Literature DB >> 20564260

MassSieve: panning MS/MS peptide data for proteins.

Douglas J Slotta1, Melinda A McFarland, Sanford P Markey.   

Abstract

We present MassSieve, a Java-based platform for visualization and parsimony analysis of single and comparative LC-MS/MS database search engine results. The success of mass spectrometric peptide sequence assignment algorithms has led to the need for a tool to merge and evaluate the increasing data set sizes that result from LC-MS/MS-based shotgun proteomic experiments. MassSieve supports reports from multiple search engines with differing search characteristics, which can increase peptide sequence coverage and/or identify conflicting or ambiguous spectral assignments.

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Year:  2010        PMID： 20564260      PMCID： PMC2997567          DOI： 10.1002/pmic.200900370

Source DB:  PubMed          Journal:  Proteomics        ISSN： 1615-9853            Impact factor:   3.984


  8 in total

1.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Authors:  Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2002-10-15       Impact factor: 6.986

2.  A statistical model for identifying proteins by tandem mass spectrometry.

Authors:  Alexey I Nesvizhskii; Andrew Keller; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2003-09-01       Impact factor: 6.986

3.  DBParser: web-based software for shotgun proteomic data analyses.

Authors:  Xiaoyu Yang; Vijay Dondeti; Rebecca Dezube; Dawn M Maynard; Lewis Y Geer; Jonathan Epstein; Xiongfong Chen; Sanford P Markey; Jeffrey A Kowalak
Journal:  J Proteome Res       Date:  2004 Sep-Oct       Impact factor: 4.466

4.  Interpretation of shotgun proteomic data: the protein inference problem.

Authors:  Alexey I Nesvizhskii; Ruedi Aebersold
Journal:  Mol Cell Proteomics       Date:  2005-07-11       Impact factor: 5.911

5.  MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results.

Authors:  Kenny Helsens; Lennart Martens; Joël Vandekerckhove; Kris Gevaert
Journal:  Proteomics       Date:  2007-02       Impact factor: 3.984

6.  DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics.

Authors:  David L Tabb; W Hayes McDonald; John R Yates
Journal:  J Proteome Res       Date:  2002 Jan-Feb       Impact factor: 4.466

7.  Proteomic parsimony through bipartite graph analysis improves accuracy and transparency.

Authors:  Bing Zhang; Matthew C Chambers; David L Tabb
Journal:  J Proteome Res       Date:  2007-08-04       Impact factor: 4.466

8.  BioJava: an open-source framework for bioinformatics.

Authors:  R C G Holland; T A Down; M Pocock; A Prlić; D Huen; K James; S Foisy; A Dräger; A Yates; M Heuer; M J Schreiber
Journal:  Bioinformatics       Date:  2008-08-08       Impact factor: 6.937
  8 in total
  24 in total

1.  The effects of chronic treatment with mood stabilizers on the rat hippocampal post-synaptic density proteome.

Authors:  Dhaval Nanavati; Daniel R Austin; Lisa A Catapano; David A Luckenbaugh; Ayse Dosemeci; Husseini K Manji; Guang Chen; Sanford P Markey
Journal:  J Neurochem       Date:  2011-09-21       Impact factor: 5.372

2.  Hierarchical clustering of shotgun proteomics data.

Authors:  Ville R Koskinen; Patrick A Emery; David M Creasy; John S Cottrell
Journal:  Mol Cell Proteomics       Date:  2011-03-29       Impact factor: 5.911

3.  RNA binding targets aminoacyl-tRNA synthetases to translating ribosomes.

Authors:  Alexandre David; Nir Netzer; Michael Brad Strader; Suman R Das; Cai Yun Chen; James Gibbs; Philippe Pierre; Jack R Bennink; Jonathan W Yewdell
Journal:  J Biol Chem       Date:  2011-04-01       Impact factor: 5.157

4.  Visualize: a free and open source multifunction tool for proteomics data analysis.

Authors:  Brian D Halligan; Andrew S Greene
Journal:  Proteomics       Date:  2011-02-07       Impact factor: 3.984

5.  Proteomic analysis of the Burkholderia pseudomallei type II secretome reveals hydrolytic enzymes, novel proteins, and the deubiquitinase TssM.

Authors:  Mary N Burtnick; Paul J Brett; David DeShazer
Journal:  Infect Immun       Date:  2014-05-27       Impact factor: 3.441

Review 6.  A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.

Authors:  Alexey I Nesvizhskii
Journal:  J Proteomics       Date:  2010-09-08       Impact factor: 4.044

7.  Familial secondary erythrocytosis due to increased oxygen affinity is caused by destabilization of the T state of hemoglobin Brigham (α₂β₂(Pro100Leu)).

Authors:  Todd L Mollan; Bindu Abraham; Michael Brad Strader; Yiping Jia; Jay N Lozier; John S Olson; Abdu I Alayash
Journal:  Protein Sci       Date:  2012-08-21       Impact factor: 6.725

8.  A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.

Authors:  Michael Brad Strader; Nina Costantino; Christopher A Elkins; Cai Yun Chen; Isha Patel; Anthony J Makusky; John S Choy; Donald L Court; Sanford P Markey; Jeffrey A Kowalak
Journal:  Mol Cell Proteomics       Date:  2010-12-17       Impact factor: 5.911

9.  Post-translational transformation of methionine to aspartate is catalyzed by heme iron and driven by peroxide: a novel subunit-specific mechanism in hemoglobin.

Authors:  Michael Brad Strader; Wayne A Hicks; Tigist Kassa; Eileen Singleton; Jayashree Soman; John S Olson; Mitchell J Weiss; Todd L Mollan; Michael T Wilson; Abdu I Alayash
Journal:  J Biol Chem       Date:  2014-06-17       Impact factor: 5.157

10.  Accumulation of non-outer segment proteins in the outer segment underlies photoreceptor degeneration in Bardet-Biedl syndrome.

Authors:  Poppy Datta; Chantal Allamargot; Joseph S Hudson; Emily K Andersen; Sajag Bhattarai; Arlene V Drack; Val C Sheffield; Seongjin Seo
Journal:  Proc Natl Acad Sci U S A       Date:  2015-07-27       Impact factor: 11.205
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