Literature DB >> 19336442

StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry.

Bas van Breukelen1, Henk W P van den Toorn, Madalina M Drugan, Albert J R Heck.   

Abstract

MOTIVATION: Mass spectrometric protein quantitation has emerged as a high-throughput tool to yield large amounts of data on peptide and protein abundances. Currently, differential abundance data can be calculated from peptide intensity ratios by several automated quantitation software packages available. There is, however, still a great need for additional processing to validate and refine the quantitation results. Here, we present a software tool, termed StatQuant, that offers a set of statistical tools to process, filter, compare and represent data from several quantitative proteomics software packages such as MSQuant. StatQuant offers the researcher post-processing methods to achieve improved confidence on the obtained protein ratios. AVAILABILITY: StatQuant can be downloaded from: (https://gforge.nbic.nl/projects/statquant/) (binary and source code).

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Year:  2009        PMID： 19336442     DOI： 10.1093/bioinformatics/btp181

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  16 in total

1.  Identification of nuclear phosphatidylinositol 4,5-bisphosphate-interacting proteins by neomycin extraction.

Authors:  Aurélia E Lewis; Lilly Sommer; Magnus Ø Arntzen; Yvan Strahm; Nicholas A Morrice; Nullin Divecha; Clive S D'Santos
Journal:  Mol Cell Proteomics       Date:  2010-11-03       Impact factor: 5.911

2.  Metabolic labeling and membrane fractionation for comparative proteomic analysis of Arabidopsis thaliana suspension cell cultures.

Authors:  Witold G Szymanski; Sylwia Kierszniowska; Waltraud X Schulze
Journal:  J Vis Exp       Date:  2013-09-28       Impact factor: 1.355

3.  In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling.

Authors:  Paul J Boersema; Leong Yan Foong; Vanessa M Y Ding; Simone Lemeer; Bas van Breukelen; Robin Philp; Jos Boekhorst; Berend Snel; Jeroen den Hertog; Andre B H Choo; Albert J R Heck
Journal:  Mol Cell Proteomics       Date:  2009-09-21       Impact factor: 5.911

4.  GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

Authors:  Kristoffer T G Rigbolt; Jens T Vanselow; Blagoy Blagoev
Journal:  Mol Cell Proteomics       Date:  2011-05-20       Impact factor: 5.911

5.  Quantitative N-linked glycoproteomics of myocardial ischemia and reperfusion injury reveals early remodeling in the extracellular environment.

Authors:  Benjamin L Parker; Giuseppe Palmisano; Alistair V G Edwards; Melanie Y White; Kasper Engholm-Keller; Albert Lee; Nichollas E Scott; Daniel Kolarich; Brett D Hambly; Nicolle H Packer; Martin R Larsen; Stuart J Cordwell
Journal:  Mol Cell Proteomics       Date:  2011-03-25       Impact factor: 5.911

6.  Quantitative phosphoproteomics after auxin-stimulated lateral root induction identifies an SNX1 protein phosphorylation site required for growth.

Authors:  Hongtao Zhang; Houjiang Zhou; Lidija Berke; Albert J R Heck; Shabaz Mohammed; Ben Scheres; Frank L H Menke
Journal:  Mol Cell Proteomics       Date:  2013-01-17       Impact factor: 5.911

7.  Protein-protein interaction network of the marine microalga Tetraselmis subcordiformis: prediction and application for starch metabolism analysis.

Authors:  Chaofan Ji; Xupeng Cao; Changhong Yao; Song Xue; Zhilong Xiu
Journal:  J Ind Microbiol Biotechnol       Date:  2014-05-31       Impact factor: 3.346

8.  The ROK family regulator Rok7B7 pleiotropically affects xylose utilization, carbon catabolite repression, and antibiotic production in streptomyces coelicolor.

Authors:  Magdalena A Świątek; Jacob Gubbens; Giselda Bucca; Eunjung Song; Yung-Hun Yang; Emma Laing; Byung-Gee Kim; Colin P Smith; Gilles P van Wezel
Journal:  J Bacteriol       Date:  2013-01-04       Impact factor: 3.490

9.  ProteoSign v2: a faster and evolved user-friendly online tool for statistical analyses of differential proteomics.

Authors:  Evangelos Theodorakis; Andreas N Antonakis; Ismini Baltsavia; Georgios A Pavlopoulos; Martina Samiotaki; Grigoris D Amoutzias; Theodosios Theodosiou; Oreste Acuto; Georgios Efstathiou; Ioannis Iliopoulos
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

Review 10.  Current challenges in software solutions for mass spectrometry-based quantitative proteomics.

Authors:  Salvatore Cappadona; Peter R Baker; Pedro R Cutillas; Albert J R Heck; Bas van Breukelen
Journal:  Amino Acids       Date:  2012-07-22       Impact factor: 3.520
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