Citing the TPP
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| == TPP Overall Latest Paper == | == TPP Overall Latest Paper == | ||
| - | Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. | + | ''Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics'' |
| Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL. | Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL. | ||
| Line 9: | Line 9: | ||
| Proteomics Clin Appl. 2015 Aug;9(7-8):745-54. doi: 10.1002/prca.201400164. Epub 2015 Apr 2. Review. | Proteomics Clin Appl. 2015 Aug;9(7-8):745-54. doi: 10.1002/prca.201400164. Epub 2015 Apr 2. Review. | ||
| - | PMID: 25631240 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/25631240 25631240] |
| == TPP Overall First Paper == | == TPP Overall First Paper == | ||
| - | A uniform proteomics MS/MS analysis platform utilizing open XML file formats. | + | ''A uniform proteomics MS/MS analysis platform utilizing open XML file formats'' |
| Keller A, Eng J, Zhang N, Li XJ, Aebersold R. | Keller A, Eng J, Zhang N, Li XJ, Aebersold R. | ||
| Line 20: | Line 20: | ||
| Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2. | Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2. | ||
| - | PMID: 16729052 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/16729052 16729052] |
| == iProphet and Combining Search Results Review == | == iProphet and Combining Search Results Review == | ||
| - | iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. | + | ''iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates'' |
| Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI. | Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI. | ||
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| Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29. | Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29. | ||
| - | PMID: 21876204 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/21876204 21876204] |
| - | Combining results of multiple search engines in proteomics. | + | ''Combining results of multiple search engines in proteomics'' |
| Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW. | Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW. | ||
| Line 40: | Line 40: | ||
| Mol Cell Proteomics. 2013 Sep;12(9):2383-93. doi: 10.1074/mcp.R113.027797. Epub 2013 May 29. Review. | Mol Cell Proteomics. 2013 Sep;12(9):2383-93. doi: 10.1074/mcp.R113.027797. Epub 2013 May 29. Review. | ||
| - | PMID: 23720762 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/23720762 23720762] |
| == PeptideProphet == | == PeptideProphet == | ||
| - | Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. | + | ''Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search'' |
| Keller A, Nesvizhskii AI, Kolker E, Aebersold R. | Keller A, Nesvizhskii AI, Kolker E, Aebersold R. | ||
| Line 51: | Line 51: | ||
| Anal Chem. 2002 Oct 15;74(20):5383-92. | Anal Chem. 2002 Oct 15;74(20):5383-92. | ||
| - | PMID: 12403597 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/12403597 12403597] |
| == ProteinProphet == | == ProteinProphet == | ||
| - | A statistical model for identifying proteins by tandem mass spectrometry. | + | ''A statistical model for identifying proteins by tandem mass spectrometry'' |
| Nesvizhskii AI, Keller A, Kolker E, Aebersold R. | Nesvizhskii AI, Keller A, Kolker E, Aebersold R. | ||
| Line 62: | Line 62: | ||
| Anal Chem. 2003 Sep 1;75(17):4646-58. | Anal Chem. 2003 Sep 1;75(17):4646-58. | ||
| - | PMID: 14632076 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/14632076 14632076] |
| == Kojak for Cross-linking analysis == | == Kojak for Cross-linking analysis == | ||
| - | Kojak: efficient analysis of chemically cross-linked protein complexes. | + | ''Kojak: efficient analysis of chemically cross-linked protein complexes'' |
| Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL. | Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL. | ||
| Line 73: | Line 73: | ||
| J Proteome Res. 2015 May 1;14(5):2190-8. doi: 10.1021/pr501321h. Epub 2015 Apr 15. | J Proteome Res. 2015 May 1;14(5):2190-8. doi: 10.1021/pr501321h. Epub 2015 Apr 15. | ||
| - | PMID: 25812159 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/25812159 25812159] |
| Line 79: | Line 79: | ||
| == StPeter Label-free Quantitation == | == StPeter Label-free Quantitation == | ||
| - | StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline. | + | ''StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline'' |
| Hoopmann MR, Winget JM, Mendoza L, Moritz RL. | Hoopmann MR, Winget JM, Mendoza L, Moritz RL. | ||
| Line 85: | Line 85: | ||
| J Proteome Res. 2018 Mar 2;17(3):1314-1320. doi: 10.1021/acs.jproteome.7b00786. Epub 2018 Feb 14. | J Proteome Res. 2018 Mar 2;17(3):1314-1320. doi: 10.1021/acs.jproteome.7b00786. Epub 2018 Feb 14. | ||
| - | PMID: 29400476 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/29400476 29400476] |
| == ASAPRatio Isotopic Labeling Quantitation (e.g. SILAC, ICAT) == | == ASAPRatio Isotopic Labeling Quantitation (e.g. SILAC, ICAT) == | ||
| - | Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. | + | ''Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry'' |
| Li XJ, Zhang H, Ranish JA, Aebersold R. | Li XJ, Zhang H, Ranish JA, Aebersold R. | ||
| Line 96: | Line 96: | ||
| Anal Chem. 2003 Dec 1;75(23):6648-57. | Anal Chem. 2003 Dec 1;75(23):6648-57. | ||
| - | PMID: 14640741 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/14640741 14640741] |
| == Libra Isobaric Labeling Quantitation (e.g TMT, iTRAQ) == | == Libra Isobaric Labeling Quantitation (e.g TMT, iTRAQ) == | ||
| - | Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. | + | ''Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software'' |
| Pedrioli PG, Raught B, Zhang XD, Rogers R, Aitchison J, Matunis M, Aebersold R. | Pedrioli PG, Raught B, Zhang XD, Rogers R, Aitchison J, Matunis M, Aebersold R. | ||
| Line 107: | Line 107: | ||
| Nat Methods. 2006 Jul;3(7):533-9. | Nat Methods. 2006 Jul;3(7):533-9. | ||
| - | PMID: 16791211 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/16791211 16791211] |
| == reSpect == | == reSpect == | ||
| - | reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra. | + | ''reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra'' |
| Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL. | Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL. | ||
| Line 118: | Line 118: | ||
| J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29. | J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29. | ||
| - | PMID: 26419769 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/26419769 26419769] |
| == THISP Human Sequence Databases == | == THISP Human Sequence Databases == | ||
| - | Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics. | + | ''Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics'' |
| Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL. | Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL. | ||
| Line 129: | Line 129: | ||
| J Proteome Res. 2016 Nov 4;15(11):4091-4100. Epub 2016 Sep 12. | J Proteome Res. 2016 Nov 4;15(11):4091-4100. Epub 2016 Sep 12. | ||
| - | PMID: 27577934 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/27577934 27577934] |
| - | + | ||
| Line 136: | Line 135: | ||
| == Proteomics Informatics Review == | == Proteomics Informatics Review == | ||
| - | Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. | + | ''Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics'' |
| Deutsch EW, Lam H, Aebersold R. | Deutsch EW, Lam H, Aebersold R. | ||
| Line 142: | Line 141: | ||
| Physiol Genomics. 2008 Mar 14;33(1):18-25. doi: 10.1152/physiolgenomics.00298.2007. Epub 2008 Jan 22. Review. | Physiol Genomics. 2008 Mar 14;33(1):18-25. doi: 10.1152/physiolgenomics.00298.2007. Epub 2008 Jan 22. Review. | ||
| - | PMID: 18212004 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/18212004 18212004] |
| == SpectraST - Library Searching == | == SpectraST - Library Searching == | ||
| - | Development and validation of a spectral library searching method for peptide identification from MS/MS. | + | ''Development and validation of a spectral library searching method for peptide identification from MS/MS'' |
| Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R. | Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R. | ||
| Line 153: | Line 152: | ||
| Proteomics. 2007 Mar;7(5):655-67. | Proteomics. 2007 Mar;7(5):655-67. | ||
| - | PMID: 17295354 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/17295354 17295354] |
| == SpectraST - Library Building == | == SpectraST - Library Building == | ||
| - | Building consensus spectral libraries for peptide identification in proteomics. | + | ''Building consensus spectral libraries for peptide identification in proteomics'' |
| Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R. | Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R. | ||
| Line 164: | Line 163: | ||
| Nat Methods. 2008 Oct;5(10):873-5. doi: 10.1038/nmeth.1254. Epub 2008 Sep 21. | Nat Methods. 2008 Oct;5(10):873-5. doi: 10.1038/nmeth.1254. Epub 2008 Sep 21. | ||
| - | PMID: 18806791 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/18806791 18806791] |
| == SpectraST - Artificial Decoys == | == SpectraST - Artificial Decoys == | ||
| - | Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics. | + | ''Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics'' |
| Lam H, Deutsch EW, Aebersold R. | Lam H, Deutsch EW, Aebersold R. | ||
| Line 175: | Line 174: | ||
| J Proteome Res. 2010 Jan;9(1):605-10. doi: 10.1021/pr900947u. | J Proteome Res. 2010 Jan;9(1):605-10. doi: 10.1021/pr900947u. | ||
| - | PMID: 19916561 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/19916561 19916561] |
| Line 181: | Line 180: | ||
| == Mass Spectrometry File Formats in General == | == Mass Spectrometry File Formats in General == | ||
| - | File formats commonly used in mass spectrometry proteomics. | + | ''File formats commonly used in mass spectrometry proteomics'' |
| Deutsch EW. | Deutsch EW. | ||
| Line 187: | Line 186: | ||
| Mol Cell Proteomics. 2012 Dec;11(12):1612-21. doi: 10.1074/mcp.R112.019695. Epub 2012 Sep 6. | Mol Cell Proteomics. 2012 Dec;11(12):1612-21. doi: 10.1074/mcp.R112.019695. Epub 2012 Sep 6. | ||
| - | PMID: 22956731 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/22956731 22956731] |
| + | |||
| == pepXML and protXML Initial Paper == | == pepXML and protXML Initial Paper == | ||
| - | A uniform proteomics MS/MS analysis platform utilizing open XML file formats. | + | ''A uniform proteomics MS/MS analysis platform utilizing open XML file formats'' |
| Keller A, Eng J, Zhang N, Li XJ, Aebersold R. | Keller A, Eng J, Zhang N, Li XJ, Aebersold R. | ||
| Line 197: | Line 197: | ||
| Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2. | Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2. | ||
| - | PMID: 16729052 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/16729052 16729052] |
| Line 203: | Line 203: | ||
| == pepXML for Cross-linking Data == | == pepXML for Cross-linking Data == | ||
| - | An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results. | + | ''An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results'' |
| Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL. | Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL. | ||
| Line 209: | Line 209: | ||
| J Am Soc Mass Spectrom. 2016 Nov;27(11):1728-1734. Epub 2016 Jul 28. | J Am Soc Mass Spectrom. 2016 Nov;27(11):1728-1734. Epub 2016 Jul 28. | ||
| - | PMID: 27469004 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/27469004 27469004] |
| == mzXML == | == mzXML == | ||
| - | A common open representation of mass spectrometry data and its application to proteomics research. | + | ''A common open representation of mass spectrometry data and its application to proteomics research'' |
| Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R. | Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R. | ||
| Line 220: | Line 220: | ||
| Nat Biotechnol. 2004 Nov;22(11):1459-66. | Nat Biotechnol. 2004 Nov;22(11):1459-66. | ||
| - | PMID: 15529173 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/15529173 15529173] |
| Line 226: | Line 226: | ||
| == TPP on Amazon Web Services == | == TPP on Amazon Web Services == | ||
| - | Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline. | + | ''Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline'' |
| Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL. | Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL. | ||
| Line 232: | Line 232: | ||
| Mol Cell Proteomics. 2015 Feb;14(2):399-404. doi: 10.1074/mcp.O114.043380. Epub 2014 Nov 23. | Mol Cell Proteomics. 2015 Feb;14(2):399-404. doi: 10.1074/mcp.O114.043380. Epub 2014 Nov 23. | ||
| - | PMID: 25418363 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/25418363 25418363] |
| == Hydra == | == Hydra == | ||
| - | Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. | + | ''Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework'' |
| Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J. | Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J. | ||
| Line 243: | Line 243: | ||
| BMC Bioinformatics. 2012 Dec 5;13:324. doi: 10.1186/1471-2105-13-324. | BMC Bioinformatics. 2012 Dec 5;13:324. doi: 10.1186/1471-2105-13-324. | ||
| - | PMID: 23216909 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/23216909 23216909] |
| == ETD analysis == | == ETD analysis == | ||
| - | Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. | + | ''Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets'' |
| Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R. | Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R. | ||
| Line 254: | Line 254: | ||
| Proteomics. 2010 Mar;10(6):1190-5. doi: 10.1002/pmic.200900567. | Proteomics. 2010 Mar;10(6):1190-5. doi: 10.1002/pmic.200900567. | ||
| - | PMID: 20082347 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/20082347 20082347] |
| Line 260: | Line 260: | ||
| == Other articles == | == Other articles == | ||
| - | A guided tour of the Trans-Proteomic Pipeline. | + | ''A guided tour of the Trans-Proteomic Pipeline'' |
| Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. | Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. | ||
| Line 266: | Line 266: | ||
| Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375. Review. | Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375. Review. | ||
| - | PMID: 20101611 | + | PMID: [https://www.ncbi.nlm.nih.gov/pubmed/20101611 20101611] |
Revision as of 02:16, 10 August 2018
If you use the TPP or any of its components in your research, please cite us in your publications. Below is a list of citations categorized by topic.
TPP Overall Latest Paper
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics
Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL.
Proteomics Clin Appl. 2015 Aug;9(7-8):745-54. doi: 10.1002/prca.201400164. Epub 2015 Apr 2. Review.
PMID: 25631240
TPP Overall First Paper
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
Keller A, Eng J, Zhang N, Li XJ, Aebersold R.
Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2.
PMID: 16729052
iProphet and Combining Search Results Review
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.
Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.
PMID: 21876204
Combining results of multiple search engines in proteomics
Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW.
Mol Cell Proteomics. 2013 Sep;12(9):2383-93. doi: 10.1074/mcp.R113.027797. Epub 2013 May 29. Review.
PMID: 23720762
PeptideProphet
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
Keller A, Nesvizhskii AI, Kolker E, Aebersold R.
Anal Chem. 2002 Oct 15;74(20):5383-92.
PMID: 12403597
ProteinProphet
A statistical model for identifying proteins by tandem mass spectrometry
Nesvizhskii AI, Keller A, Kolker E, Aebersold R.
Anal Chem. 2003 Sep 1;75(17):4646-58.
PMID: 14632076
Kojak for Cross-linking analysis
Kojak: efficient analysis of chemically cross-linked protein complexes
Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL.
J Proteome Res. 2015 May 1;14(5):2190-8. doi: 10.1021/pr501321h. Epub 2015 Apr 15.
PMID: 25812159
StPeter Label-free Quantitation
StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline
Hoopmann MR, Winget JM, Mendoza L, Moritz RL.
J Proteome Res. 2018 Mar 2;17(3):1314-1320. doi: 10.1021/acs.jproteome.7b00786. Epub 2018 Feb 14.
PMID: 29400476
ASAPRatio Isotopic Labeling Quantitation (e.g. SILAC, ICAT)
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry
Li XJ, Zhang H, Ranish JA, Aebersold R.
Anal Chem. 2003 Dec 1;75(23):6648-57.
PMID: 14640741
Libra Isobaric Labeling Quantitation (e.g TMT, iTRAQ)
Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software
Pedrioli PG, Raught B, Zhang XD, Rogers R, Aitchison J, Matunis M, Aebersold R.
Nat Methods. 2006 Jul;3(7):533-9.
PMID: 16791211
reSpect
reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra
Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL.
J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29.
PMID: 26419769
THISP Human Sequence Databases
Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics
Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL.
J Proteome Res. 2016 Nov 4;15(11):4091-4100. Epub 2016 Sep 12.
PMID: 27577934
Proteomics Informatics Review
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
Deutsch EW, Lam H, Aebersold R.
Physiol Genomics. 2008 Mar 14;33(1):18-25. doi: 10.1152/physiolgenomics.00298.2007. Epub 2008 Jan 22. Review.
PMID: 18212004
SpectraST - Library Searching
Development and validation of a spectral library searching method for peptide identification from MS/MS
Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R.
Proteomics. 2007 Mar;7(5):655-67.
PMID: 17295354
SpectraST - Library Building
Building consensus spectral libraries for peptide identification in proteomics
Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R.
Nat Methods. 2008 Oct;5(10):873-5. doi: 10.1038/nmeth.1254. Epub 2008 Sep 21.
PMID: 18806791
SpectraST - Artificial Decoys
Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics
Lam H, Deutsch EW, Aebersold R.
J Proteome Res. 2010 Jan;9(1):605-10. doi: 10.1021/pr900947u.
PMID: 19916561
Mass Spectrometry File Formats in General
File formats commonly used in mass spectrometry proteomics
Deutsch EW.
Mol Cell Proteomics. 2012 Dec;11(12):1612-21. doi: 10.1074/mcp.R112.019695. Epub 2012 Sep 6.
PMID: 22956731
pepXML and protXML Initial Paper
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
Keller A, Eng J, Zhang N, Li XJ, Aebersold R.
Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2.
PMID: 16729052
pepXML for Cross-linking Data
An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results
Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL.
J Am Soc Mass Spectrom. 2016 Nov;27(11):1728-1734. Epub 2016 Jul 28.
PMID: 27469004
mzXML
A common open representation of mass spectrometry data and its application to proteomics research
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.
Nat Biotechnol. 2004 Nov;22(11):1459-66.
PMID: 15529173
TPP on Amazon Web Services
Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline
Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL.
Mol Cell Proteomics. 2015 Feb;14(2):399-404. doi: 10.1074/mcp.O114.043380. Epub 2014 Nov 23.
PMID: 25418363
Hydra
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Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets
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A guided tour of the Trans-Proteomic Pipeline
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