A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments

Journal of the American Society for Mass Spectrometry

Volumn 27, Issue 10, 2016, Pages 1620-1625

  Paulo, Joao A ^a   O’Connell, Jeremy D ^a   Gygi, Steven P ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Ion interference; Lumos; MS standard; MuiltiNotch; Orbitrap Fusion; SPS MS3; TMT

Indexed keywords

DRUG PRODUCTS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PEPTIDES;

LUMOS; MAXIMUM SENSITIVITY; MUILTINOTCH; ORBITRAP; PEPTIDE QUANTIFICATION; QUANTITATIVE MASS SPECTROMETRIES; SPS-MS3; TRIPLE STAGE MASS SPECTROMETRY;

IONS;

FUNGAL PROTEIN; ION; MET6 PROTEIN; PFK2 PROTEIN; PROTEOME; UNCLASSIFIED DRUG; URA2 PROTEIN; PEPTIDE;

ANALYTIC METHOD; ARTICLE; MASS SPECTROMETRY; MEASUREMENT ACCURACY; NONHUMAN; PROTEOMICS; QUANTITATIVE ANALYSIS; YEAST; CHEMISTRY; SACCHAROMYCES CEREVISIAE; TANDEM MASS SPECTROMETRY;

MASS SPECTROMETRY; PEPTIDES; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; TANDEM MASS SPECTROMETRY;

EID: 84986617578     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-016-1434-9     Document Type: Article

References (21)

1. Dayon, L., Hainard, A., Licker, V., Turck, N., Kuhn, K., Hochstrasser, D.F., Burkhard, P.R., Sanchez, J.C.: Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal. Chem. 80, 2921–2931 (2008)
2. Thompson, A., Schafer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., Johnstone, R., Mohammed, A.K., Hamon, C.: Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895–1904 (2003)
3. 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.: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154–1169 (2004)
4. Ting, L., Rad, R., Gygi, S.P., Haas, W.: MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods 8, 937–940 (2011)
5. McAlister, G.C., Nusinow, D.P., Jedrychowski, M.P., Wuhr, M., Huttlin, E.L., Erickson, B.K., Rad, R., Haas, W., Gygi, S.P.: MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Anal. Chem. 86, 7150–7158 (2014)
6. Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J.D., Bussey, H., Chu, A.M., Connelly, C., Davis, K., Dietrich, F., Dow, S.W., El Bakkoury, M., Foury, F., Friend, S.H., Gentalen, E., Giaever, G., Hegemann, J.H., Jones, T., Laub, M., Liao, H., Liebundguth, N., Lockhart, D.J., Lucau-Danila, A., Lussier, M., M’Rabet, N., Menard, P., Mittmann, M., Pai, C., Rebischung, C., Revuelta, J.L., Riles, L., Roberts, C.J., Ross-MacDonald, P., Scherens, B., Snyder, M., Sookhai-Mahadeo, S., Storms, R.K., Veronneau, S., Voet, M., Volckaert, G., Ward, T.R., Wysocki, R., Yen, G.S., Yu, K., Zimmermann, K., Philippsen, P., Johnston, M., Davis, R.W.: Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999)
7. Chu, A.M., Davis, R.W.: High-throughput creation of a whole-genome collection of yeast knockout strains. Methods Mol. Biol. 416, 205–220 (2008)
8. Baudin, A., Ozier-Kalogeropoulos, O., Denouel, A., Lacroute, F., Cullin, C.: A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21, 3329–3330 (1993)
9. Masselot, M., De Robichon-Szulmajster, H.: Methionine biosynthesis in Saccharomyces cerevisiae. I. Genetical analysis of auxotrophic mutants. Mol. Gen. Genet. 139, 121–132 (1975)
10. Parmar, L., Lobo, Z., Nadkarni, M., Maitra, P.K.: Multiple genes control particulate phosphofructokinase of yeast. Mol. Gen. Genet. 197, 515–516 (1984)
11. Lacroute, F.: Regulation of pyrimidine biosynthesis in Saccharomyces cerevisiae. J. Bacteriol. 95, 824–832 (1968)
12. Paulo, J.A., Gygi, S.P.: A comprehensive proteomic and phosphoproteomic analysis of yeast deletion mutants of 14-3-3 orthologs and associated effects of rapamycin. Proteomics 15, 474–486 (2015)
13. Paulo, J.A., McAllister, F.E., Everley, R.A., Beausoleil, S.A., Banks, A.S., Gygi, S.P.: Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics. Proteomics 15, 462–473 (2015)
14. Paulo, J.A., O’Connell, J.D., Gaun, A., Gygi, S.P.: Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. Mol. Biol. Cell. 26, 4063–4074 (2015)
15. Paulo, J.A., Gaun, A., Gygi, S.P.: Global analysis of protein expression and phosphorylation levels in nicotine-treated pancreatic stellate cells. J. Proteome Res. 14, 4246–4256 (2015)
16. Huttlin, E.L., Jedrychowski, M.P., Elias, J.E., Goswami, T., Rad, R., Beausoleil, S.A., Villen, J., Haas, W., Sowa, M.E., Gygi, S.P.: A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143, 1174–1189 (2010)
17. Elias, J.E., Gygi, S.P.: Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol. Biol. 604, 55–71 (2010)
18. Elias, J.E., Gygi, S.P.: Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207–214 (2007)
19. Krzywinski, M., Altman, N.: Visualizing samples with box plots. Nat. Methods 11, 119–120 (2014)
20. Chong, Y.T., Koh, J.L., Friesen, H., Duffy, S.K., Cox, M.J., Moses, A., Moffat, J., Boone, C., Andrews, B.J.: Yeast proteome dynamics from single cell imaging and automated analysis. Cell 161, 1413–1424 (2015)
21. Ryu, S.Y.: Bioinformatics tools to identify and quantify proteins using mass spectrometry data. Adv. Protein Chem. Struct. Biol. 94, 1–17 (2014)