A Skyline Plugin for Pathway-Centric Data Browsing

Journal of the American Society for Mass Spectrometry

Volumn 27, Issue 11, 2016, Pages 1752-1757

  Degan, Michael G ^a   Ryadinskiy, Lillian ^a   Fujimoto, Grant M ^a   Wilkins, Christopher S ^a   Lichti, Cheryl F ^b   Payne, Samuel H ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b University of Texas Medical Branch School of Medicine   (United States)

Author keywords

Bioinformatics; Data analysis; Systems biology; Targeted proteomics

Indexed keywords

BIODIVERSITY; BIOINFORMATICS; DATA HANDLING; DATA REDUCTION; DESIGN OF EXPERIMENTS; INFORMATION ANALYSIS; LABORATORIES; MASS SPECTROMETRY; MOLECULAR BIOLOGY;

BIOLOGICAL HYPOTHESIS; EXPERIMENTAL PROTOCOLS; MASS SPECTROMETRY DATA; PACIFIC NORTHWEST NATIONAL LABORATORIES; QUANTITATIVE EXPERIMENTS; SELECTED REACTION MONITORING; SYSTEMS BIOLOGY; TARGETED PROTEOMICS;

PROTEINS;

PEPTIDE; PROTEIN; PROTEOME;

ARTICLE; BIODIVERSITY; INFORMATION PROCESSING; MASS SPECTROMETRY; NONHUMAN; ORGANISMS; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEOMICS; SOFTWARE; HUMAN; STATISTICS;

HUMANS; MASS SPECTROMETRY; PEPTIDES; PROTEOME; PROTEOMICS; SOFTWARE; STATISTICS AS TOPIC;

EID: 84991074946     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-016-1448-3     Document Type: Article

References (19)

1. Liebler, D.C., Zimmerman, L.J.: Targeted quantitation of proteins by mass spectrometry. Biochemistry 52(22), 3797–3806 (2013)
2. Prakash, A., Tomazela, D.M., Frewen, B., Maclean, B., Merrihew, G., Peterman, S., Maccoss, M.J.: Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J. Proteome Res. 8(6), 2733–2739 (2009)
3. Picotti, P., Aebersold, R.: Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 9(6), 555–566 (2012)
4. Wu, C., Shi, T., Brown, J.N., He, J., Gao, Y., Fillmore, T.L., Shukla, A.K., Moore, R.J., Camp II, D.G., Rodland, K.D., Qian, W.J., Liu, T., Smith, R.D.: Expediting SRM assay development for large-scale targeted proteomics experiments. J. Proteome Res. 13(10), 4479–4487 (2014)
5. Vizcaino, J.A., Cote, R.G., Csordas, A., Dianes, J.A., Fabregat, A., Foster, J.M., Griss, J., Alpi, E., Birim, M., Contell, J., O'Kelly, G., Schoenegger, A., Ovelleiro, D., Perez-Riverol, Y., Reisinger, F., Rios, D., Wang, R., Hermjakob, H.: The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41(Database issue), D1063–D1069 (2013)
6. Vizcaino, J.A., Deutsch, E.W., Wang, R., Csordas, A., Reisinger, F., Rios, D., Dianes, J.A., Sun, Z., Farrah, T., Bandeira, N., Binz, P.A., Xenarios, I., Eisenacher, M., Mayer, G., Gatto, L.: ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol. 32(3), 223–226 (2014)
7. Craig, R., Cortens, J.P., Beavis, R.C.: Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 3(6), 1234–1242 (2004)
8. Egertson, J.D., Kuehn, A., Merrihew, G.E., Bateman, N.W., MacLean, B.X., Ting, Y.S., Canterbury, J.D., Marsh, D.M., Kellmann, M., Zabrouskov, V., Wu, C.C., MacCoss, M.J.: Multiplexed MS/MS for improved data-independent acquisition. Nat. Methods 10(8), 744–746 (2013)
9. 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 (Oxford, Engl.) 26(7), 966–968 (2010)
10. Schilling, B., MacLean, B., Held, J.M., Sahu, A.K., Rardin, M.J., Sorensen, D.J., Peters, T., Wolfe, A.J., Hunter, C.L., MacCoss, M.J., Gibson, B.W.: Multiplexed, scheduled, high-resolution parallel reaction monitoring on a full scan QqTOF Instrument with integrated data-dependent and targeted mass spectrometric workflows. Anal. Chem. 87(20), 10222–10229 (2015)
11. Schilling, B., Rardin, M.J., MacLean, B.X., Zawadzka, A.M., Frewen, B.E., Cusack, M.P., Sorensen, D.J., Bereman, M.S., Jing, E., Wu, C.C., Verdin, E., Kahn, C.R., Maccoss, M.J., Gibson, B.W.: Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol. Cell. Proteom. 11(5), 202–214 (2012)
12. Egertson, J.D., MacLean, B., Johnson, R., Xuan, Y., MacCoss, M.J.: Multiplexed peptide analysis using data-independent acquisition and Skyline. Nat. Protoc. 10(6), 887–903 (2015)
13. 2 (SWATH) data independent acquisitions. improving post acquisition analysis of proteomic experiments. Mol. Cell. Proteom. 14(9), 2405–2419 (2015)
14. Payne, S.H., Monroe, M.E., Overall, C.C., Kiebel, G.R., Degan, M., Gibbons, B.C., Fujimoto, G.M., Purvine, S.O., Adkins, J.N., Lipton, M.S., Smith, R.D.: The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. Scientific Data 2, 150041 (2015)
15. Kim, M.S., Pinto, S.M., Getnet, D., Nirujogi, R.S., Manda, S.S., Chaerkady, R., Madugundu, A.K., Kelkar, D.S., Isserlin, R., Jain, S., Thomas, J.K., Muthusamy, B., Leal-Rojas, P., Kumar, P., Sahasrabuddhe, N.A., Balakrishnan, L., Advani, J., George, B., Renuse, S., Selvan, L.D., Patil, A.H., Nanjappa, V., Radhakrishnan, A., Prasad, S., Subbannayya, T., Raju, R., Kumar, M., Sreenivasamurthy, S.K., Marimuthu, A., Sathe, G.J., Chavan, S., Datta, K.K., Subbannayya, Y., Sahu, A., Yelamanchi, S.D., Jayaram, S., Rajagopalan, P., Sharma, J., Murthy, K.R., Syed, N., Goel, R., Khan, A.A., Ahmad, S., Dey, G., Mudgal, K., Chatterjee, A., Huang, T.C., Zhong, J., Wu, X., Shaw, P.G., Freed, D., Zahari, M.S., Mukherjee, K.K., Shankar, S., Mahadevan, A., Lam, H., Mitchell, C.J., Shankar, S.K., Satishchandra, P., Schroeder, J.T., Sirdeshmukh, R., Maitra, A., Leach, S.D., Drake, C.G., Halushka, M.K., Prasad, T.S., Hruban, R.H., Kerr, C.L., Bader, G.D., Iacobuzio-Donahue, C.A., Gowda, H., Pandey, A.: A draft map of the human proteome. Nature 509(7502), 575–581 (2014)
16. Kanehisa, M., Goto, S.: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1), 27–30 (2000)
17. Searle, B.C., Egertson, J.D., Bollinger, J.G., Stergachis, A.B., MacCoss, M.J.: Using data independent acquisition (DIA) to model high-responding peptides for targeted proteomics experiments. Mol. Cell. Proteom. 14(9), 2331–2340 (2015)
18. Escher, C., Reiter, L., MacLean, B., Ossola, R., Herzog, F., Chilton, J., MacCoss, M.J., Rinner, O.: Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 12(8), 1111–1121 (2012)
19. Parker, S.J., Rost, H., Rosenberger, G., Collins, B.C., Malmstrom, L., Amodei, D., Venkatraman, V., Raedschelders, K., Van Eyk, J.E., Aebersold, R.: Identification of a set of conserved eukaryotic internal retention time standards for data-independent acquisition mass spectrometry. Mol. Cell. Proteom. 14(10), 2800–2813 (2015)