Literature DB >> 19275241

SLoMo: automated site localization of modifications from ETD/ECD mass spectra.

Christopher M Bailey1, Steve M M Sweet, Debbie L Cunningham, Martin Zeller, John K Heath, Helen J Cooper.   

Abstract

Recently, software has become available to automate localization of phosphorylation sites from CID data and to assign associated confidence scores. We present an algorithm, SLoMo (Site Localization of Modifications), which extends this capability to ETD/ECD mass spectra. Furthermore, SLoMo caters for both high and low resolution data and allows for site-localization of any UniMod post-translational modification. SLoMo accepts input data from a variety of formats (e.g., Sequest, OMSSA). We validate SLoMo with high and low resolution ETD, ECD, and CID data.

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Year:  2009        PMID： 19275241     DOI： 10.1021/pr800917p

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  34 in total

Review 1.  Modification site localization scoring: strategies and performance.

Authors:  Robert J Chalkley; Karl R Clauser
Journal:  Mol Cell Proteomics       Date:  2012-02-11       Impact factor: 5.911

2.  Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16.

Authors:  Tuo Li; Benjamin A Diner; Jin Chen; Ileana M Cristea
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-12       Impact factor: 11.205

3.  Comparative assessment of site assignments in CID and electron transfer dissociation spectra of phosphopeptides discloses limited relocation of phosphate groups.

Authors:  Nikolai Mischerikow; A F Maarten Altelaar; J Daniel Navarro; Shabaz Mohammed; Albert J R Heck
Journal:  Mol Cell Proteomics       Date:  2010-03-16       Impact factor: 5.911

4.  Confident phosphorylation site localization using the Mascot Delta Score.

Authors:  Mikhail M Savitski; Simone Lemeer; Markus Boesche; Manja Lang; Toby Mathieson; Marcus Bantscheff; Bernhard Kuster
Journal:  Mol Cell Proteomics       Date:  2010-11-06       Impact factor: 5.911

5.  Identification of tandem mass spectra of mixtures of isomeric peptides.

Authors:  Xi Chen; Paul Drogaris; Marshall Bern
Journal:  J Proteome Res       Date:  2010-06-04       Impact factor: 4.466

6.  LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach.

Authors:  Damian Fermin; Scott J Walmsley; Anne-Claude Gingras; Hyungwon Choi; Alexey I Nesvizhskii
Journal:  Mol Cell Proteomics       Date:  2013-08-05       Impact factor: 5.911

Review 7.  The coming of age of phosphoproteomics--from large data sets to inference of protein functions.

Authors:  Philippe P Roux; Pierre Thibault
Journal:  Mol Cell Proteomics       Date:  2013-09-13       Impact factor: 5.911

8.  What does the future hold for Top Down mass spectrometry?

Authors:  Benjamin A Garcia
Journal:  J Am Soc Mass Spectrom       Date:  2009-10-29       Impact factor: 3.109

9.  Modification site localization scoring integrated into a search engine.

Authors:  Peter R Baker; Jonathan C Trinidad; Robert J Chalkley
Journal:  Mol Cell Proteomics       Date:  2011-04-13       Impact factor: 5.911

10.  Differential phosphoproteomics of fibroblast growth factor signaling: identification of Src family kinase-mediated phosphorylation events.

Authors:  Debbie L Cunningham; Steve M M Sweet; Helen J Cooper; John K Heath
Journal:  J Proteome Res       Date:  2010-05-07       Impact factor: 4.466
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