1. The MassChroQ user manual contains information about installing and using MassChroQ, together with a detailed explanation of the algorithms it uses [pdf]
2. An FAQ is available here.
3. The manpage.
4. The latest masschroqML (MassChroQ's input/output XML file format) version 2.2 schema is available here.
To get the latest news about MassChroQ, but also to ask question and get help about it, subscribe to the pappso-tools mailing list.

Academic Publications

1. MassChroQ: A versatile tool for mass spectrometry quantification, B. Valot, O. Langella, E. Nano, M. Zivy. Proteomics, 2011, 11:3572–3577. [pdf] [bib]
The data analyzed in this paper are available in this archive.

Conference talks and posters

1. MassChroQ : logiciel de quantification par spectrométrie de masse, slides of a talk given at Rencontres bioinformaticiens et statisticiens de l'INRA in march 2011. [pdf in french]
2. MassChroQ: a complete tool for mass spectrometry-based proteomic quantification, a poster presented at the Final COST Meeting(EUPP) 2011 and at the SMAP 2011 congress. [pdf]