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Literature DB >> 18543960

PhosphoScore: an open-source phosphorylation site assignment tool for MSn data.

Brian E Ruttenberg¹, Trairak Pisitkun, Mark A Knepper, Jason D Hoffert.

Abstract

Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MS(n)). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95% correct MS(2) assignments from known synthetic data, > 98% agreement with an established MS(2) assignment algorithm (Ascore), and >92% agreement with visual inspection of MS(3) and MS(4) spectra.

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Year: 2008 PMID： 18543960 PMCID： PMC2562657 DOI： 10.1021/pr800169k

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

15 in total

1. SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database.

Authors: V Bafna; N Edwards
Journal: Bioinformatics Date: 2001 Impact factor: 6.937

2. Large-scale characterization of HeLa cell nuclear phosphoproteins.

Authors: Sean A Beausoleil; Mark Jedrychowski; Daniel Schwartz; Joshua E Elias; Judit Villén; Jiaxu Li; Martin A Cohn; Lewis C Cantley; Steven P Gygi
Journal: Proc Natl Acad Sci U S A Date: 2004-08-09 Impact factor: 11.205

3. Stochastic relaxation, gibbs distributions, and the bayesian restoration of images.

Authors: S Geman; D Geman
Journal: IEEE Trans Pattern Anal Mach Intell Date: 1984-06 Impact factor: 6.226

4. Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway.

Authors: Greg T Cantin; John D Venable; Daniel Cociorva; John R Yates
Journal: J Proteome Res Date: 2006-01 Impact factor: 4.466

5. A probability-based approach for high-throughput protein phosphorylation analysis and site localization.

Authors: Sean A Beausoleil; Judit Villén; Scott A Gerber; John Rush; Steven P Gygi
Journal: Nat Biotechnol Date: 2006-09-10 Impact factor: 54.908

6. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.

Authors: Henrik Molina; David M Horn; Ning Tang; Suresh Mathivanan; Akhilesh Pandey
Journal: Proc Natl Acad Sci U S A Date: 2007-02-07 Impact factor: 11.205

7. Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites.

Authors: Jason D Hoffert; Trairak Pisitkun; Guanghui Wang; Rong-Fong Shen; Mark A Knepper
Journal: Proc Natl Acad Sci U S A Date: 2006-04-25 Impact factor: 11.205

8. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.

Authors: Albrecht Gruhler; Jesper V Olsen; Shabaz Mohammed; Peter Mortensen; Nils J Faergeman; Matthias Mann; Ole N Jensen
Journal: Mol Cell Proteomics Date: 2005-01-22 Impact factor: 5.911

9. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.

Authors: Jesper V Olsen; Blagoy Blagoev; Florian Gnad; Boris Macek; Chanchal Kumar; Peter Mortensen; Matthias Mann
Journal: Cell Date: 2006-11-03 Impact factor: 41.582

10. An automated platform for analysis of phosphoproteomic datasets: application to kidney collecting duct phosphoproteins.

Authors: Jason D Hoffert; Guanghui Wang; Trairak Pisitkun; Rong-Fong Shen; Mark A Knepper
Journal: J Proteome Res Date: 2007-08-07 Impact factor: 4.466

41 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. Large-scale phosphotyrosine proteomic profiling of rat renal collecting duct epithelium reveals predominance of proteins involved in cell polarity determination.

Authors: Boyang Zhao; Mark A Knepper; Chung-Lin Chou; Trairak Pisitkun
Journal: Am J Physiol Cell Physiol Date: 2011-09-21 Impact factor: 4.249

Review 3. What can we learn about cardioprotection from the cardiac mitochondrial proteome?

Authors: Marjan Gucek; Elizabeth Murphy
Journal: Cardiovasc Res Date: 2010-08-30 Impact factor: 10.787

4. 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

5. 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

Review 6. Toward a complete in silico, multi-layered embryonic stem cell regulatory network.

Authors: Huilei Xu; Christoph Schaniel; Ihor R Lemischka; Avi Ma'ayan
Journal: Wiley Interdiscip Rev Syst Biol Med Date: 2010 Nov-Dec

7. 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