Nonparametric bayesian evaluation of differential protein quantification

Journal of Proteome Research

Volumn 12, Issue 10, 2013, Pages 4556-4565

  Serang, Oliver ^a   Cansizoglu, A Ertugrul ^b   Käll, Lukas ^c   Steen, Hanno ^b   Steen, Judith A ^b  

^a THERMO FISHER SCIENTIFIC   (Germany)

^b BOSTON CHILDREN S HOSPITAL   (United States)

^c ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

control control; fold change; LC MS MS; npCI; null distribution; PSM; TMT labeling

Indexed keywords

ANAPHASE PROMOTING COMPLEX; PEPTIDE; PROTEIN;

ARTICLE; BAYES THEOREM; CONTROLLED STUDY; DIFFERENTIAL PROTEIN QUANTIFICATION; FEMALE; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; KERNEL METHOD; LIQUID CHROMATOGRAPHY; MITOSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY;

ACTINS; ALGORITHMS; BAYES THEOREM; CASE-CONTROL STUDIES; CELL CYCLE PROTEINS; DATA INTERPRETATION, STATISTICAL; HELA CELLS; HUMANS; PROTEOME; PROTEOMICS; STATISTICS, NONPARAMETRIC; TANDEM MASS SPECTROMETRY; TUBULIN;

EID: 84885230259     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400678m     Document Type: Article

References (67)

1. Nesvizhskii, A. I. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics J. Proteomics 2010, 73 (11) 2092-2123
2. Serang, O.; Noble, W. S. A review of statistical methods for protein identification using tandem mass spectrometry Stat. Interface 2012, 5 (1) 3-20
3. Li, Y. F.; Radivojac, P. Computational approaches to protein inference in shotgun proteomics BMC Bioinf. 2012, 13 (Suppl 16) S4
4. Huang, T.; Wang, J.; Yu, W.; He, Z. Protein inference: a review Briefings Bioinf. 2012, 13 (5) 586-614
5. Sandberg, R.; Yasuda, R.; Pankratz, D. G.; Carter, T. A.; Del Rio, J. A.; Wodicka, L.; Mayford, M.; Lockhart, D. J.; Barlow, C. Regional and strain-specific gene expression mapping in the adult mouse brain Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 11038-11043
6. Roxas, B. A. P.; Li., Q. Significance analysis of microarray for relative quantitation of lc/ms data in proteomics BMC Bioinf. 2008, 9 (1) 187
7. Oberg, A. L.; Mahoney, D. W.; Eckel-Passow, J. E.; Malone, C. J.; Wolfinger, R. D.; Hill, E. G.; Cooper, L. T.; Onuma, O. K.; Spiro, C.; Therneau, T. M Statistical analysis of relative labeled mass spectrometry data from complex samples using anova J. Proteome Res. 2008, 7 (1) 225-233
8. Ishihama, Y.; Schmidt, T.; Rappsilber, J.; Mann, M.; Hartl, F. U.; Kerner, M. J.; Frishman, D. Protein abundance profiling of the escherichia coli cytosol BMC Genomics 2008, 9 (1) 102
9. Granholm, V.; Noble, W. S.; Käll, L. On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics J. Proteome Res. 2011, 10 (5) 2671-2678
10. Serang, O.; Paulo, J.; Steen, H.; Steen, J. A. A non-parametric cutout index for robust evaluation of identified proteins Mol. Cell. Proteomics 2013, 12 (3) 807-812
11. Alm, H.; Scholz, B.; Fischer, C.; Kultima, K.; Viberg, H.; Eriksson, P.; Dencker, L.; Stigson, M. Proteomic evaluation of neonatal exposure to 2, 2, 4, 4, 5-pentabromodiphenyl ether Environ. Health Perspect. 2006, 114 (2) 254
12. Corzett, T. H.; Fodor, I. K.; Choi, M. W.; Walsworth, V. L.; Chromy, B. A.; Turteltaub, K. W.; McCutchen-Maloney, S. L. Statistical analysis of the experimental variation in the proteomic characterization of human plasma by two-dimensional difference gel electrophoresis J. Proteome Res. 2006, 5 (10) 2611-2619
13. Nissom, P. M.; Sanny, A.; Kok, Y. J.; Hiang, Y. T.; Chuah, S. H.; Shing, T. K.; Lee, Y. Y.; Wong, T. K.; Hu, W.; Sim, M. Transcriptome and proteome profiling to understanding the biology of high productivity cho cells Mol. Biotechnol. 2006, 34 (2) 125-140
14. Keenan, J.; Murphy, L.; Henry, M.; Meleady, P.; Clynes, M. Proteomic analysis of multidrug-resistance mechanisms in adriamycin-resistant variants of dlkp, a squamous lung cancer cell line Proteomics 2009, 9 (6) 1556-1566
15. Dore, S.; Kar, S.; Quirion, R. Rediscovering an old friend, igf-i: potential use in the treatment of neurodegenerative diseases Trends Neurosci. 1997, 20 (8) 326
16. Kohno, K.; Izumi, H.; Uchiumi, T.; Ashizuka, M.; Kuwano, M. The pleiotropic functions of the y-box-binding protein, yb-1 Bioessays 2003, 25 (7) 691-698
17. Tusher, V. G.; Tibshirani, R.; Chu, G. Significance analysis of microarrays applied to the ionizing radiation response Proc. Natl. Acad. Sci. 2001, 98 (9) 5116-5121
18. Yang, I. V.; Chen, E.; Hasseman, J. P.; Liang, W.; Frank, B. C.; Wang, S.; Sharov, V.; Saeed, A. I.; White, J.; Li, J.; Lee, N. H.; Yeatman, T. J.; Quackenbush, J. Within the fold: assessing differential expression measures and reproducibility in microarray assays Genome Biol. 2002, 3 (11) 1-0062
19. Serang, O.; Moruz, L.; Hoopmann., M. R.; Käll, L. Recognizing uncertainty increases robustness and reproducibility of mass spectrometry-based protein inferences J. Proteome Res. 2012, 11 (12) 5586-91
20. Granholm, V.; Navarro, J.; Noble, W. S.; Käll, L. Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics J. Proteomics 2012, 80, 123-131
21. Searle, B. C.; Dasari, S.; Wilmarth, P. A.; Turner, M.; Reddy, A. P.; David, L. L.; Nagalla, S. R. Identification of protein modifications using ms/ms de novo sequencing and the opensea alignment algorithm J. Proteome Res. 2005, 4 (2) 546-554
22. Käll, L.; Canterbury, J.; Weston, J.; Noble, W. S.; MacCoss, M. J. A semi-supervised machine learning technique for peptide identification from shotgun proteomics datasets Nat. Methods 2007, 4, 923-25
23. Käll, L.; Storey, J.; Noble, W. S. Nonparametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry Bioinformatics 2008, 24 (16) i42-i48
24. Choi, H.; Nesvizhskii, A. I. Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics J. Proteome Res. 2008, 7 (1) 254-265
25. Kessner, D.; Chambers, M.; Burke, R.; Agus, D.; Mallick, P. Proteowizard: open source software for rapid proteomics tools development Bioinformatics 2008, 24 (21) 2534-2536
26. Chambers, M. C.; Maclean, B.; Burke, R.; Amodei, D.; Ruderman, D. L.; Neumann, S.; Gatto, L.; Fischer, B.; Pratt, P.; Egertson, J. A cross-platform toolkit for mass spectrometry and proteomics Nat. Biotechnol. 2012, 30 (10) 918-920
27. Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20, 3551-3567
28. Searle, B. C. Scaffold: A bioinformatic tool for validating ms/ms-based proteomic studies Proteomics 2010, 10 (6) 1265-1269
29. Keller, B. O.; Sui, J.; Young, A. B.; Whittal, R. M. Interferences and contaminants encountered in modern mass spectrometry Anal. Chim. Acta 2008, 627 (1) 71-81
30. Cui, X.; Churchill, G. A. Statistical tests for differential expression in cdna microarray experiments Genome Biol. 2003, 4 (4) 210
31. Parzen, E. On estimation of a probability density function and mode Ann. Math. Stat. 1962, 33 (3) 1065-1076
32. Rosenblatt, M. Remarks on some nonparametric estimates of a density function Ann. Math. Stat. 1956, 832-837
33. Nislow, C.; Lombillo, V. A.; Kuriyama, R.; Mclntosh, J. R. A plus-end-directed motor enzyme that moves antiparallel microtubules in vitro localizes to the interzone of mitotic spindles Nature 1992, 359, 543-547
34. Garnett, M. J.; Mansfeld, J.; Godwin, C.; Matsusaka, T.; Wu, J.; Russell, P.; Pines, J.; Venkitaraman, A. R. Ube2s elongates ubiquitin chains on apc/c substrates to promote mitotic exit Nat. Cell Biol. 2009, 11 (11) 1363-1369
35. van der Vaart, B.; Manatschal, C.; Grigoriev, I.; Olieric, V.; Gouveia, S. M.; Bjelić, S.; Demmers, J.; Vorobjev, I.; Hoogenraad, C. C; Michel, O. S. Slain2 links microtubule plus end-tracking proteins and controls microtubule growth in interphase J. Cell Biol. 2011, 193 (6) 1083-1099
36. Oceguera-Yanez, F.; Kimura, K.; Yasuda, S.; Higashida, C.; Kitamura, T.; Hiraoka, Y.; Haraguchi, T.; Narumiya., S. Ect2 and mgcracgap regulate the activation and function of cdc42 in mitosis J. Cell Biol. 2005, 168 (2) 221-232
37. Olsen, J. V.; Vermeulen, M.; Santamaria, A.; Kumar, C.; Miller, M. L.; Jensen, L. J.; Gnad, F.; Cox, J.; Jensen, T. S.; Nigg, E. A. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis Sci. Signaling 2010, 3 (104) ra3
38. Honda, K.; Mihara, H.; Kato, Y.; Yamaguchi, A.; Tanaka, H.; Yasuda, H.; Furukawa, K.; Urano, T. Degradation of human aurora2 protein kinase by the anaphase-promoting complex-ubiquitin-proteasome pathway Oncogene 2000, 19 (24) 2812
39. Feine, O.; Zur, A.; Mahbubani, H.; Brandeis, M. Human kid is degraded by the apc/ccdh1 but not by the apc/ccdc20 Cell Cycle 2007, 6 (20) 2516-2523
40. Rape, M.; Kirschner, M. W. Autonomous regulation of the anaphase-promoting complex couples mitosis to s-phase entry Nature 2004, 432 (7017) 588-595
41. Seki, A.; Fang, G. Ckap2 is a spindle-associated protein degraded by apc/c-cdh1 during mitotic exit J. Biol. Chem. 2007, 282 (20) 15103-15113
42. Pfleger, C. M.; Kirschner, M. W. The ken box: an apc recognition signal distinct from the d box targeted by cdh1 Genes Dev. 2000, 14 (6) 655-665
43. Bashir, T.; Dorrello, N. V.; Amador, V.; Guardavaccaro, D.; Pagano, M. Control of the scfskp2-cks1 ubiquitin ligase by the apc/ccdh1 ubiquitin ligase Nature 2004, 428 (6979) 190-193
44. Rankin, S.; Ayad, N. G.; Kirschner, M. W. Sororin, a substrate of the anaphase-promoting complex, is required for sister chromatid cohesion in vertebrates Mol. Cell 2005, 18 (2) 185-200
45. CDH1 and Promote S Phase Entry Mol. Cell 2011, 42 (4) 511-523
46. Casaletto, J. B.; Nutt, L. K.; Wu, Q.; Moore, J. D.; Etkin, L. D.; Jackson, P. K.; Hunt, T.; Kornbluth, S. Inhibition of the anaphase-promoting complex by the Xnf7 ubiquitin ligase J. Cell Biol. 2005, 169 (1) 61-71
47. Gurden, M. D.; Holland, A. J.; van Zon, W.; Tighe, A.; Vergnolle, M. A.; Andres, D. A.; Spielmann, H. P.; Malumbres, M.; Wolthuis, R. M.; Cleveland, D. W. Cdc20 is required for the post-anaphase, KEN-dependent degradation of centromere protein F J. Cell Sci. 2010, 123 (3) 321-330
48. Bassermann, F.; Frescas, D.; Guardavaccaro, D.; Busino, L.; Peschiaroli, A.; Pagano, M. The cdc14b-cdh1-plk1 axis controls the g2 dna-damage-response checkpoint Cell 2008, 134 (2) 256-267
49. Zhao, W.; Fang, G. Anillin is a substrate of anaphase-promoting complex/cyclosome (apc/c) that controls spatial contractility of myosin during late cytokinesis J. Biol. Chem. 2005, 280 (39) 33516-33524
50. Colombo, S. L.; Palacios-Callender, M.; Frakich, N.; De Leon, J.; Schmitt, C. A.; Boorn, L.; Davis, N.; Moncada, S. Anaphase-promoting complex/cyclosome-cdh1 coordinates glycolysis and glutaminolysis with transition to s phase in human t lymphocytes Proc. Natl. Acad. Sci. 2010, 107 (44) 18868-18873
51. Harley, M. E.; Allan, L. A.; Sanderson, H. S.; Clarke, P. R. Phosphorylation of mcl-1 by cdk1-cyclin b1 initiates its cdc20-dependent destruction during mitotic arrest EMBO J. 2010, 29 (14) 2407-2420
52. Merbl, Y.; Kirschner, M. W. Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays Proc. Natl. Acad. Sci. 2009, 106 (8) 2543-2548
53. Wang, Y.; Zhan, Q. Cell cycle-dependent expression of centrosomal ninein-like protein in human cells is regulated by the anaphase-promoting complex J. Biol. Chem. 2007, 282 (24) 17712-17719
54. Tudzarova, S.; Colombo, S. L.; Stoeber, K.; Carcamo, S.; Williams, G. H.; Moncada, S. Two ubiquitin ligases, apc/c-cdh1 and skp1-cul1-f (scf)-β-trcp, sequentially regulate glycolysis during the cell cycle Proc. Natl. Acad. Sci. 2011, 108 (13) 5278-5283
55. Cotto-Rios, X. M.; Jones, M. J.; Busino, L.; Pagano, M.; Huang, T. T. APC/CCdh1-dependent proteolysis of USP1 regulates the response to UV-mediated DNA damage J. Cell Biol. 2011, 194 (2) 177-186
56. Karamysheva, Z.; Diaz-Martinez, L. A.; Crow, S. E.; Li, B.; Yu, H. Multiple anaphase-promoting complex/cyclosome degrons mediate the degradation of human sgo1 J. Biol. Chem. 2009, 284 (3) 1772-1780
57. Ohoka, N.; Sakai, S.; Onozaki, K.; Nakanishi, M.; Hayashi, H. Anaphase-promoting complex/cyclosome-cdh1 mediates the ubiquitination and degradation of trb3 Biochem. Biophys. Res. Commun. 2010, 392 (3) 289-294
58. Thellin, O.; Zorzi, W.; Lakaye, B.; De Borman, B.; Coumans, B.; Hennen, G.; Grisar, T.; Igout, A.; Heinen, E. Housekeeping genes as internal standards: use and limits J. Biotechnol. 1999, 75 (2) 291-295
59. Ke, P.; Kuo, Y.; Hu, C.; Chang, Z. Control of dttp pool size by anaphase promoting complex/cyclosome is essential for the maintenance of genetic stability Genes Dev. 2005, 19 (16) 1920-1933
60. Lindon, C.; Pines, J. Ordered proteolysis in anaphase inactivates plk1 to contribute to proper mitotic exit in human cells J. Cell Biol. 2004, 164 (2) 233-241
61. Stewart, S.; Fang, G. Anaphase-promoting complex/cyclosome controls the stability of tpx2 during mitotic exit Mol. Cell. Biol. 2005, 25 (23) 10516-10527
62. Zhu, C.; Lau, E.; Schwarzenbacher, R.; Bossy-Wetzel, E.; Jiang, W. Spatiotemporal control of spindle midzone formation by prc1 in human cells Proc. Natl. Acad. Sci. 2006, 103 (16) 6196-6201
63. Li, L.; Zhou, Y.; Sun, L.; Xing, G.; Tian, C.; Sun, J.; Zhang, L.; He, F. Nusap is degraded by apc/c-cdh1 and its overexpression results in mitotic arrest dependent of its microtubules' affinity Cell. Signal. 2007, 19 (10) 2046-2055
64. Qi, W.; Yu, H. Ken-box-dependent degradation of the bub1 spindle checkpoint kinase by the anaphase-promoting complex/cyclosome J. Biol. Chem. 2007, 282 (6) 3672-3679
65. Ghoshal, K.; Datta, J.; Majumder, S.; Bai, S.; Kutay, H.; Motiwala, T.; Jacob, S. T. 5-aza-deoxycytidine induces selective degradation of dna methyltransferase 1 by a proteasomal pathway that requires the ken box, bromo-adjacent homology domain, and nuclear localization signal Mol. Cell. Biol. 2005, 25 (11) 4727-4741
66. Noble, W. S. Support Vector Machine Applications in Computational Biology. In Kernel Methods in Computational Biology; Schoelkopf, B.; Tsuda, K.; Vert, J.-P., Eds.; MIT Press: Cambridge, MA, 2004; pp 71-92.
67. Ting, L.; Rad, R.; Gygi, S. P.; Haas, W. Ms3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics Nat. Methods 2011, 8 (11) 937-940