zhang B, VerBerkmoes NC, Langston MA, Uberbacher E, Hettich RL, Samatova NF (2006) J Proteome Res 5(11):2909–2918. doi:10.1021/pr0600273
Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG (2005) Mol Cell Proteomics 4(10):1487–1502. doi:10.1074/mcp.M500084-MCP200
Cooper B, Feng J, Garrett WM (2010) J Am Soc Mass Spectrom 21(9):1534–1546. doi:10.1016/j.jasms.2010.05.001
Zhou JY, Schepmoes AA, Zhang X, Moore RJ, Monroe ME, Lee JH, Camp DG, Smith RD, Qian WJ (2010) J Proteome Res 9(11):5698–5704. doi:10.1021/pr100508p
Choi H, Fermin D, Nesvizhskii AI (2008) Mol Cell Proteomics 7(12):2373–2385. doi:10.1074/mcp.M800203-MCP200
Nesvizhskii AI, Aebersold R (2005) Mol Cell Proteomics 4(10):1419–1440. doi:10.1074/mcp.R500012-MCP200
Zhang Y, Wen Z, Washburn MP, Florens L (2010) Anal Chem 82(6):2272–2281. doi:10.1021/ac9023999
Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP (2006) J Proteome Res 5(9):2339–2347. doi:10.1021/pr060161n
Asara JM, Christofk HR, Freimark LM, Cantley LC (2008) Proteomics 8(5):994–999. doi:10.1002/pmic.200700426
Griffin NM, Yu J, Long F, Oh P, Shore S, Li Y, Koziol JA, Schnitzer JE (2010) Nat Biotechnol 28(1):83–89. doi:10.1038/nbt.1592
Colaert N, Gevaert K, Martens L (2011) J Proteome Res 10(7):3183–3189. doi:10.1021/pr200219x
Bondarenko PV, Chelius D, Shaler TA (2002) Anal Chem 74(18):4741–4749
Chelius D, Bondarenko PV (2002) J Proteome Res 1(4):317–323
Sandra K, Moshir M, D'Hondt F, Tuytten R, Verleysen K, Kas K, Francois I, Sandra P (2009) J Chromatogr B Anal Technol Biomed Life Sci 877(11–12):1019–1039. doi:10.1016/j.jchromb.2009.02.050
Sandra K, Moshir M, D'Hondt F, Verleysen K, Kas K, Sandra P (2008) J Chromatogr B Anal Technol Biomed Life Sci 866(1–2):48–63. doi:10.1016/j.jchromb.2007.10.034
Sun W, Wu S, Wang X, Zheng D, Gao Y (2005) Eur J Mass Spectrom (Chichester, Eng) 11(6):575–580. doi:10.1255/ejms.776
Radulovic D, Jelveh S, Ryu S, Hamilton TG, Foss E, Mao Y, Emili A (2004) Mol Cell Proteomics 3(10):984–997. doi:10.1074/mcp.M400061-MCP200
Conrads TP, Anderson GA, Veenstra TD, Pasa-Tolic L, Smith RD (2000) Anal Chem 72(14):3349–3354
Stanley JR, Adkins JN, Slysz GW, Monroe ME, Purvine SO, Karpievitch YV, Anderson GA, Smith RD, Dabney AR (2011) Anal Chem 83(16):6135–6140. doi:10.1021/ac2009806
Monroe ME, Tolic N, Jaitly N, Shaw JL, Adkins JN, Smith RD (2007) Bioinformatics 23(15):2021–2023. doi:10.1093/bioinformatics/btm281
Fang R, Elias DA, Monroe ME, Shen Y, McIntosh M, Wang P, Goddard CD, Callister SJ, Moore RJ, Gorby YA, Adkins JN, Fredrickson JK, Lipton MS, Smith RD (2006) Mol Cell Proteomics 5(4):714–725. doi:10.1074/mcp.M500301-MCP200
Varnum SM, Webb-Robertson BJ, Hessol NA, Smith RD, Zangar RC (2011) PLoS One 6(12):e29263. doi:10.1371/journal.pone.0029263
Silva JC, Denny R, Dorschel C, Gorenstein MV, Li GZ, Richardson K, Wall D, Geromanos SJ (2006) Mol Cell Proteomics 5(4):589–607. doi:10.1074/mcp.M500321-MCP200
Silva JC, Gorenstein MV, Li GZ, Vissers JP, Geromanos SJ (2006) Mol Cell Proteomics 5(1):144–156. doi:10.1074/mcp.M500230-MCP200
Li GZ, Vissers JP, Silva JC, Golick D, Gorenstein MV, Geromanos SJ (2009) Proteomics 9(6):1696–1719. doi:10.1002/pmic.200800564
Blackburn K, Cheng FY, Williamson JD, Goshe MB (2010) Rapid Commun Mass Spectrom 24(7):1009–1016. doi:10.1002/rcm.4476
Blackburn K, Mbeunkui F, Mitra SK, Mentzel T, Goshe MB (2010) J Proteome Res 9(7):3621–3637. doi:10.1021/pr100144z
Kohlbacher O, Reinert K, Gropl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M (2007) Bioinformatics 23(2):e191–197. doi:10.1093/bioinformatics/btl299
Reinert K, Kohlbacher O (2010) Methods Mol Biol 604:201–211. doi:10.1007/978-1-60761-444-9_14
Sturm M, Bertsch A, Gropl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O (2008) BMC Bioinforma 9:163. doi:10.1186/1471-2105-9-163
Luber CA, Cox J, Lauterbach H, Fancke B, Selbach M, Tschopp J, Akira S, Wiegand M, Hochrein H, O'Keeffe M, Mann M (2010) Immunity 32(2):279–289. doi:10.1016/j.immuni.2010.01.013
Leptos KC, Sarracino DA, Jaffe JD, Krastins B, Church GM (2006) Proteomics 6(6):1770–1782. doi:10.1002/pmic.200500201
Park SK, Venable JD, Xu T, Yates JR 3rd (2008) Nat Methods 5(4):319–322. doi:10.1038/nmeth.1195
Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Muller M (2007) Proteomics 7(19):3470–3480. doi:10.1002/pmic.200700057
America AH, Cordewener JH (2008) Proteomics 8(4):731–749. doi:10.1002/pmic.200700694
Christin C, Bischoff R, Horvatovich P (2011) Talanta 83(4):1209–1224. doi:10.1016/j.talanta.2010.10.029
Neilson KA, Ali NA, Muralidharan S, Mirzaei M, Mariani M, Assadourian G, Lee A, van Sluyter SC, Haynes PA (2011) Proteomics 11(4):535–553. doi:10.1002/pmic.201000553
Choi H, Glatter T, Gstaiger M, Nesvizhskii AI (2012) J Proteome Res 11(4):2619–2624. doi:10.1021/pr201185r
Grossmann J, Roschitzki B, Panse C, Fortes C, Barkow-Oesterreicher S, Rutishauser D, Schlapbach R (2010) J Proteomics 73(9):1740–1746. doi:10.1016/j.jprot.2010.05.011
Costenoble R, Picotti P, Reiter L, Stallmach R, Heinemann M, Sauer U, Aebersold R (2011) Mol Syst Biol 7:464. doi:10.1038/msb.2010.122
Kitteringham NR, Jenkins RE, Lane CS, Elliott VL, Park BK (2009) J Chromatogr B Anal Technol Biomed Life Sci 877(13):1229–1239. doi:10.1016/j.jchromb.2008.11.013
Malmstrom J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R (2009) Nature 460(7256):762–765. doi:10.1038/nature08184
Gallien S, Duriez E, Domon B (2011) J Mass Spectrom 46(3):298–312. doi:10.1002/jms.1895
Lange V, Picotti P, Domon B, Aebersold R (2008) Mol Syst Biol 4:222. doi:10.1038/msb.2008.61
Duncan MW, Yergey AL, Patterson SD (2009) Proteomics 9(5):1124–1127. doi:10.1002/pmic.200800739
Deutsch EW (2010) Methods Mol Biol 604:285–296. doi:10.1007/978-1-60761-444-9_19
Deutsch EW, Lam H, Aebersold R (2008) EMBO Rep 9(5):429–434. doi:10.1038/embor.2008.56
Jones P, Cote RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H (2008) Nucleic Acids Res 36(Suppl 1):D878–D883. doi:10.1093/nar/gkm1021
Jones P, Cote RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R (2006) Nucleic Acids Res 34(Suppl 1):D659–D663. doi:10.1093/nar/gkj138
Wang R, Fabregat A, Rios D, Ovelleiro D, Foster JM, Cote RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaino JA (2012) Nat Biotechnol 30(2):135–137. doi:10.1038/nbt.2112
Fusaro VA, Mani DR, Mesirov JP, Carr SA (2009) Nat Biotechnol 27(2):190–198. doi:10.1038/nbt.1524
Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R (2007) Nat Biotechnol 25(1):125–131. doi:10.1038/nbt1275
Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R (2008) Nat Methods 5(11):913–914. doi:10.1038/nmeth1108-913
Reiter L, Rinner O, Picotti P, Huttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R (2011) Nat Methods 8(5):430–435. doi:10.1038/nmeth.1584
Cham Mead JA, Bianco L, Bessant C (2010) Proteomics 10(6):1106–1126. doi:10.1002/pmic.200900396
MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR 3rd (2003) Anal Chem 75(24):6912–6921. doi:10.1021/ac034790h
Unwin RD, Griffiths JR, Leverentz MK, Grallert A, Hagan IM, Whetton AD (2005) Mol Cell Proteomics 4(8):1134–1144. doi:10.1074/mcp.M500113-MCP200
Kiyonami R, Schoen A, Prakash A, Peterman S, Zabrouskov V, Picotti P, Aebersold R, Huhmer A, Domon B (2010) Mol Cell Proteomics 10(2):M110.002931. doi:10.1074/mcp.M110.002931
Stahl-Zeng J, Lange V, Ossola R, Eckhardt K, Krek W, Aebersold R, Domon B (2007) Mol Cell Proteomics 6(10):1809–1817. doi:10.1074/mcp.M700132-MCP200
Klaassen T, Szwandt S, Kapron JT, Roemer A (2009) Rapid Commun Mass Spectrom 23(15):2301–2306. doi:10.1002/rcm.4147
Fortin T, Salvador A, Charrier JP, Lenz C, Bettsworth F, Lacoux X, Choquet-Kastylevsky G, Lemoine J (2009) Anal Chem 81(22):9343–9352. doi:10.1021/ac901447h
Bennett EJ, Rush J, Gygi SP, Harper JW (2010) Cell 143(6):951–965. doi:10.1016/j.cell.2010.11.017
Kuepfer L, Peter M, Sauer U, Stelling J (2007) Nat Biotechnol 25(9):1001–1006. doi:10.1038/nbt1330
Lu P, Vogel C, Wang R, Yao X, Marcotte EM (2007) Nat Biotechnol 25(1):117–124. doi:10.1038/nbt1270
Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M (2011) Nature 473(7347):337–342. doi:10.1038/nature10098
Holzmann J, Pichler P, Madalinski M, Kurzbauer R, Mechtler K (2009) Anal Chem 81(24):10254–10261. doi:10.1021/ac902286m
Nanavati D, Gucek M, Milne JL, Subramaniam S, Markey SP (2008) Mol Cell Proteomics 7(2):442–447. doi:10.1074/mcp.M700345-MCP200
Schmidt C, Lenz C, Grote M, Luhrmann R, Urlaub H (2010) Anal Chem 82(7):2784–2796. doi:10.1021/ac902710k
Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M (2009) Nat Methods 6(3):203–205. doi:10.1038/nmeth.1302
Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003) Proc Natl Acad Sci USA 100(12):6940–6945. doi:10.1073/pnas.0832254100
Kirkpatrick DS, Gerber SA, Gygi SP (2005) Methods 35(3):265–273. doi:10.1016/j.ymeth.2004.08.018
Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ (2005) Nat Methods 2(8):587–589. doi:10.1038/nmeth774
Brun V, Dupuis A, Adrait A, Marcellin M, Thomas D, Court M, Vandenesch F, Garin J (2007) Mol Cell Proteomics 6(12):2139–2149. doi:10.1074/mcp.M700163-MCP200
Singh S, Springer M, Steen J, Kirschner MW, Steen H (2009) J Proteome Res 8(5):2201–2210. doi:10.1021/pr800654s
Carroll KM, Simpson DM, Eyers CE, Knight CG, Brownridge P, Dunn WB, Winder CL, Lanthaler K, Pir P, Malys N, Kell DB, Oliver SG, Gaskell SJ, Beynon RJ (2011) Mol Cell Proteomics 10(12):M111.007633. doi:10.1074/mcp.M111.007633
Adrait A, Lebert D, Trauchessec M, Dupuis A, Louwagie M, Masselon C, Jaquinod M, Chevalier B, Vandenesch F, Garin J, Bruley C, Brun V (2012) J Proteomics 75(10):3041–3049. doi:10.1016/j.jprot.2011.11.031
Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M (2012) Mol Cell Proteomics 11:O111.009613. doi:10.1074/mcp.O111.009613
Persson A, Hober S, Uhlen M (2006) Curr Opin Mol Ther 8(3):185–190
Uhlen M, Bjorling E, Agaton C, Szigyarto CA, Amini B, Andersen E, Andersson AC, Angelidou P, Asplund A, Asplund C, Berglund L, Bergstrom K, Brumer H, Cerjan D, Ekstrom M, Elobeid A, Eriksson C, Fagerberg L, Falk R, Fall J, Forsberg M, Bjorklund MG, Gumbel K, Halimi A, Hallin I, Hamsten C, Hansson M, Hedhammar M, Hercules G, Kampf C, Larsson K, Lindskog M, Lodewyckx W, Lund J, Lundeberg J, Magnusson K, Malm E, Nilsson P, Odling J, Oksvold P, Olsson I, Oster E, Ottosson J, Paavilainen L, Persson A, Rimini R, Rockberg J, Runeson M, Sivertsson A, Skollermo A, Steen J, Stenvall M, Sterky F, Stromberg S, Sundberg M, Tegel H, Tourle S, Wahlund E, Walden A, Wan J, Wernerus H, Westberg J, Wester K, Wrethagen U, Xu LL, Hober S, Ponten F (2005) Mol Cell Proteomics 4(12):1920–1932. doi:10.1074/mcp.M500279-MCP200
Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Bjorling L, Ponten F (2010) Nat Biotechnol 28(12):1248–1250. doi:10.1038/nbt1210-1248
Blondeau F, Ritter B, Allaire PD, Wasiak S, Girard M, Hussain NK, Angers A, Legendre-Guillemin V, Roy L, Boismenu D, Kearney RE, Bell AW, Bergeron JJ, McPherson PS (2004) Proc Natl Acad Sci USA 101(11):3833–3838. doi:10.1073/pnas.0308186101
Powell DW, Weaver CM, Jennings JL, McAfee KJ, He Y, Weil PA, Link AJ (2004) Mol Cell Biol 24(16):7249–7259. doi:10.1128/MCB.24.16.7249-7259.2004
Rappsilber J, Ryder U, Lamond AI, Mann M (2002) Genome Res 12(8):1231–1245. doi:10.1101/gr.473902
Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M (2005) Mol Cell Proteomics 4(9):1265–1272. doi:10.1074/mcp.M500061-MCP200
Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R (2008) Bioinformatics 9:529. doi:10.1186/1471-2105-9-529
Kuntumalla S, Braisted JC, Huang ST, Parmar PP, Clark DJ, Alami H, Zhang Q, Donohue-Rolfe A, Tzipori S, Fleischmann RD, Peterson SN, Pieper R (2009) Proteome Sci 7:22. doi:10.1186/1477-5956-7-22
Trudgian DC, Ridlova G, Fischer R, Mackeen MM, Ternette N, Acuto O, Kessler BM, Thomas B (2011) Proteomics 11(14):2790–2797. doi:10.1002/pmic.201000800
Schmidt A, Beck M, Malmstrom J, Lam H, Claassen M, Campbell D, Aebersold R (2011) Mol Syst Biol 7:510. doi:10.1038/msb.2011.37
Ludwig C, Claassen M, Schmidt A, Aebersold R (2011) Mol Cell Proteomics 11(3):M111.013987. doi:10.1074/mcp.M111.013987
Sanz-Medel A (2008) Anal Bioanal Chem 391(3):885–894. doi:10.1007/s00216-008-2083-z
Sanz-Medel A, Montes-Bayon M, de la Campa del Rosario Fernandez M, Encinar JR, Bettmer J (2008) Anal Bioanal Chem 390(1):3–16. doi:10.1007/s00216-007-1615-2
Ahrends R, Pieper S, Neumann B, Scheler C, Linscheid MW (2009) Anal Chem 81(6):2176–2184. doi:10.1021/ac802310c
El-Khatib AH, Esteban-Fernandez D, Linscheid MW (2012) Anal Bioanal Chem 403(8):2255–2267. doi:10.1007/s00216-012-5910-1
Zinn N, Hahn B, Pipkorn R, Schwarzer D, Lehmann WD (2009) J Proteome Res 8(10):4870–4875. doi:10.1021/pr900494m
Zinn N, Winter D, Lehmann WD (2010) Anal Chem 82(6):2334–2340. doi:10.1021/ac9025412
Esteban-Fernandez D, Scheler C, Linscheid MW (2011) Anal Bioanal Chem 401(2):657–666. doi:10.1007/s00216-011-5104-2
Wind M, Edler M, Jakubowski N, Linscheid M, Wesch H, Lehmann WD (2001) Anal Chem 73(1):29–35
Rubbi L, Titz B, Brown L, Galvan E, Komisopoulou E, Chen SS, Low T, Tahmasian M, Skaggs B, Muschen M, Pellegrini M, Graeber TG (2011) Sci Signal 4(166):ra18. doi:10.1126/scisignal.2001314
Hilger M, Bonaldi T, Gnad F, Mann M (2009) Mol Cell Proteomics 8(8):1908–1920. doi:10.1074/mcp.M800559-MCP200
Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M (2006) Cell 127(3):635–648. doi:10.1016/j.cell.2006.09.026
Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M (2010) Sci Signal 3(104):ra3. doi:10.1126/scisignal.2000475
Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B (2011) Sci Signal 4(164):rs3. doi:10.1126/scisignal.2001570
Kettenbach AN, Schweppe DK, Faherty BK, Pechenick D, Pletnev AA, Gerber SA (2011) Sci Signal 4(179):rs5. doi:10.1126/scisignal.2001497
Eyrich B, Sickmann A, Zahedi RP (2011) Proteomics 11(4):554–570. doi:10.1002/pmic.201000489
Wu CJ, Chen YW, Tai JH, Chen SH (2011) J Proteome Res 10(3):1088–1097. doi:10.1021/pr100864b
Oberprieler NG, Lemeer S, Kalland ME, Torgersen KM, Heck AJ, Tasken K (2010) Blood 116(13):2253–2265. doi:10.1182/blood-2010-01-266650
Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ (2010) Mol Cell Proteomics 9(1):84–99. doi:10.1074/mcp.M900291-MCP200
Ding VM, Boersema PJ, Foong LY, Preisinger C, Koh G, Natarajan S, Lee DY, Boekhorst J, Snel B, Lemeer S, Heck AJ, Choo A (2011) PLoS One 6(3):e17538. doi:10.1371/journal.pone.0017538
Boja ES, Phillips D, French SA, Harris RA, Balaban RS (2009) J Proteome Res 8(10):4665–4675. doi:10.1021/pr900387b
Iwai LK, Benoist C, Mathis D, White FM (2010) J Proteome Res 9(6):3135–3145. doi:10.1021/pr100035b
Jones AM, Nuhse TS (2011) Methods Mol Biol 779:287–302. doi:10.1007/978-1-61779-264-9_17
Wu J, Warren P, Shakey Q, Sousa E, Hill A, Ryan TE, He T (2010) Proteomics 10(11):2224–2234. doi:10.1002/pmic.200900788
Montoya A, Beltran L, Casado P, Rodriguez-Prados JC, Cutillas PR (2011) Methods 54(4):370–378. doi:10.1016/j.ymeth.2011.02.004
Mortensen P, Gouw JW, Olsen JV, Ong SE, Rigbolt KT, Bunkenborg J, Cox J, Foster LJ, Heck AJ, Blagoev B, Andersen JS, Mann M (2010) J Proteome Res 9(1):393–403. doi:10.1021/pr900721e
Mueller LN, Brusniak MY, Mani DR, Aebersold R (2008) J Proteome Res 7(1):51–61. doi:10.1021/pr700758r
Olsen JV, Ong SE, Mann M (2004) Mol Cell Proteomics 3(6):608–614. doi:10.1074/mcp.T400003-MCP200
Haas W, Faherty BK, Gerber SA, Elias JE, Beausoleil SA, Bakalarski CE, Li X, Villen J, Gygi SP (2006) Mol Cell Proteomics 5(7):1326–1337. doi:10.1074/mcp.M500339-MCP200
Cutillas PR, Vanhaesebroeck B (2007) Mol Cell Proteomics 6(9):1560–1573. doi:10.1074/mcp.M700037-MCP200
Casado P, Cutillas PR (2011) Mol Cell Proteomics 10(1):M110.003079. doi:10.1074/mcp.M110.003079
Ow SY, Salim M, Noirel J, Evans C, Rehman I, Wright PC (2009) J Proteome Res 8(11):5347–5355. doi:10.1021/pr900634c
Savitski MM, Sweetman G, Askenazi M, Marto JA, Lang M, Zinn N, Bantscheff M (2011) Anal Chem 83(23):8959–8967. doi:10.1021/ac201760x
Nielsen ML, Savitski MM, Zubarev RA (2005) Mol Cell Proteomics 4(6):835–845. doi:10.1074/mcp.T400022-MCP200
van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kuhner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stulke J, Serrano L, Russell RB, Heck AJ, Bork P, Gavin AC (2012) Mol Syst Biol 8:571. doi:10.1038/msb.2012.4
Bantscheff M, Hopf C, Savitski MM, Dittmann A, Grandi P, Michon AM, Schlegl J, Abraham Y, Becher I, Bergamini G, Boesche M, Delling M, Dumpelfeld B, Eberhard D, Huthmacher C, Mathieson T, Poeckel D, Reader V, Strunk K, Sweetman G, Kruse U, Neubauer G, Ramsden NG, Drewes G (2011) Nat Biotechnol 29(3):255–265. doi:10.1038/nbt.1759
Breitwieser FP, Muller A, Dayon L, Kocher T, Hainard A, Pichler P, Schmidt-Erfurth U, Superti-Furga G, Sanchez JC, Mechtler K, Bennett KL, Colinge J (2011) J Proteome Res 10(6):2758–2766. doi:10.1021/pr1012784
Wu Z, Doondeea JB, Moghaddas Gholami A, Janning MC, Lemeer S, Kramer K, Eccles SA, Gollin SM, Grenman R, Walch A, Feller SM, Kuster B (2011) Mol Cell Proteomics 10(12):M111.011635. doi:10.1074/mcp.M111.011635
Wang H, Alvarez S, Hicks LM (2012) J Proteome Res 11(1):487–501. doi:10.1021/pr2008225
Savitski MM, Fischer F, Mathieson T, Sweetman G, Lang M, Bantscheff M (2010) J Am Soc Mass Spectrom 21(10):1668–1679. doi:10.1016/j.jasms.2010.01.012
Olsen JV, Schwartz JC, Griep-Raming J, Nielsen ML, Damoc E, Denisov E, Lange O, Remes P, Taylor D, Splendore M, Wouters ER, Senko M, Makarov A, Mann M, Horning S (2009) Mol Cell Proteomics 8(12):2759–2769. doi:10.1074/mcp.M900375-MCP200
Olsen JV, de Godoy LM, Li G, Macek B, Mortensen P, Pesch R, Makarov A, Lange O, Horning S, Mann M (2005) Mol Cell Proteomics 4(12):2010–2021. doi:10.1074/mcp.T500030-MCP200
Li Z, Adams RM, Chourey K, Hurst GB, Hettich RL, Pan C (2012) J Proteome Res 11(3):1582–1590. doi:10.1021/pr200748h
Falick AM, Lane WS, Lilley KS, MacCoss MJ, Phinney BS, Sherman NE, Weintraub ST, Witkowska HE, Yates NA (2011) J Biomol Tech 22(1):21–26
Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP (2008) Mol Cell Proteomics 7(4):631–644. doi:10.1074/mcp.M700240-MCP200
Diz AP, Carvajal-Rodriguez A, Skibinski DO (2011) Mol Cell Proteomics 10(3):M110.004374. doi:10.1074/mcp.M110.004374
Bauer A, Kuster B (2003) Eur J Biochem 270(4):570–578
Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, Croughton K, Cruciat C, Eberhard D, Gagneur J, Ghidelli S, Hopf C, Huhse B, Mangano R, Michon AM, Schirle M, Schlegl J, Schwab M, Stein MA, Bauer A, Casari G, Drewes G, Gavin AC, Jackson DB, Joberty G, Neubauer G, Rick J, Kuster B, Superti-Furga G (2004) Nat Cell Biol 6(2):97–105. doi:10.1038/ncb1086
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G (2006) Nature 440(7084):631–636. doi:10.1038/nature04532
Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002) Nature 415(6868):141–147. doi:10.1038/415141a
Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, Conaway JW, Florens L, Washburn MP (2006) Proc Natl Acad Sci USA 103(50):18928–18933. doi:10.1073/pnas.0606379103
Pardo M, Choudhary JS (2012) J Proteome Res 11(3):1462–1474. doi:10.1021/pr2011632
Sardiu ME, Florens L, Washburn MP (2009) J Proteome Res 8(6):2944–2952. doi:10.1021/pr900073d
Choi H, Kim S, Gingras AC, Nesvizhskii AI (2010) Mol Syst Biol 6:385. doi:10.1038/msb.2010.41
Choi H, Larsen B, Lin ZY, Breitkreutz A, Mellacheruvu D, Fermin D, Qin ZS, Tyers M, Gingras AC, Nesvizhskii AI (2010) Nat Methods 8(1):70–73. doi:10.1038/nmeth.1541
Dawson MA, Prinjha RK, Dittmann A, Giotopoulos G, Bantscheff M, Chan WI, Robson SC, Chung CW, Hopf C, Savitski MM, Huthmacher C, Gudgin E, Lugo D, Beinke S, Chapman TD, Roberts EJ, Soden PE, Auger KR, Mirguet O, Doehner K, Delwel R, Burnett AK, Jeffrey P, Drewes G, Lee K, Huntly BJ, Kouzarides T (2011) Nature 478(7370):529–533. doi:10.1038/nature10509
Schiess R, Wollscheid B, Aebersold R (2009) Mol Oncol 3(1):33–44. doi:10.1016/j.molonc.2008.12.001
Hilario M, Kalousis A, Pellegrini C, Muller M (2006) Mass Spectrom Rev 25(3):409–449. doi:10.1002/mas.20072
Byvatov E, Schneider G (2003) Appl Bioinformatics 2(2):67–77
Boulesteix AL, Strimmer K (2007) Brief Bioinform 8(1):32–44. doi:10.1093/bib/bbl016
Ong SE, Mann M (2005) Nat Chem Biol 1(5):252–262. doi:10.1038/nchembio736
Sun A, Zhang J, Wang C, Yang D, Wei H, Zhu Y, Jiang Y, He F (2009) J Proteome Res 8(11):4934–4942. doi:10.1021/pr900252n
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The authors wish to thank Frank Weissbrodt for help with creating the graphics. We apologize to all authors whose interesting work could not be cited owing to space or conceptual constraints.
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Published in the topical issue Quantitative Mass Spectrometry in Proteomics with guest editors Bernhard Kuster and Marcus Bantscheff.
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Bantscheff, M., Lemeer, S., Savitski, M.M. et al. Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal Bioanal Chem 404, 939–965 (2012). https://doi.org/10.1007/s00216-012-6203-4
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DOI: https://doi.org/10.1007/s00216-012-6203-4