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

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

DOI

  • Anders Dahl Knudsen, Danmark
  • Tue Bennike, Aalborg Universitet, Danmark
  • Henrik Kjeldal, Aalborg Universitet, Danmark
  • Svend Birkelund, Aalborg Universitet, Danmark
  • Daniel Otzen
  • Allan Stensballe, Aalborg Universitet
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/
OriginalsprogEngelsk
TidsskriftJournal of Proteomics
Vol/bind103
Sider (fra-til)261-266
Antal sider6
ISSN1874-3919
DOI
StatusUdgivet - 30 maj 2014

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