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Quantitation of MALDI peptides


MALDIPepQuant is a tool to quantify MALDI peptides (SILAC) from Phenyx output.

This tool has been developed as a service of the Bioinformatics Core Facility for Proteomics, within a collaboration between the Proteome Informatics Group from the Swiss Institute of Bioinformatics (SIB) and the Biomedical Proteomics Research Group (BPRG).

MALDIPepQuant v3.1 is written in Java 1.5, using the Java Swing technology for its Graphical User Interface.

Reference to the publication :
Coute Y., Hernandez C., Appel R. D., Sanchez J.-C., Margolles A. 2007. Labeling of Bifidobacterium longum Cells with 13C-Substituted Leucine for Quantitative Proteomic Analyses. Appl. Environ. Microbiol. 2007 Sep;73(17):5653-6. Epub 2007 Jun 29
PubMed Id : 17601805.
PDF version of the full text is available on the Applied And Environmental Microbiology web site.

Screenshot of MALDIPepQuant

Test it online

The Java Web Start technology can be used to run MALDIPepQuant directly from the Expasy website.
Be sure to have at least version 1.5 of Java Runtime Environment (JRE) installed on your computer. Otherwise, you can download the latest version from the Sun website.
It has been fully tested on Windows 2000/XP (Firefox 2.0, IE 6.0), Linux (Firefox 2.0), Mac OS X (Safari 3.0). Do not hesitate to contact us with your configuration (OS & browser name and version) if you encountered some troubles.

In order to test MALDIPepQuant, you can use one of the following test sets:

  • Test set 1 : labeled 13C-Leu (aminoacid:L, shift:6Da) with intermediary peaks; data acquired on MALDI-TOF/TOF 4700 from Applied Biosystems
  • Test set 2 : labeled 13C-Leu (aminoacid:L, shift:6Da) and 13C6/15N2-Lys (aminoacid:K, shift:8Da), without intermediary peaks ; data acquired on MALDI-TOF/TOF 4800 from Applied Biosystems
Download one of the test sets and extract it. After extraction, you can use the files as parameters for MALDIPepQuant as specified in the help page.

Run MALDIPepQuant with Java Web Start


Download the source code

By following this link you may download the complete source code of MALDIPepQuant, including Java source code, libraries, and build file.
This distribution also contains the help page of MALDIPepQuant.

Download	MALDIPepQuant