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Forum: MassChroQ: new release version 1.2

Posted by: Edlira Nano
Date: 2012-02-16 16:42
Summary: MassChroQ: new release version 1.2
Project: MassChroQ


Version 1.2 of MassChroQ, called \"Longteeth Crocklet\" is now released. What is new in this version?

  • The peak post-matching feature: before version 1.2 peak matching in MassChroQ was performed peak by peak during quantification. The peak matching mode adds a new peak matching step at the end of the quantification of each group of MS runs: for each peptide to be quantified, its previously unmatched peaks are rematched by taking into account the retention times of the previously matched peaks for this peptide in the group. This gives more accurate retention times allowing the matching of some previously missed peaks. The peak post-matching mode is recommended only in high resolution experiments. See the manual for more details.
  • The comparison result file: the tsv result files produced by MassChroQ are well suited for automatic statistical analysis in external tools, like the R software. But they are not well suited for simple manual or visual overview or comparison purposes. Therefore, in version 1.2, we have added a new type of tsv result file, the comparison result file, which is well suited for immediate visual comparison of results and simple manual statistical analysis on them. The comparison type of file is automatically generated with the other old tsv result files.
  • The masschroqML schema has changed, the current schema version being 1.2 (the same version number as MassChroQ). Older masschroqML files stay functional with the new schema, but new masschroqML files (containing the post matching feature for example) will not work with older schema and MassChroQ versions. This new schema is automatically installed with this new version.

The new release version can be downloaded from the MassChroQ download page at

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