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Using ProHits to Store, Annotate, and Analyze Affinity Purificationâ Mass Spectrometry (APâ MS) Data
dc.contributor.authorLiu, Guomin
dc.contributor.authorZhang, Jianping
dc.contributor.authorChoi, Hyungwon
dc.contributor.authorLambert, Jean‐philippe
dc.contributor.authorSrikumar, Tharan
dc.contributor.authorLarsen, Brett
dc.contributor.authorNesvizhskii, Alexey I.
dc.contributor.authorRaught, Brian
dc.contributor.authorTyers, Mike
dc.contributor.authorGingras, Anne‐claude
dc.date.accessioned2020-01-13T15:03:18Z
dc.date.available2020-01-13T15:03:18Z
dc.date.issued2012-09
dc.identifier.citationLiu, Guomin; Zhang, Jianping; Choi, Hyungwon; Lambert, Jean‐philippe ; Srikumar, Tharan; Larsen, Brett; Nesvizhskii, Alexey I.; Raught, Brian; Tyers, Mike; Gingras, Anne‐claude (2012). "Using ProHits to Store, Annotate, and Analyze Affinity Purificationâ Mass Spectrometry (APâ MS) Data." Current Protocols in Bioinformatics 39(1): 8.16.1-8.16.32.
dc.identifier.issn1934-3396
dc.identifier.issn1934-340X
dc.identifier.urihttps://hdl.handle.net/2027.42/152510
dc.description.abstractAffinity purification coupled with mass spectrometry (APâ MS) is a robust technique used to identify proteinâ protein interactions. With recent improvements in sample preparation, and dramatic advances in MS instrumentation speed and sensitivity, this technique is becoming more widely used throughout the scientific community. To meet the needs of research groups both large and small, we have developed software solutions for tracking, scoring and analyzing APâ MS data. Here, we provide details for the installation and utilization of ProHits, a Laboratory Information Management System designed specifically for APâ MS interaction proteomics. This protocol explains: (i) how to install the complete ProHits system, including modules for the management of mass spectrometry files and the analysis of interaction data, and (ii) alternative options for the use of preâ existing search results in simpler versions of ProHits, including a virtual machine implementation of our ProHits Lite software. We also describe how to use the main features of the software to analyze APâ MS data. Curr. Protoc. Bioinform. 39:8.16.1â 8.16.32. © 2012 by John Wiley & Sons, Inc.
dc.publisherWiley Periodicals, Inc.
dc.subject.otheraffinity purification coupled with mass spectrometry
dc.subject.otherdata analysis
dc.subject.othervirtual machine
dc.subject.otherstatistical models
dc.subject.otherproteinâ protein interactions
dc.titleUsing ProHits to Store, Annotate, and Analyze Affinity Purificationâ Mass Spectrometry (APâ MS) Data
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelBiological Chemistry
dc.subject.hlbsecondlevelGenetics
dc.subject.hlbsecondlevelMolecular, Cellular and Developmental Biology
dc.subject.hlbtoplevelHealth Sciences
dc.subject.hlbtoplevelScience
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/152510/1/cpbi0816.pdf
dc.identifier.doi10.1002/0471250953.bi0816s39
dc.identifier.sourceCurrent Protocols in Bioinformatics
dc.identifier.citedreferencePerkins, D.N., Pappin, D.J., Creasy, D.M., and Cottrell, J.S. 1999. Probabilityâ based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551 â 3567.
dc.identifier.citedreferenceBreitkreutz, A., Choi, H., Sharom, J.R., Boucher, L., Neduva, V., Larsen, B., Lin, Z.Y., Breitkreutz, B.J., Stark, C., Liu, G., Ahn, J., Dewarâ Darch, D., Reguly, T., Tang, X., Almeida, R., Qin, Z.S., Pawson, T., Gingras, A.C., Nesvizhskii, A.I., and Tyers, M. 2010. A global protein kinase and phosphatase interaction network in yeast. Science 328: 1043 â 1046.
dc.identifier.citedreferenceChoi, H., Larsen, B., Lin, Z.Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z.S., Tyers, M., Gingras, A.C., and Nesvizhskii, A.I. 2011. SAINT: Probabilistic scoring of affinity purificationâ mass spectrometry data. Nat. Methods 8: 70 â 73.
dc.identifier.citedreferenceCraig, R. and Beavis, R.C. 2004. TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20: 1466 â 1467.
dc.identifier.citedreferenceCsordas, A., Ovelleiro, D., Wang, R., Foster, J.M., Rios, D., Vizcaino, J.A., and Hermjakob, H. 2012. PRIDE: Quality control in a proteomics data repository. Database (Oxford) 2012: bas004.
dc.identifier.citedreferenceDeutsch, E.W., Mendoza, L., Shteynberg, D., Farrah, T., Lam, H., Tasman, N., Sun, Z., Nilsson, E., Pratt, B., Prazen, B., Eng, J.K., Martin, D.B., Nesvizhskii, A.I., and Aebersold, R. 2010. A guided tour of the Transâ Proteomic Pipeline. Proteomics 10: 1150 â 1159.
dc.identifier.citedreferenceEng, J.K., McCormack, A.L., and Yates, J.R. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 5: 976 â 989.
dc.identifier.citedreferenceGavin, A.C., Maeda, K., and Kuhner, S. 2011. Recent advances in charting proteinâ protein interaction: Mass spectrometryâ based approaches. Curr. Opin. Biotechnol. 22: 42 â 49.
dc.identifier.citedreferenceGingras, A.C., Gstaiger, M., Raught, B., and Aebersold, R. 2007. Analysis of protein complexes using mass spectrometry. Nat. Rev. Mol. Cell. Biol. 8: 645 â 654.
dc.identifier.citedreferenceKeller, A., Nesvizhskii, A.I., Kolker, E., and Aebersold, R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74: 5383 â 5392.
dc.identifier.citedreferenceKerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackesâ Carter, F., Chen, C., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U., Jandrasits, C., Jimenez, R.C., Khadake, J., Mahadevan, U., Masson, P., Pedruzzi, I., Pfeiffenberger, E., Porras, P., Raghunath, A., Roechert, B., Orchard, S., and Hermjakob, H. 2012. The IntAct molecular interaction database in 2012. Nucleic Acids Res. 40: D841 â D846.
dc.identifier.citedreferenceKessner, D., Chambers, M., Burke, R., Agus, D., and Mallick, P. 2008. ProteoWizard: Open source software for rapid proteomics tools development. Bioinformatics 24: 2534 â 2536.
dc.identifier.citedreferenceLicata, L., Briganti, L., Peluso, D., Perfetto, L., Iannuccelli, M., Galeota, E., Sacco, F., Palma, A., Nardozza, A.P., Santonico, E., Castagnoli, L., and Cesareni, G. 2012. MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 40: D857 â D861.
dc.identifier.citedreferenceLiu, G., Zhang, J., Larsen, B., Stark, C., Breitkreutz, A., Lin, Z.Y., Breitkreutz, B.J., Ding, Y., Colwill, K., Pasculescu, A., Pawson, T., Wrana, J.L., Nesvizhskii, A.I., Raught, B., Tyers, M., and Gingras, A.C. 2010. ProHits: Integrated software for mass spectrometryâ based interaction proteomics. Nat. Biotechnol. 28: 1015 â 1017.
dc.identifier.citedreferenceLopes, C.T., Franz, M., Kazi, F., Donaldson, S.L., Morris, Q., and Bader, G.D. 2010. Cytoscape Web: An interactive webâ based network browser. Bioinformatics 26: 2347 â 2348.
dc.identifier.citedreferenceMaglott, D., Ostell, J., Pruitt, K.D., and Tatusova, T. 2011. Entrez Gene: Geneâ centered information at NCBI. Nucleic Acids Res. 39: D52 â D57.
dc.identifier.citedreferenceNesvizhskii, A.I., Keller, A., Kolker, E., and Aebersold, R. 2003. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75: 4646 â 4658.
dc.identifier.citedreferenceOrchard, S., Salwinski, L., Kerrien, S., Montecchiâ Palazzi, L., Oesterheld, M., Stumpflen, V., Ceol, A., Chatrâ aryamontri, A., Armstrong, J., Woollard, P., Salama, J.J., Moore, S., Wojcik, J., Bader, G.D., Vidal, M., Cusick, M.E., Gerstein, M., Gavin, A.C., Supertiâ Furga, G., Greenblatt, J., Bader, J., Uetz, P., Tyers, M., Legrain, P., Fields, S., Mulder, N., Gilson, M., Niepmann, M., Burgoon, L., De Las Rivas, J., Prieto, C., Perreau, V.M., Hogue, C., Mewes, H.W., Apweiler, R., Xenarios, I., Eisenberg, D., Cesareni, G., and Hermjakob, H. 2007. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat. Biotechnol. 25: 894 â 898.
dc.identifier.citedreferenceOrchard, S., Aranda, B., and Hermjakob, H. 2010. The publication and database deposition of molecular interaction data. Curr. Protoc. Protein Sci. 60: 25.3.1 â 25.3.13.
dc.identifier.citedreferencePruitt, K.D., Tatusova, T., Brown, G.R., and Maglott, D.R. 2012. NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy. Nucleic Acids Res. 40: D130 â D135.
dc.identifier.citedreferenceSkarra, D.V., Goudreault, M., Choi, H., Mullin, M., Nesvizhskii, A.I., Gingras, A.C., and Honkanen, R.E. 2011. Labelâ free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5. Proteomics 11: 1508 â 1516.
dc.identifier.citedreferenceStark, C., Breitkreutz, B.J., Chatrâ Aryamontri, A., Boucher, L., Oughtred, R., Livstone, M.S., Nixon, J., Van Auken, K., Wang, X., Shi, X., Reguly, T., Rust, J.M., Winter, A., Dolinski, K., and Tyers, M. 2011. The BioGRID interaction database: 2011 update. Nucleic Acids Res. 39: D698 â D704.
dc.identifier.citedreferenceTaylor, C.F., Paton, N.W., Lilley, K.S., Binz, P.A., Julian, R.K. Jr., Jones, A.R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E.W., Dunn, M.J., Heck, A.J., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T.A., Patterson, S.D., Ping, P., Seymour, S.L., Souda, P., Tsugita, A., Vandekerckhove, J., Vondriska, T.M., Whitelegge, J.P., Wilkins, M.R., Xenarios, I., Yates, J.R. 3rd, and Hermjakob, H. 2007. The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 25: 887 â 893.
dc.identifier.citedreferencehttp://prohitsms.com/Prohits_download/list.php
dc.identifier.citedreferenceProHits source code.
dc.identifier.citedreferencehttp://www.cytoscape.org/
dc.identifier.citedreferencehttp://cytoscapeweb.cytoscape.org/
dc.identifier.citedreferencehttp://thebiogrid.org/
dc.identifier.citedreferencehttp://proteowizard.sourceforge.net/
dc.identifier.citedreferencehttp://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
dc.identifier.citedreferencehttp://www.thegpm.org/
dc.identifier.citedreferencehttp://www.ncbi.nlm.nih.gov/RefSeq/
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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