Comparative study of targeted and label-free mass spectrometry methods for protein quantification

Journal of Proteome Research

Volumn 12, Issue 4, 2013, Pages 2005-2011

  Ijsselstijn, Linda ^a   Stoop, Marcel P ^a   Stingl, Christoph ^a   Sillevis Smitt, Peter A E ^a   Luider, Theo M ^a   Dekker, Lennard J M ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

mass spectrometry; multiple reaction monitoring; protein quantification; qual quant; targeted

Indexed keywords

ALBUMIN; ALTERNATIVE COMPLEMENT PATHWAY C3 C5 CONVERTASE; APOLIPOPROTEIN E; COMPLEMENT COMPONENT C3; CYSTEINE; GALECTIN 3; METHIONINE; VITAMIN D BINDING PROTEIN;

ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; HUMAN; HUMAN TISSUE; ION TRAP MASS SPECTROMETRY; MASS SPECTROMETRY; PARTICLE SIZE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; PROTEOMICS;

AMINO ACID SEQUENCE; BLOOD PROTEINS; CEREBROSPINAL FLUID; HUMANS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PROTEINS; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 84875943685     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr301221f     Document Type: Article

References (23)

1. Baty, J. D.; Robinson, P. R. Single and multiple ion recording techniques for the analysis of diphenylhydantoin and its major metabolite in plasma Biomed. Mass Spectrom. 1977, 4 (1) 36-41
2. Gallien, S.; Duriez, E.; Domon, B. Selected reaction monitoring applied to proteomics J. Mass Spectrom. 2011, 46 (3) 298-312
3. Anderson, L.; Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins Mol. Cell. Proteomics 2006, 5 (4) 573-88
4. Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics 2002, 1 (5) 376-86
5. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 1999, 17 (10) 994-9
6. DeSouza, L. V.; Taylor, A. M.; Li, W.; Minkoff, M. S.; Romaschin, A. D.; Colgan, T. J.; Siu, K. W. 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. 2008, 7 (8) 3525-34
7. Yao, X.; Freas, A.; Ramirez, J.; Demirev, P. A.; Fenselau, C. Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus Anal. Chem. 2001, 73 (13) 2836-42
8. Gerber, S. A.; Rush, J.; Stemman, O.; Kirschner, M. W.; Gygi, S. P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (12) 6940-5
9. IJsselstijn, L.; Dekker, L. J.; Koudstaal, P. J.; Hofman, A.; Sillevis Smitt, P.; Breteler, M. M.; Luider, T. Serum clusterin levels are not increased in presymptomatic Alzheimer's disease J. Proteome Res. 2011, 10 (4) 2006-10
10. Addona, T. A.; Abbatiello, S. E.; Schilling, B.; Skates, S. J.; Mani, D. R.; Bunk, D. M.; Spiegelman, C. H.; Zimmerman, L. J.; Ham, A. J.; Keshishian, H.; Hall, S. C.; Allen, S.; Blackman, R. K.; Borchers, C. H.; Buck, C.; Cardasis, H. L.; Cusack, M. P.; Dodder, N. G.; Gibson, B. W.; Held, J. M.; Hiltke, T.; Jackson, A.; Johansen, E. B.; Kinsinger, C. R.; Li, J.; Mesri, M.; Neubert, T. A.; Niles, R. K.; Pulsipher, T. C.; Ransohoff, D.; Rodriguez, H.; Rudnick, P. A.; Smith, D.; Tabb, D. L.; Tegeler, T. J.; Variyath, A. M.; Vega-Montoto, L. J.; Wahlander, A.; Waldemarson, S.; Wang, M.; Whiteaker, J. R.; Zhao, L.; Anderson, N. L.; Fisher, S. J.; Liebler, D. C.; Paulovich, A. G.; Regnier, F. E.; Tempst, P.; Carr, S. A. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma Nat. Biotechnol. 2009, 27 (7) 633-41
11. Domon, B.; Aebersold, R. Options and considerations when selecting a quantitative proteomics strategy Nat. Biotechnol. 2010, 28 (7) 710-21
12. de Groot, C. J.; Guzel, C.; Steegers-Theunissen, R. P.; de Maat, M.; Derkx, P.; Roes, E. M.; Heeren, R. M.; Luider, T. M.; Steegers, E. A. Specific peptides identified by mass spectrometry in placental tissue from pregnancies complicated by early onset preeclampsia attained by laser capture dissection Proteomics Clin. Appl. 2007, 1 (3) 325-35
13. Guzel, C.; Ursem, N. T.; Dekker, L. J.; Derkx, P.; Joore, J.; van Dijk, E.; Ligtvoet, G.; Steegers, E. A.; Luider, T. M. Multiple reaction monitoring assay for pre-eclampsia related calcyclin peptides in formalin fixed paraffin embedded placenta J Proteome Res 2011, 10 (7) 3274-82
14. IJsselstijn, L.; Dekker, L. J.; Stingl, C.; van der Weiden, M. M.; Hofman, A.; Kros, J. M.; Koudstaal, P. J.; Sillevis Smitt, P. A.; Ikram, M. A.; Breteler, M. M.; Luider, T. M. Serum levels of pregnancy zone protein are elevated in presymptomatic Alzheimer's disease J Proteome Res 2011, 10 (11) 4902-10
15. Stoop, M. P.; Coulier, L.; Rosenling, T.; Shi, S.; Smolinska, A. M.; Buydens, L.; Ampt, K.; Stingl, C.; Dane, A.; Muilwijk, B.; Luitwieler, R. L.; Sillevis Smitt, P. A.; Hintzen, R. Q.; Bischoff, R.; Wijmenga, S. S.; Hankemeier, T.; van Gool, A. J.; Luider, T. M. Quantitative proteomics and metabolomics analysis of normal human cerebrospinal fluid samples Mol. Cell. Proteomics 2010, 9 (9) 2063-75
16. Stoop, M. P.; Singh, V.; Dekker, L. J.; Titulaer, M. K.; Stingl, C.; Burgers, P. C.; Sillevis Smitt, P. A.; Hintzen, R. Q.; Luider, T. M. Proteomics comparison of cerebrospinal fluid of relapsing remitting and primary progressive multiple sclerosis PLoS One 2010, 5 (8) e12442
17. MacLean, B.; Tomazela, D. M.; Shulman, N.; Chambers, M.; Finney, G. L.; Frewen, B.; Kern, R.; Tabb, D. L.; Liebler, D. C.; MacCoss, M. J. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments Bioinformatics 2010, 26 (7) 966-8
18. Han, B.; Higgs, R. E. Proteomics: from hypothesis to quantitative assay on a single platform. Guidelines for developing MRM assays using ion trap mass spectrometers Brief Funct. Genomic Proteomic 2008, 7 (5) 340-54
19. Gallien, S.; Duriez, E.; Crone, C.; Kellmann, M.; Moehring, T.; Domon, B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer Mol. Cell. Proteomics 2012, 11 (12) 1709-23
20. Geiger, T.; Cox, J.; Mann, M. Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation Mol. Cell. Proteomics 2010, 9 (10) 2252-61
21. Levin, Y.; Hradetzky, E.; Bahn, S. Quantification of proteins using data-independent analysis (MSE) in simple and complex samples: a systematic evaluation Proteomics 2011, 11 (16) 3273-87
22. Ramanathan, R.; Jemal, M.; Ramagiri, S.; Xia, Y. Q.; Humpreys, W. G.; Olah, T.; Korfmacher, W. A. It is time for a paradigm shift in drug discovery bioanalysis: from SRM to HRMS J. Mass Spectrom. 2011, 46 (6) 595-601
23. Kaufmann, A.; Butcher, P.; Maden, K.; Walker, S.; Widmer, M. Quantitative and confirmative performance of liquid chromatography coupled to high-resolution mass spectrometry compared to tandem mass spectrometry Rapid Commun. Mass Spectrom. 2011, 25 (7) 979-92