S
Stephen Tanner
Researcher at University of California, San Diego
Publications - 12
Citations - 1874
Stephen Tanner is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Proteome & Gene prediction. The author has an hindex of 11, co-authored 12 publications receiving 1802 citations. Previous affiliations of Stephen Tanner include University of California, Los Angeles & Ludwig Institute for Cancer Research.
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Journal ArticleDOI
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra.
Stephen Tanner,Hongjun Shu,Ari Frank,Ling-Chi Wang,Ebrahim Zandi,Marc C. Mumby,Pavel A. Pevzner,Vineet Bafna +7 more
TL;DR: A tool is described, InsPecT, to identify posttranslational modifications using tandem mass spectrometry data, which identifies modified peptides with better or equivalent accuracy than other database search tools while being 2 orders of magnitude faster than SEQUEST, and substantially faster than X!TANDEM on complex mixtures.
Journal ArticleDOI
Identification of post-translational modifications by blind search of mass spectra
TL;DR: This work describes an unrestrictive PTM search algorithm, MS-Alignment, that searches for all types of PTMs at once in a blind mode, that is, without knowing which PTMs exist in nature.
Journal ArticleDOI
Clustering Millions of Tandem Mass Spectra
Ari Frank,Nuno Bandeira,Zhouxin Shen,Stephen Tanner,Steven P. Briggs,Richard D. Smith,Pavel A. Pevzner +6 more
TL;DR: This work presents an efficient clustering approach for analyzing large MS/MS data sets (over 10 million spectra) with a capability to reduce the number of spectra submitted to further analysis by an order of magnitude.
Journal ArticleDOI
Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
Nitin Gupta,Stephen Tanner,Navdeep Jaitly,Joshua N. Adkins,Mary S. Lipton,Robert Edwards,Robert Edwards,Margaret F. Romine,Andrei L. Osterman,Vineet Bafna,Vineet Bafna,Richard D. Smith,Pavel A. Pevzner,Pavel A. Pevzner +13 more
TL;DR: This study provides the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavage of N-terminal methionine residues.
Journal ArticleDOI
Improving gene annotation using peptide mass spectrometry
Stephen Tanner,Zhouxin Shen,Julio Ng,Liliana Florea,Roderic Guigó,Steven P. Briggs,Vineet Bafna +6 more
TL;DR: By searching a corpus of 18.5 million tandem mass spectra from human proteomic samples, this work validate 39,000 exons and 11,000 introns at the level of translation and demonstrates that proteomic profiling should play a role in any genome sequencing project.