Accurate annotation of peptide modifications through unrestrictive database search.

@article{citeulike:2721960, abstract = {Proteins are extensively modified after translation due to cellular regulation, signal transduction, or chemical damage. Peptide tandem mass spectrometry can discover post-translational modifications, as well as sequence polymorphisms. Recent efforts have studied modifications at the proteomic scale. In this context, it becomes crucial to assess the accuracy of modification discovery. We discuss methods to quantify the false discovery rate from a search and demonstrate how several features can be used to distinguish valid modifications from search artifacts. We present a tool, PTMFinder, which implements these methods. We summarize the corpus of post-translational modifications identified on large data sets. Thousands of known and novel modification sites are identified, including site-specific modifications conserved over vast evolutionary distances.}, address = {Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA. stanner@ucsd.edu}, author = {Tanner, S. and Payne, S. H. and Dasari, S. and Shen, Z. and Wilmarth, P. A. and David, L. L. and Loomis, W. F. and Briggs, S. P. and Bafna, V. }, citeulike-article-id = {2721960}, doi = {10.1021/pr070444v}, issn = {1535-3893}, journal = {Journal of proteome research}, month = {January}, number = {1}, pages = {170--181}, posted-at = {2008-04-26 16:13:04}, priority = {2}, title = {Accurate annotation of peptide modifications through unrestrictive database search.}, url = {http://dx.doi.org/10.1021/pr070444v}, volume = {7}, year = {2008} }

TY - JOUR ID - citeulike:2721960 L3 - citeulike-article-id:2721960 TI - Accurate annotation of peptide modifications through unrestrictive database search. JF - Journal of proteome research VL - 7 IS - 1 SP - 170 EP - 181 AD - Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA. stanner@ucsd.edu SN - 1535-3893 N2 - Proteins are extensively modified after translation due to cellular regulation, signal transduction, or chemical damage. Peptide tandem mass spectrometry can discover post-translational modifications, as well as sequence polymorphisms. Recent efforts have studied modifications at the proteomic scale. In this context, it becomes crucial to assess the accuracy of modification discovery. We discuss methods to quantify the false discovery rate from a search and demonstrate how several features can be used to distinguish valid modifications from search artifacts. We present a tool, PTMFinder, which implements these methods. We summarize the corpus of post-translational modifications identified on large data sets. Thousands of known and novel modification sites are identified, including site-specific modifications conserved over vast evolutionary distances. AU - Tanner, S AU - Payne, SH AU - Dasari, S AU - Shen, Z AU - Wilmarth, PA AU - David, LL AU - Loomis, WF AU - Briggs, SP AU - Bafna, V PY - 2008/01// UR - http://dx.doi.org/10.1021/pr070444v ER -