Condenser: A statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller™

Anders Dahl Knudsen; Tue Bennike; Henrik Kjeldal; Svend Birkelund; Daniel Otzen; Allan Stensballe

doi:10.1016/j.jprot.2014.02.001

Condenser: A statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller™

Anders Dahl Knudsen, Tue Bennike, Henrik Kjeldal, Svend Birkelund, Daniel Otzen, Allan Stensballe

Interdisciplinary Nanoscience Center - INANO-MBG, iNANO-huset

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

6 Citations (Scopus)

Abstract

We describe Condenser, a freely available, comprehensive open-source tool for merging multidimensional quantitative proteomics data from the Matrix Science Mascot Distiller Quantitation Toolbox into a common format ready for subsequent bioinformatic analysis. A number of different relative quantitation technologies, such as metabolic (15)N and amino acid stable isotope incorporation, label-free and chemical-label quantitation are supported. The program features multiple options for curative filtering of the quantified peptides, allowing the user to choose data quality thresholds appropriate for the current dataset, and ensure the quality of the calculated relative protein abundances. Condenser also features optional global normalization, peptide outlier removal, multiple testing and calculation of t-test statistics for highlighting and evaluating proteins with significantly altered relative protein abundances. Condenser provides an attractive addition to the gold-standard quantitative workflow of Mascot Distiller, allowing easy handling of larger multi-dimensional experiments. Source code, binaries, test data set and documentation are available at http://condenser.googlecode.com/

Original language	English
Journal	Journal of Proteomics
Volume	103
Pages (from-to)	261-266
Number of pages	6
ISSN	1874-3919
DOIs	https://doi.org/10.1016/j.jprot.2014.02.001
Publication status	Published - 30 May 2014

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@article{e2641f3aa7344bad8d5a7000490e070f,

title = "Condenser: A statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller{\texttrademark}",

abstract = "We describe Condenser, a freely available, comprehensive open-source tool for merging multidimensional quantitative proteomics data from the Matrix Science Mascot Distiller Quantitation Toolbox into a common format ready for subsequent bioinformatic analysis. A number of different relative quantitation technologies, such as metabolic (15)N and amino acid stable isotope incorporation, label-free and chemical-label quantitation are supported. The program features multiple options for curative filtering of the quantified peptides, allowing the user to choose data quality thresholds appropriate for the current dataset, and ensure the quality of the calculated relative protein abundances. Condenser also features optional global normalization, peptide outlier removal, multiple testing and calculation of t-test statistics for highlighting and evaluating proteins with significantly altered relative protein abundances. Condenser provides an attractive addition to the gold-standard quantitative workflow of Mascot Distiller, allowing easy handling of larger multi-dimensional experiments. Source code, binaries, test data set and documentation are available at http://condenser.googlecode.com/",

author = "Knudsen, {Anders Dahl} and Tue Bennike and Henrik Kjeldal and Svend Birkelund and Daniel Otzen and Allan Stensballe",

year = "2014",

month = may,

day = "30",

doi = "10.1016/j.jprot.2014.02.001",

language = "English",

volume = "103",

pages = "261--266",

journal = "Journal of Proteomics",

issn = "1874-3919",

publisher = "Elsevier B.V.",

}

Condenser: A statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller™. / Knudsen, Anders Dahl; Bennike, Tue; Kjeldal, Henrik et al.
In: Journal of Proteomics, Vol. 103, 30.05.2014, p. 261-266.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - Condenser

T2 - A statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller™

AU - Knudsen, Anders Dahl

AU - Bennike, Tue

AU - Kjeldal, Henrik

AU - Birkelund, Svend

AU - Otzen, Daniel

AU - Stensballe, Allan

PY - 2014/5/30

Y1 - 2014/5/30

N2 - We describe Condenser, a freely available, comprehensive open-source tool for merging multidimensional quantitative proteomics data from the Matrix Science Mascot Distiller Quantitation Toolbox into a common format ready for subsequent bioinformatic analysis. A number of different relative quantitation technologies, such as metabolic (15)N and amino acid stable isotope incorporation, label-free and chemical-label quantitation are supported. The program features multiple options for curative filtering of the quantified peptides, allowing the user to choose data quality thresholds appropriate for the current dataset, and ensure the quality of the calculated relative protein abundances. Condenser also features optional global normalization, peptide outlier removal, multiple testing and calculation of t-test statistics for highlighting and evaluating proteins with significantly altered relative protein abundances. Condenser provides an attractive addition to the gold-standard quantitative workflow of Mascot Distiller, allowing easy handling of larger multi-dimensional experiments. Source code, binaries, test data set and documentation are available at http://condenser.googlecode.com/

AB - We describe Condenser, a freely available, comprehensive open-source tool for merging multidimensional quantitative proteomics data from the Matrix Science Mascot Distiller Quantitation Toolbox into a common format ready for subsequent bioinformatic analysis. A number of different relative quantitation technologies, such as metabolic (15)N and amino acid stable isotope incorporation, label-free and chemical-label quantitation are supported. The program features multiple options for curative filtering of the quantified peptides, allowing the user to choose data quality thresholds appropriate for the current dataset, and ensure the quality of the calculated relative protein abundances. Condenser also features optional global normalization, peptide outlier removal, multiple testing and calculation of t-test statistics for highlighting and evaluating proteins with significantly altered relative protein abundances. Condenser provides an attractive addition to the gold-standard quantitative workflow of Mascot Distiller, allowing easy handling of larger multi-dimensional experiments. Source code, binaries, test data set and documentation are available at http://condenser.googlecode.com/

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DO - 10.1016/j.jprot.2014.02.001

M3 - Journal article

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SN - 1874-3919

VL - 103

SP - 261

EP - 266

JO - Journal of Proteomics

JF - Journal of Proteomics

ER -

Condenser: A statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller™

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