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

B. van Breukelen; H.W.P. van den Toorn; M.M. Drugan; A.J.R. Heck

doi:10.1093/bioinformatics/btp181

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

B. van Breukelen, H.W.P. van den Toorn, M.M. Drugan, A.J.R. Heck

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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).

Original language	English
Pages (from-to)	1472-3
Number of pages	2
Journal	Bioinformatics
Volume	25
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btp181
Publication status	Published - 1 Jun 2009

Keywords

Databases, Protein
Mass Spectrometry
Proteins
Proteomics
Software

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10.1093/bioinformatics/btp181

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title = "StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry",

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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author = "{van Breukelen}, B. and {van den Toorn}, H.W.P. and M.M. Drugan and A.J.R. Heck",

year = "2009",

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doi = "10.1093/bioinformatics/btp181",

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T2 - a post-quantification analysis toolbox for improving quantitative mass spectrometry

AU - van Breukelen, B.

AU - van den Toorn, H.W.P.

AU - Drugan, M.M.

AU - Heck, A.J.R.

PY - 2009/6/1

Y1 - 2009/6/1

N2 - 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).

AB - 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).

KW - Databases, Protein

KW - Mass Spectrometry

KW - Proteins

KW - Proteomics

KW - Software

U2 - 10.1093/bioinformatics/btp181

DO - 10.1093/bioinformatics/btp181

M3 - Article

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JO - Bioinformatics

JF - Bioinformatics

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ER -

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

Abstract

Keywords

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