REVIEW

Advances in quantitative proteomics

  • Yuguang WANG 1 ,
  • Haiying LI 1 ,
  • Sixue CHEN , 1,2
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  • 1. College of Life Sciences, Heilongjiang University, Harbin 150080, China
  • 2. Department of Biology, Genetics Institute, The Plant Molecular and Cellular Biology Program, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA

Received date: 29 Mar 2010

Accepted date: 12 Apr 2010

Published date: 01 Jun 2010

Copyright

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg

Abstract

Large-scale protein quantification has become a major proteomics application in many areas of biological and medical research. During the past years, different techniques have been developed, including gel-based such as differential in-gel electrophoresis (DIGE) and liquid chromatography-based such as isotope labeling and label-free quantification. These quantitative proteomics tools hold significant promise for biomarker discovery, diagnostic and therapeutic applications. They are also important for research in functional genomics and systems biology towards basic understanding of molecular networks and pathway interactions. In this review, we summarize current technologies in quantitative proteomics and discuss recent applications of the technologies.

Cite this article

Yuguang WANG , Haiying LI , Sixue CHEN . Advances in quantitative proteomics[J]. Frontiers in Biology, 2010 , 5(3) : 195 -203 . DOI: 10.1007/s11515-010-0049-y

Acknowledgements

The proteomics work in our collaborative orted by funding from the University of Florida, the National Science Foundation (MCB 0818051,CAREER 0845162onal Institute of Health (1S10RR025418-01) of the USA to S CHEN, and the National Science Foundation of China (No. 30871566) and the Natural Science Foundation of Heilongjiang Province (No. C2007-37) to H LI.
1
Alban A, David S O, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I (2003). A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics, 3(1): 36-44

DOI

2
America A H, Cordewener J H (2008). Comparative LC-MS: a landscape of peaks and valleys. Proteomics, 8(4): 731-749

DOI

4
Anderson K S, Ramachandran N, Wong J, Raphael J V, Hainsworth E, Demirkan G, Cramer D, Aronzon D, Hodi F S, Harris L, Logvinenko T, LaBaer J (2008). Application of protein microarrays for multiplexed detection of antibodies to tumor antigens in breast cancer. J Proteome Res, 7(4): 1490-1499

DOI

3
Anderson L, Hunter C L (2006). Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics, 5(4): 573-588

DOI

5
Asara J M, Christofk H R, Freimark L M, Cantley L C (2008). A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics, 8(5): 994-999

DOI

6
Bertone P, Snyder M (2005). Advances in functional protein microarray technology. FEBS J, 272(21): 5400-5411

DOI

7
Blackburn J M, Hart D J (2005). Fabrication of protein function microarrays for systems-oriented proteomic analysis. Methods Mol Biol, 310: 197-216

DOI

8
Bosch G, Skovran E, Xia Q, Wang T, Taub F, Miller J A, Lidstrom M E, Hackett M (2008). Comprehensive proteomics of Methylobacterium extorquens AM1 metabolism under single carbon and nonmethylotrophic conditions. Proteomics, 8(17): 3494-3505

DOI

9
Casati P, Zhang X, Burlingame A L, Walbot V (2005). Analysis of leaf proteome after UV-B irradiation in maize lines differing in sensitivity. Mol Cell Proteomics, 4(11): 1673-1685

9
Chen S, Harmon A (2006). Advances in plant proteomics. Proteomics, 6(20): 5504–5516

DOI

10
Cheng F Y, Blackburn K, Lin Y M, Goshe M B, Williamson J D (2009). Absolute protein quantification by LC/MS(E) for global analysis of salicylic acid-induced plant protein secretion responses. J Proteome Res, 8(1): 82-93

DOI

11
Cravatt B F, Simon G M, Yates J R 3rd (2007). The biological impact of mass-spectrometry-based proteomics. Nature, 450(7172): 991-1000

DOI

12
Cretich M, Damin F, Pirri G, Chiari M (2006). Protein and peptide arrays: recent trends and new directions. Biomol Eng, 23(2-3): 77-88

13
Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser D F, Burkhard P R, Sanchez J C (2008). Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal Chem, 80(8): 2921-2931

DOI

14
DeSouza L V, Taylor A M, Li W, Minkoff M S, Romaschin A D, Colgan T J, Siu K W (2008). Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues. J Proteome Res, 7(8): 3525-3534

DOI

15
Fu C, Hu J, Liu T, Ago T, Sadoshima J, Li H (2008). Quantitative analysis of redox-sensitive proteome with DIGE and ICAT. J Proteome Res, 7(9): 3789-3802

DOI

16
Gevaert K, Impens F, Ghesquière B, Van Damme P, Lambrechts A, Vandekerckhove J (2008). Stable isotopic labeling in proteomics. Proteomics, 8(23-24): 4873-4885

17
Gharbi S, Gaffney P, Yang A, Zvelebil M J, Cramer R, Waterfield M D, Timms J F (2002). Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol Cell Proteomics, 1(2): 91-98

DOI

18
Görg A, Weiss W, Dunn M J (2004). Current two-dimensional electrophoresis technology for proteomics. Proteomics, 4(12): 3665-3685

DOI

19
Graumann J, Hubner N C, Kim J B, Ko K, Moser M, Kumar C, Cox J, Schöler H, Mann M (2008). Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Mol Cell Proteomics, 7(4): 672-683

DOI

20
Greengauz-Roberts O, Stöppler H, Nomura S, Yamaguchi H, Goldenring J R, Podolsky R H, Lee J R, Dynan W S (2005). Saturation labeling with cysteine-reactive cyanine fluorescent dyes provides increased sensitivity for protein expression profiling of laser-microdissected clinical specimens. Proteomics, 5(7): 1746-1757

DOI

21
Gruhler A, Olsen J V, Mohammed S, Mortensen P, Faergeman N J, Mann M, Jensen O N (2005). Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics, 4: 310-327

DOI

22
Gu S, Pan S, Bradbury E M, Chen X (2003). Precise peptide sequencing and protein quantification in the human proteome through in vivo lysine-specific mass tagging. J Am Soc Mass Spectrom, 14(1): 1-7

DOI

23
Gygi S P, Rist B, Gerber S A, Turecek F, Gelb M H, Aebersold R (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol, 17(10): 994-999

DOI

24
Gygi S P, Corthals G L, Zhang Y, Rochon Y, Aebersold R (2000). Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci U S A, 97(17): 9390-9395

DOI

25
Hamelinck D, Zhou H, Li L, Verweij C, Dillon D, Feng Z, Costa J, Haab B B (2005). Optimized normalization for antibody microarrays and application to serum-protein profiling. Mol Cell Proteomics, 4(6): 773-784

DOI

26
Hansen K C, Schmitt-Ulms G, Chalkley R J, Hirsch J, Baldwin M A, Burlingame A L (2003). Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol Cell Proteomics, 2(5): 299-314

27
Hjernø K, Alm R, Canbäck B, Matthiesen R, Trajkovski K, Björk L, Roepstorff P, Emanuelsson C (2006). Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colorless strawberry mutant. Proteomics, 6(5): 1574-1587

DOI

28
Hurd T R, Prime T A, Harbour M E, Lilley K S, Murphy M P (2007). Detection of reactive oxygen species-sensitive thiol proteins by redox difference gel electrophoresis: implications for mitochondrial redox signaling. J Biol Chem, 282(30): 22040-22051

DOI

29
Iliuk A, Galan J, Tao W A (2009). Playing tag with quantitative proteomics. Anal Bioanal Chem, 393(2): 503-513

DOI

30
Karp N A, Spencer M, Lindsay H, O’Dell K, Lilley K S (2005). Impact of replicate types on proteomic expression analysis. J Proteome Res, 4(5): 1867-1871

DOI

31
Kitteringham N R, Jenkins R E, Lane C S, Elliott V L, Park B K (2009). Multiple reaction monitoring for quantitative biomarker analysis in proteomics and metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci, 877(13): 1229-1239

DOI

32
Krüger M, Moser M, Ussar S, Thievessen I, Luber C A, Forner F, Schmidt S, Zanivan S, Fässler R, Mann M (2008). SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell, 134(2): 353-364

DOI

33
Langenfeld E, Zanger U M, Jung K, Meyer H E, Marcus K (2009). Mass spectrometry-based absolute quantification of microsomal cytochrome P450 2D6 in human liver. Proteomics, 9(9): 2313-2323

DOI

34
Letarte S, Brusniak M Y, Campbell D, Eddes J, Kemp C J, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt K S, Vitek O, Zhang H, Aebersold R, Watts J D (2008). Differential plasma glycoproteome of p19ARF skin cancer mouse model using the corra label-free LC-MS proteomics platform. Clin Proteomics, 4(3-4): 105-116

DOI

35
Li X J, Yi E C, Kemp C J, Zhang H, Aebersold R (2005). A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol Cell Proteomics, 4(9): 1328-1340

36
Liu H, Sadygov R G, Yates J R 3rd (2004). A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem, 76(14): 4193-4201

37
Lucitt M B, Price T S, Pizarro A, Wu W, Yocum A K, Seiler C, Pack M A, Blair I A, Fitzgerald G A, Grosser T (2008). Analysis of the zebrafish proteome during embryonic development. Mol Cell Proteomics, 7(5): 981-994

38
Neubert H, Bonnert T P, Rumpel K, Hunt B T, Henle E S, James I T (2008). Label-free detection of differential protein expression by LC/MALDI mass spectrometry. J Proteome Res, 7(6): 2270-2279

39
Oda Y, Huang K, Cross F R, Cowburn D, Chait B T (1999). Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A, 96(12): 6591-6596

40
Old W M, Meyer-Arendt K, Aveline-Wolf L, Pierce K G, Mendoza A, Sevinsky J R, Resing K A, Ahn N G (2005). Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics, 4(10): 1487-1502

42
Ong S E, Blagoev B, Kratchmarova I, Kristensen D B, Steen H, Pandey A, Mann M (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics, 1(5): 376-386

43
Ong S E, Kratchmarova I, Mann M (2003). Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res, 2(2): 173-181

41
Ong S E, Mann M (2006). A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc, 1(6): 2650-2660

44
Ong S E, Mittler G, Mann M (2004). Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nat Methods, 1(2): 119-126

45
Orenes-Piñero E, Cortón M, González-Peramato P, Algaba F, Casal I, Serrano A, Sánchez-Carbayo M (2007). Searching urinary tumor markers for bladder cancer using a two-dimensional differential gel electrophoresis (2D-DIGE) approach. J Proteome Res, 6(11): 4440-4448

46
Ow S Y, Cardona T, Taton A, Magnuson A, Lindblad P, Stensjö K, Wright P C (2008). Quantitative shotgun proteomics of enriched heterocysts from Nostoc sp. PCC 7120 using 8-plex isobaric peptide tags. J Proteome Res, 7(4): 1615-1628

47
Patel V J, Thalassinos K, Slade S E, Connolly J B, Crombie A, Murrell J C, Scrivens J H (2009). A comparison of labeling and label-free mass spectrometry-based proteomics approaches. J Proteome Res, 8(7): 3752-3759

48
Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney R R, Schmidt M C, Rachidi N, Lee S J, Mah A S, Meng L, Stark M J, Stern D F, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki P F, Snyder M (2005). Global analysis of protein phosphorylation in yeast. Nature, 438(7068): 679-684

49
Rajcevic U, Petersen K, Knol J C, Loos M, Bougnaud S, Klychnikov O, Li K W, Pham T V, Wang J, Miletic H, Peng Z, Bjerkvig R, Jimenez C R, Niclou S P (2009). iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype. Mol Cell Proteomics, 8(11): 2595-2612

50
Ramachandran N, Larson D N, Stark P R, Hainsworth E, LaBaer J (2005). Emerging tools for real-time label-free detection of interactions on functional protein microarrays. FEBS J, 272(21): 5412-5425

51
Rao P V, Reddy A P, Lu X, Dasari S, Krishnaprasad A, Biggs E, Roberts C T, Nagalla S R (2009). Proteomic identification of salivary biomarkers of type-2 diabetes. J Proteome Res, 8(1): 239-245

52
Ross P L, Huang Y N, Marchese J N, 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 D J (2004). Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics, 3(12): 1154-1169

53
Shaw J, Rowlinson R, Nickson J, Stone T, Sweet A, Williams K, Tonge R (2003). Evaluation of saturation labelling two-dimensional difference gel electrophoresis fluorescent dyes. Proteomics, 3(7): 1181-1195

54
Shevchenko A, Jensen O N, Podtelejnikov A V, Sagliocco F, Wilm M, Vorm O, Mortensen P, Shevchenko A, Boucherie H, Mann M (1996). Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc Natl Acad Sci U S A, 93(25): 14440-14445

55
Shui W, Gilmore S A, Sheu L, Liu J, Keasling J D, Bertozzi C R (2009). Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. J Proteome Res, 8(1): 282-289

56
Silva J C, Denny R, Dorschel C, Gorenstein M V, Li G Z, Richardson K, Wall D, Geromanos S J (2006). Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale. Mol Cell Proteomics, 5(4): 589-607

57
Tang W, Deng Z, Oses-Prieto J A, Suzuki N, Zhu S, Zhang X, Burlingame A L, Wang Z Y (2008). Proteomics studies of brassinosteroid signal transduction using prefractionation and two-dimensional DIGE. Mol Cell Proteomics, 7(4): 728-738

58
Thelen J J, Peck S C (2007). Quantitative proteomics in plants: choices in abundance. Plant Cell, 19(11): 3339-3346

59
Thompson A, Schäfer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed A K, Hamon C (2003). Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem, 75(8): 1895-1904

60
Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M (2001). Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics, 1(3): 377-396

DOI

61
Unlü M, Morgan M E, Minden J S (1997). Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis, 18(11): 2071-2077

DOI

62
Unwin R D, Griffiths J R, Leverentz M K, Grallert A, Hagan I M, Whetton A D (2005). Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity. Mol Cell Proteomics, 4(8): 1134-1144

DOI

63
Wang Y, Ao X, Vuong H, Konanur M, Miller F R, Goodison S, Lubman D M (2008). Membrane glycoproteins associated with breast tumor cell progression identified by a lectin affinity approach. J Proteome Res, 7(10): 4313-4325

DOI

64
Whiteaker J R, Zhang H, Zhao L, Wang P, Kelly-Spratt K S, Ivey R G, Piening B D, Feng L C, Kasarda E, Gurley K E, Eng J K, Chodosh L A, Kemp C J, McIntosh M W, Paulovich A G (2007). Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res, 6(10): 3962-3975

DOI

65
Zhang R, Regnier F E (2002). Minimizing resolution of isotopically coded peptides in comparative proteomics. J Proteome Res, 1(2): 139-147

DOI

66
Zhang B, VerBerkmoes N C, Langston M A, Uberbacher E, Hettich R L, Samatova N F (2006). Detecting differential and correlated protein expression in label-free shotgun proteomics. J Proteome Res, 5: 2909-2918

DOI

68
Zhou F, Galan J, Geahlen R L, Tao W A (2007). A novel quantitative proteomics strategy to study phosphorylation-dependent peptide-protein interactions. J Proteome Res, 6(1): 133-140

DOI

67
Zhou H, Ranish J A, Watts J D, Aebersold R (2002). Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol, 20(5): 512-515

DOI

69
Zhu M, Simons B, Zhu N, Oppenheimer D G, Chen S (2010). Analysis of abscisic acid responsive proteins in Brassica napus guard cells by multiplexed isobaric tagging. J Proteomics, 73(4): 790-805

DOI

70
Zybailov B, Friso G, Kim J, Rudella A, Rodríguez V R, Asakura Y, Sun Q, van Wijk K J (2009). Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism. Mol Cell Proteomics, 8(8): 1789-1810

DOI

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