title: Condenser: a statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller™.
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/.
authors: Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.
authors: Anders Dahl
authors: AD
authors: Knudsen
authors: Department of Biotechnology and Chemistry, Aalborg University, Denmark; Department of Health Science and Technology, Aalborg University, Denmark.
authors: Tue
authors: T
authors: Bennike
authors: Department of Biotechnology and Chemistry, Aalborg University, Denmark.
authors: Henrik
authors: H
authors: Kjeldal
authors: Department of Health Science and Technology, Aalborg University, Denmark.
authors: Svend
authors: S
authors: Birkelund
authors: Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.
authors: Daniel Erik
authors: DE
authors: Otzen
authors: Department of Health Science and Technology, Aalborg University, Denmark. Electronic address: as@hst.aau.dk.
authors: Allan
authors: A
authors: Stensballe
mesh_terms: D030562:Databases, Protein; D010455:Peptides / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D010455:Peptides
keywords: Mascot Distiller; Proteomics; Quantitation; SQL; Statistics