Literature DB >> 25574629

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

Marc Vaudel1, Julia M Burkhart2, René P Zahedi2, Eystein Oveland3, Frode S Berven4, Albert Sickmann2, Lennart Martens5, Harald Barsnes6.   

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Year:  2015        PMID： 25574629     DOI： 10.1038/nbt.3109

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  19 in total

Review 1.  Combining results of multiple search engines in proteomics.

Authors:  David Shteynberg; Alexey I Nesvizhskii; Robert L Moritz; Eric W Deutsch
Journal:  Mol Cell Proteomics       Date:  2013-05-29       Impact factor: 5.911

2.  In need of an upgrade.

Authors: 
Journal:  Nat Biotechnol       Date:  2013-10       Impact factor: 54.908

3.  SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

Authors:  Marc Vaudel; Harald Barsnes; Frode S Berven; Albert Sickmann; Lennart Martens
Journal:  Proteomics       Date:  2011-01-31       Impact factor: 3.984

4.  A global analysis of peptide fragmentation variability.

Authors:  Harald Barsnes; Ingvar Eidhammer; Lennart Martens
Journal:  Proteomics       Date:  2011-02-16       Impact factor: 3.984

Review 5.  PROTEINCHALLENGE: crowd sourcing in proteomics analysis and software development.

Authors:  Sarah F Martin; Heiner Falkenberg; Thomas F Dyrlund; Guennadi A Khoudoli; Craig J Mageean; Rune Linding
Journal:  J Proteomics       Date:  2012-12-07       Impact factor: 4.044

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.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors:  Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal:  Genome Biol       Date:  2010-08-25       Impact factor: 13.583

8.  The mzIdentML data standard for mass spectrometry-based proteomics results.

Authors:  Andrew R Jones; Martin Eisenacher; Gerhard Mayer; Oliver Kohlbacher; Jennifer Siepen; Simon J Hubbard; Julian N Selley; Brian C Searle; James Shofstahl; Sean L Seymour; Randall Julian; Pierre-Alain Binz; Eric W Deutsch; Henning Hermjakob; Florian Reisinger; Johannes Griss; Juan Antonio Vizcaíno; Matthew Chambers; Angel Pizarro; David Creasy
Journal:  Mol Cell Proteomics       Date:  2012-02-27       Impact factor: 5.911

9.  Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites.

Authors:  Ivan Matic; Ivan Ahel; Ronald T Hay
Journal:  Nat Methods       Date:  2012-07-30       Impact factor: 28.547

10.  The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.

Authors:  Richard G Côté; Johannes Griss; José A Dianes; Rui Wang; James C Wright; Henk W P van den Toorn; Bas van Breukelen; Albert J R Heck; Niels Hulstaert; Lennart Martens; Florian Reisinger; Attila Csordas; David Ovelleiro; Yasset Perez-Rivevol; Harald Barsnes; Henning Hermjakob; Juan Antonio Vizcaíno
Journal:  Mol Cell Proteomics       Date:  2012-09-04       Impact factor: 5.911
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  176 in total

1.  Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry.

Authors:  Barry M Zee; Artyom A Alekseyenko; Kyle A McElroy; Mitzi I Kuroda
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-01       Impact factor: 11.205

2.  Supramolecular Polymeric Assemblies for the Selective Depletion of Abundant Acidic Proteins in Serum.

Authors:  Mahalia A C Serrano; Jingjing Gao; Katrina A Kelly; S Thayumanavan; Richard W Vachet
Journal:  ACS Appl Mater Interfaces       Date:  2018-11-15       Impact factor: 9.229

3.  Tracking Effects of SIL1 Increase: Taking a Closer Look Beyond the Consequences of Elevated Expression Level.

Authors:  Thomas Labisch; Stephan Buchkremer; Vietxuan Phan; Laxmikanth Kollipara; Christian Gatz; Chris Lentz; Kay Nolte; Jörg Vervoorts; José Andrés González Coraspe; Albert Sickmann; Stephanie Carr; René P Zahedi; Joachim Weis; Andreas Roos
Journal:  Mol Neurobiol       Date:  2017-04-11       Impact factor: 5.590

4.  Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins.

Authors:  Sondos Samandi; Annie V Roy; Vivian Delcourt; Jean-François Lucier; Jules Gagnon; Maxime C Beaudoin; Benoît Vanderperre; Marc-André Breton; Julie Motard; Jean-François Jacques; Mylène Brunelle; Isabelle Gagnon-Arsenault; Isabelle Fournier; Aida Ouangraoua; Darel J Hunting; Alan A Cohen; Christian R Landry; Michelle S Scott; Xavier Roucou
Journal:  Elife       Date:  2017-10-30       Impact factor: 8.140

5.  Production of Hypoallergenic Antibacterial Peptides from Defatted Soybean Meal in Membrane Bioreactor: A Bioprocess Engineering Study with Comprehensive Product Characterization.

Authors:  Arijit Nath; Gábor Szécsi; Barbara Csehi; Zsuzsa Mednyánszky; Gabriella Kiskó; Éva Bányai; Mihály Dernovics; András Koris
Journal:  Food Technol Biotechnol       Date:  2017-09       Impact factor: 3.918

6.  A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer.

Authors:  Xinxin Peng; Xiaoyan Xu; Yumeng Wang; David H Hawke; Shuangxing Yu; Leng Han; Zhicheng Zhou; Kamalika Mojumdar; Kang Jin Jeong; Marilyne Labrie; Yiu Huen Tsang; Minying Zhang; Yiling Lu; Patrick Hwu; Kenneth L Scott; Han Liang; Gordon B Mills
Journal:  Cancer Cell       Date:  2018-04-26       Impact factor: 31.743

7.  Two functionally distinct NADP+-dependent ferredoxin oxidoreductases maintain the primary redox balance of Pyrococcus furiosus.

Authors:  Diep M N Nguyen; Gerrit J Schut; Oleg A Zadvornyy; Monika Tokmina-Lukaszewska; Saroj Poudel; Gina L Lipscomb; Leslie A Adams; Jessica T Dinsmore; William J Nixon; Eric S Boyd; Brian Bothner; John W Peters; Michael W W Adams
Journal:  J Biol Chem       Date:  2017-07-13       Impact factor: 5.157

8.  The Electron Bifurcating FixABCX Protein Complex from Azotobacter vinelandii: Generation of Low-Potential Reducing Equivalents for Nitrogenase Catalysis.

Authors:  Rhesa N Ledbetter; Amaya M Garcia Costas; Carolyn E Lubner; David W Mulder; Monika Tokmina-Lukaszewska; Jacob H Artz; Angela Patterson; Timothy S Magnuson; Zackary J Jay; H Diessel Duan; Jacquelyn Miller; Mary H Plunkett; John P Hoben; Brett M Barney; Ross P Carlson; Anne-Frances Miller; Brian Bothner; Paul W King; John W Peters; Lance C Seefeldt
Journal:  Biochemistry       Date:  2017-08-03       Impact factor: 3.162

9.  metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes.

Authors:  Caleb W Easterly; Ray Sajulga; Subina Mehta; James Johnson; Praveen Kumar; Shane Hubler; Bart Mesuere; Joel Rudney; Timothy J Griffin; Pratik D Jagtap
Journal:  Mol Cell Proteomics       Date:  2019-06-24       Impact factor: 5.911

Review 10.  Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.

Authors:  Mak A Saito; Erin M Bertrand; Megan E Duffy; David A Gaylord; Noelle A Held; William Judson Hervey; Robert L Hettich; Pratik D Jagtap; Michael G Janech; Danie B Kinkade; Dagmar H Leary; Matthew R McIlvin; Eli K Moore; Robert M Morris; Benjamin A Neely; Brook L Nunn; Jaclyn K Saunders; Adam I Shepherd; Nicholas I Symmonds; David A Walsh
Journal:  J Proteome Res       Date:  2019-03-12       Impact factor: 4.466
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