Abstract
There are a large number of search engines designed to take mass spectrometry fragmentation spectra and match them to peptides from proteins in a database. These peptides could be unmodified, but they could also bear modifications that were added biologically or during sample preparation. As a measure of reliability for the peptide identification, software normally calculates how likely a given quality of match could have been achieved at random, most commonly through the use of target-decoy database searching (Elias and Gygi, Nat Methods 4(3): 207–214, 2007). Matching the correct peptide but with the wrong modification localization is not a random match, so results with this error will normally still be assessed as reliable identifications by the search engine. Hence, an extra step is required to determine site localization reliability, and the software approaches to measure this are the subject of this part of the chapter.
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References
Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4(3):207–214
Chalkley RJ, Clauser KR (2012) Modification site localization scoring: strategies and performance. Mol Cell Proteomics 11(5):3–14
Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B (2011) Confident phosphorylation site localization using the Mascot Delta Score. Mol Cell Proteomics 10(2):M110.003830
Baker PR, Trinidad JC, Chalkley RJ (2011) Modification site localization scoring integrated into a search engine. Mol Cell Proteomics 10(7):M111 008078
Spectrum Mill – Agilent Technologies Inc. Available from: http://www.chem.agilent.com/en-US/Products/software/chromatography/ms/spectrummillformassh unterworkstation/pages/default.aspx
Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24(10):1285–1292
Scaffold – Proteome Software. Available from: http://www.proteomesoftware.com/products/ptm/
Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127(3):635–648
Taus T, Kocher T, Pichler P, Paschke C, Schmidt A, Henrich C, Mechtler K (2011) Universal and confident phosphorylation site localization using phosphoRS. J Proteome Res 10(12):5354–5362
Proteome Discoverer – Thermo Scientific. Available from: http://www.thermoscientific.com/en/product/proteome-discoverer-software.html
Marx H, Lemeer S, Schliep JE, Matheron L, Mohammed S, Cox J, Mann M, Heck AJ, Kuster B (2013) A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat Biotechnol 31(6):557–564
Kapp EA, Schutz F, Reid GE, Eddes JS, Moritz RL, O’Hair RA, Speed TP, Simpson RJ (2003) Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal Chem 75(22):6251–6264
Baker PR, Chalkley RJ (2014) MS-viewer: a web-based spectral viewer for proteomics results. Mol Cell Proteomics 13(5):1392–1396
Moore KE, Gozani O (2014) An unexpected journey: lysine methylation across the proteome. Biochim Biophys Acta 1839(12):1395–1403
Chalkley RJ (2013) When target-decoy false discovery rate estimations are inaccurate and how to spot instances. J Proteome Res 12(2):1062–1064
Acknowledgement
This work was supported by NIH NIGMS grant 8P41GM103481.
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Chalkley, R.J. (2016). Modification Site Localization in Peptides. In: Mirzaei, H., Carrasco, M. (eds) Modern Proteomics – Sample Preparation, Analysis and Practical Applications. Advances in Experimental Medicine and Biology, vol 919. Springer, Cham. https://doi.org/10.1007/978-3-319-41448-5_13
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DOI: https://doi.org/10.1007/978-3-319-41448-5_13
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