Improving qualitative and quantitative performance for MSE-based label-free proteomics

Journal of Proteome Research

Volumn 12, Issue 6, 2013, Pages 2340-2353

  Bond, Nicholas J ^a,b   Shliaha, Pavel V ^a   Lilley, Kathryn S ^a   Gatto, Laurent ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b MRC HUMAN NUTRITION RESEARCH   (United Kingdom)

Author keywords

data combination; data independent acquisition; false discovery rate; identification transfer; missing values; quantitation

Indexed keywords

PROTEOME;

ARTICLE; COMPUTER PROGRAM; DATA PROCESSING; MASS SPECTROMETRY; PERFORMANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS;

EID: 84879391561     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300776t     Document Type: Article

References (49)

1. Schulze, W. X.; Usadel, B. Quantitation in mass-spectrometry-based proteomics Annu. Rev. Plant Biol. 2010, 61, 491-516
2. Gevaert, K.; Impens, F.; Ghesquière, B.; Van Damme, P.; Lambrechts, A.; Vandekerckhove, J. Stable isotopic labeling in proteomics Proteomics 2008, 8, 4873-4885
3. Neilson, K. A.; Ali, N. A.; Muralidharan, S.; Mirzaei, M.; Mariani, M.; Assadourian, G.; Lee, A.; van Sluyter, S. C.; Haynes, P. A. Less label, more free: approaches in label-free quantitative mass spectrometry Proteomics 2011, 11, 535-553
4. Evans, C.; Noirel, J.; Ow, S. Y.; Salim, M.; Pereira-Medrano, A. G.; Couto, N.; Pandhal, J.; Smith, D.; Pham, T. K.; Karunakaran, E.; Zou, X.; Biggs, C. A.; Wright, P. C. An insight into iTRAQ: where do we stand now? Anal. Bioanal. Chem. 2012, 404 (4) 1011-1027
5. Ting, L.; Rad, R.; Gygi, S. P.; Haas, W. MS3 eliminates ratio distortion in isobaric labeling-based multiplexed quantitative proteomics Nat. Methods 2011, 8, 937-940
6. Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein Mol. Cell. Proteomics 2005, 4, 1265-1272
7. Levin, Y.; Hradetzky, E.; Bahn, S. Quantification of proteins using data-independent analysis (MSE) in simple andcomplex samples: a systematic evaluation Proteomics 2011, 11, 3273-3287
8. Silva, J. C.; Gorenstein, M. V.; Li, G.-Z.; Vissers, J. P. C.; Geromanos, S. J. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition Mol. Cell. Proteomics 2006, 5, 144-156
9. Silva, J. C.; Denny, R.; Dorschel, C. A.; Gorenstein, M.; Kass, I. J.; Li, G.-Z.; McKenna, T.; Nold, M. J.; Richardson, K.; Young, P.; Geromanos, S. Quantitative proteomic analysis by accurate mass retention time pairs Anal. Chem. 2005, 77, 2187-2200
10. Geromanos, S. J.; Vissers, J. P. C.; Silva, J. C.; Dorschel, C. A.; Li, G.-Z.; Gorenstein, M. V.; Bateman, R. H.; Langridge, J. I. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS Proteomics 2009, 9, 1683-1695
11. Krishnamurthy, D.; Levin, Y.; Harris, L. W.; Umrania, Y.; Bahn, S.; Guest, P. C. Analysis of the human pituitary proteome by data independent label-free liquid chromatography tandem mass spectrometry Proteomics 2011, 11, 495-500
12. Kennedy, J.; Yi, E. C. Use of gas-phase fractionation to increase protein identifications: application to the peroxisome Methods Mol. Biol. 2008, 432, 217-228
13. Hoopmann, M. R.; Finney, G. L.; MacCoss, M. J. High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry Anal. Chem. 2007, 79, 5620-5632
14. Luethy, R.; Kessner, D. E.; Katz, J. E.; Maclean, B.; Grothe, R.; Kani, K.; Faça, V.; Pitteri, S.; Hanash, S.; Agus, D. B.; Mallick, P. Precursor-ion mass re-estimation improves peptide identification on hybrid instruments J. Proteome Res. 2008, 7, 4031-4039
15. Li, G.-Z.; Vissers, J. P. C.; Silva, J. C.; Golick, D.; Gorenstein, M. V.; Geromanos, S. J. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures Proteomics 2009, 9, 1696-1719
16. Gillet, L. C.; Navarro, P.; Tate, S.; Roest, H.; Selevsek, N.; Reiter, L.; Bonner, R.; Aebersold, R. 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 2012, 11 (6 O111.016717
17. Panchaud, A.; Scherl, A.; Shaffer, S. A.; von Haller, P. D.; Kulasekara, H. D.; Miller, S. I.; Goodlett, D. R. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean Anal. Chem. 2009, 81, 6481-6488
18. Geiger, T.; Cox, J.; Mann, M. Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation Mol. Cell. Proteomics 2010, 9, 2252-2261
19. Masselon, C.; Anderson, G. A.; Harkewicz, R.; Bruce, J. E.; Pasa-Tolic, L.; Smith, R. D. Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures Anal. Chem. 2000, 72 (8) 1918-1924
20. Michalski, A.; Cox, J.; Mann, M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS J. Proteome Res. 2011, 10, 1785-1793
21. Vandenbogaert, M.; Li-Thiao-Té, S.; Kaltenbach, H.-M.; Zhang, R.; Aittokallio, T.; Schwikowski, B. Alignment of LC-MS images, with applications to biomarker discovery and protein identification Proteomics 2008, 8, 650-672
22. Conrads, T. P.; Anderson, G. A.; Veenstra, T. D.; Pasa-Tolić, L.; Smith, R. D. Utility of accurate mass tags for proteome-wide protein identification Anal. Chem. 2000, 72, 3349-3354
23. Lipton, M. S.; Pasa-Tolic', L.; Anderson, G. A.; Anderson, D. J.; Auberry, D. L.; Battista, J. R.; Daly, M. J.; Fredrickson, J.; Hixson, K. K.; Kostandarithes, H.; Masselon, C.; Markillie, L. M.; Moore, R. J.; Romine, M. F.; Shen, Y.; Stritmatter, E.; Tolic', N.; Udseth, H. R.; Venkateswaran, A.; Wong, K.-K.; Zhao, R.; Smith, R. D. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11049-11054
24. Strittmatter, E. F.; Ferguson, P. L.; Tang, K.; Smith, R. D. Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry J. Am. Soc. Mass Spectrom. 2003, 14, 980-991
25. Pasa-Tolić, L.; Masselon, C.; Barry, R. C.; Shen, Y.; Smith, R. D. Proteomic analyses using an accurate mass and time tag strategy BioTechniques 2004, 37, 621-624, 626-633, 636 passim
26. Myung, S.; Lee, Y. J.; Moon, M. H.; Taraszka, J.; Sowell, R.; Koeniger, S.; Hilderbrand, A. E.; Valentine, S. J.; Cherbas, L.; Cherbas, P.; Kaufmann, T. C.; Miller, D. F.; Mechref, Y.; Novotny, M. V.; Ewing, M. A.; Sporleder, C. R.; Clemmer, D. E. Development of high-sensitivity ion trap ion mobility spectrometry time-of-flight techniques: a high-throughput nano-LC-IMS-TOF separation of peptides arising from a Drosophila protein extract Anal. Chem. 2003, 75, 5137-5145
27. Pringle, S. D.; Giles, K.; Wildgoose, J. L.; Williams, J. P.; Slade, S. E.; Thalassinos, K.; Bateman, R. H.; Bowers, M. T.; Scrivens, J. H. An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument Int. J. Mass Spectrom. 2007, 261, 1-12
28. Hoaglund, C. S.; Valentine, S. J.; Clemmer, D. E. An ion trap interface for esi-ion mobility experiments Anal. Chem. 1997, 69, 4156-4161
29. Ibrahim, Y. M.; Prior, D. C.; Baker, E. S.; Smith, R. D.; Belov, M. E. Characterization of an ion mobility-multiplexed collision induced dissociation-tandem time-of-flight mass spectrometry approach Int. J. Mass Spectrom. 2010, 293, 34-44
30. Shliaha, P. V.; Bond, N. J.; Gatto, L.; Lilley, K. S. Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies J. Proteome Res. 2013, pr300775k
31. Neubert, H.; Bonnert, T. P.; Rumpel, K.; Hunt, B. T.; Henle, E. S.; James, I. T. Label-free detection of differential protein expression by LC/MALDI mass spectrometry J. Proteome Res. 2008, 7, 2270-2279
32. 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. E.; 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, 2063-2075
33. R Development Core Team R: A language and environment for statistical computing; R Foundation for Statistical Computing: Vienna, Austria, 2011.
34. Gatto, L.; Lilley, K. S. MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation Bioinformatics 2011, 28, 288-289
35. Katajamaa, M.; Oresic, M. Processing methods for differential analysis of LC/MS profile data BMC Bioinform. 2005, 6, 179
36. Käll, L.; Storey, J. D.; MacCoss, M. J.; Noble, W. S. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases J. Proteome Res. 2008, 7, 29-34
37. Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing J. R. Stat. Soc., Ser. B 1995, 57, 289-300
38. Storey, J. D.; Tibshirani, R. Statistical significance for genomewide studies Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 9440-9445
39. Olsen, J. V.; Ong, S.-E.; Mann, M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues Mol. Cell. Proteomics 2004, 3, 608-614
40. Thiede, B.; Lamer, S.; Mattow, J.; Siejak, F.; Dimmler, C.; Rudel, T.; Jungblut, P. R. Analysis of missed cleavage sites, tryptophan oxidation and N-terminal pyroglutamylation after in-gel tryptic digestion Rapid Commun. Mass Spectrom. 2000, 14, 496-502
41. Cleveland, W. S. Robust locally weighted regression and smoothing scatterplots J. Am. Stat. Assoc. 1979, 74, 829-836
42. Mueller, L. N.; Rinner, O.; Schmidt, A.; Letarte, S.; Bodenmiller, B.; Brusniak, M.-Y.; Vitek, O.; Aebersold, R.; Müller, M. SuperHirn-a novel tool for high resolution LC-MS-based peptide/protein profiling Proteomics 2007, 7, 3470-3480
43. Geromanos, S. J.; Hughes, C.; Golick, D.; Ciavarini, S.; Gorenstein, M. V.; Richardson, K.; Hoyes, J. B.; Vissers, J. P. C.; Langridge, J. I. Simulating and validating proteomics data and search results Proteomics 2011, 11, 1189-1211
44. Geromanos, S. J.; Hughes, C.; Ciavarini, S.; Vissers, J. P. C.; Langridge, J. I. Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples Anal. Bioanal. Chem. 2012, 404 (4) 1127-1139
45. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74, 5383-5392
46. Prakash, A.; Mallick, P.; Whiteaker, J.; Zhang, H.; Paulovich, A.; Flory, M.; Lee, H.; Aebersold, R.; Schwikowski, B. Signal Maps for Mass Spectrometry-based Comparative Proteomics Mol. Cell. Proteomics 2006, 5, 423-432
47. Stanley, J. R.; Adkins, J. N.; Slysz, G. W.; Monroe, M. E.; Purvine, S. O.; Karpievitch, Y. V.; Anderson, G. A.; Smith, R. D.; Dabney, A. R. A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics Anal. Chem. 2011, 83 (16) 6135-6140
48. Dabney, A.; Storey, J. D. and with assistance from Warnes, G. R. qvalue: Q-value estimation for false discovery rate control, version 1.35.0.
49. Gentleman, R. C.; Carey, V. J.; Bates, D. M.; Bolstad, B.; Dettling, M.; Dudoit, S.; Ellis, B.; Gautier, L.; Ge, Y.; Gentry, J.; Hornik, K.; Hothorn, T.; Huber, W.; Iacus, S.; Irizarry, R.; Leisch, F.; Li, C.; Maechler, M.; Rossini, A. J.; Sawitzki, G.; Smith, C.; Smyth, G.; Tierney, L.; Yang, J. Y. H.; Zhang, J. Bioconductor: open software development for computational biology and bioinformatics Genome Biol. 2004, 5, R80