Literature DB >> 18345006

A quantitative analysis software tool for mass spectrometry-based proteomics.

Sung Kyu Park1, John D Venable, Tao Xu, John R Yates.   

Abstract

We describe Census, a quantitative software tool compatible with many labeling strategies as well as with label-free analyses, single-stage mass spectrometry (MS1) and tandem mass spectrometry (MS/MS) scans, and high- and low-resolution mass spectrometry data. Census uses robust algorithms to address poor-quality measurements and improve quantitative efficiency, and it can support several input file formats. We tested Census with stable-isotope labeling analyses as well as label-free analyses.

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Year:  2008        PMID： 18345006      PMCID： PMC3509211          DOI： 10.1038/nmeth.1195

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  14 in total

1.  GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model.

Authors:  David L Tabb; Anita Saraf; John R Yates
Journal:  Anal Chem       Date:  2003-12-01       Impact factor: 6.986

2.  A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases.

Authors:  Rovshan G Sadygov; John R Yates
Journal:  Anal Chem       Date:  2003-08-01       Impact factor: 6.986

3.  Selective detection of membrane proteins without antibodies: a mass spectrometric version of the Western blot.

Authors:  David Arnott; Adrianne Kishiyama; Elizabeth A Luis; Sarah G Ludlum; James C Marsters; John T Stults
Journal:  Mol Cell Proteomics       Date:  2002-02       Impact factor: 5.911

4.  A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.

Authors:  Michael J MacCoss; Christine C Wu; Hongbin Liu; Rovshan Sadygov; John R Yates
Journal:  Anal Chem       Date:  2003-12-15       Impact factor: 6.986

5.  Open mass spectrometry search algorithm.

Authors:  Lewis Y Geer; Sanford P Markey; Jeffrey A Kowalak; Lukas Wagner; Ming Xu; Dawn M Maynard; Xiaoyu Yang; Wenyao Shi; Stephen H Bryant
Journal:  J Proteome Res       Date:  2004 Sep-Oct       Impact factor: 4.466

6.  Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap.

Authors:  Jesper V Olsen; Lyris M F de Godoy; Guoqing Li; Boris Macek; Peter Mortensen; Reinhold Pesch; Alexander Makarov; Oliver Lange; Stevan Horning; Matthias Mann
Journal:  Mol Cell Proteomics       Date:  2005-10-24       Impact factor: 5.911

7.  Performance of a linear ion trap-Orbitrap hybrid for peptide analysis.

Authors:  John R Yates; Daniel Cociorva; Lujian Liao; Vlad Zabrouskov
Journal:  Anal Chem       Date:  2006-01-15       Impact factor: 6.986

8.  Characterization of mouse spleen cells by subtractive proteomics.

Authors:  Francisco J Dieguez-Acuna; Scott A Gerber; Shohta Kodama; Joshua E Elias; Sean A Beausoleil; Denise Faustman; Steven P Gygi
Journal:  Mol Cell Proteomics       Date:  2005-07-21       Impact factor: 5.911

9.  Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors.

Authors:  Leonard J Foster; Carmen L De Hoog; Matthias Mann
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-30       Impact factor: 11.205

10.  A proteomic strategy for gaining insights into protein sumoylation in yeast.

Authors:  Carilee Denison; Adam D Rudner; Scott A Gerber; Corey E Bakalarski; Danesh Moazed; Steven P Gygi
Journal:  Mol Cell Proteomics       Date:  2004-11-12       Impact factor: 5.911
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  170 in total

1.  15N-labeled brain enables quantification of proteome and phosphoproteome in cultured primary neurons.

Authors:  Lujian Liao; Richard C Sando; John B Farnum; Peter W Vanderklish; Anton Maximov; John R Yates
Journal:  J Proteome Res       Date:  2011-12-02       Impact factor: 4.466

2.  Toward objective evaluation of proteomic algorithms.

Authors:  John R Yates; Sung Kyu Robin Park; Claire M Delahunty; Tao Xu; Jeffrey N Savas; Daniel Cociorva; Paulo Costa Carvalho
Journal:  Nat Methods       Date:  2012-04-27       Impact factor: 28.547

3.  Protein turnover quantification in a multilabeling approach: from data calculation to evaluation.

Authors:  Christian Trötschel; Stefan P Albaum; Daniel Wolff; Simon Schröder; Alexander Goesmann; Tim W Nattkemper; Ansgar Poetsch
Journal:  Mol Cell Proteomics       Date:  2012-04-06       Impact factor: 5.911

4.  Label-free quantification and shotgun analysis of complex proteomes by one-dimensional SDS-PAGE/NanoLC-MS: evaluation for the large scale analysis of inflammatory human endothelial cells.

Authors:  Violette Gautier; Emmanuelle Mouton-Barbosa; David Bouyssié; Nicolas Delcourt; Mathilde Beau; Jean-Philippe Girard; Corinne Cayrol; Odile Burlet-Schiltz; Bernard Monsarrat; Anne Gonzalez de Peredo
Journal:  Mol Cell Proteomics       Date:  2012-04-19       Impact factor: 5.911

5.  A posttranslational modification code for CFTR maturation is altered in cystic fibrosis.

Authors:  Sandra Pankow; Casimir Bamberger; John R Yates
Journal:  Sci Signal       Date:  2019-01-01       Impact factor: 8.192

6.  SILAC peptide ratio calculator: a tool for SILAC quantitation of peptides and post-translational modifications.

Authors:  Xiaoyan Guan; Neha Rastogi; Mark R Parthun; Michael A Freitas
Journal:  J Proteome Res       Date:  2014-01-09       Impact factor: 4.466

7.  ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies.

Authors:  Jing Tang; Jianbo Fu; Yunxia Wang; Bo Li; Yinghong Li; Qingxia Yang; Xuejiao Cui; Jiajun Hong; Xiaofeng Li; Yuzong Chen; Weiwei Xue; Feng Zhu
Journal:  Brief Bioinform       Date:  2020-03-23       Impact factor: 11.622

8.  Phosphoproteomic Analyses Reveal Early Signaling Events in the Osmotic Stress Response.

Authors:  Kelly E Stecker; Benjamin B Minkoff; Michael R Sussman
Journal:  Plant Physiol       Date:  2014-05-07       Impact factor: 8.340

9.  Quantitative proteomic study of arsenic treated mouse liver sinusoidal endothelial cells using a reverse super-SILAC method.

Authors:  Wenbo Li; Jiyang Zhang; Yongzhuang Lv; Nader Sheibani
Journal:  Biochem Biophys Res Commun       Date:  2019-05-02       Impact factor: 3.575

10.  Tracking brain palmitoylation change: predominance of glial change in a mouse model of Huntington's disease.

Authors:  Junmei Wan; Jeffrey N Savas; Amy F Roth; Shaun S Sanders; Roshni R Singaraja; Michael R Hayden; John R Yates; Nicholas G Davis
Journal:  Chem Biol       Date:  2013-11-07
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