• It is much faster. It takes no more than 3 minutes to fully analyse 1Go of profile mzXML data and only a few seconds for 1Go of centroid ones.
• It is much lighter. At most 400 Mo of RAM (Random Access Memory) are used by MassChroQ. In comparison, in previous versions the RAM usage size was equivalent to the size of the MS-run being analysed, which could be up to 1.5 Go. As a consequence, your personal computer stays fully functional during MassChroQ analysis.
• It uses much less disk space. The maximum disk space used by MassChroQ is equal to the size of the biggest MS-run of your analysis. This version needs to duplicate on disk only the MS-run being analysed, this disk space being automatically freed when the analysis of the MS-run is finished. In comparison, previous versions needed a disk space size equal to the sum of all the MS-runs being analysed.

• The peak post-matching feature : before version 1.2 peak matching in MassChroQ was performed peak by peak during quantification, by matching peptide retention times (MS/MS level retention times) to the peak's retention time interval (MS level retention time). However, a flaw in this method is that sometimes the peptide retention times (MS/MS) are not necessarily close to the peak's retention time interval (MS). This can cause match failure of relevant peaks. The peak post-matching mode adds a second peak matching pass at the end of the quantification of each group of MS-runs. This second peak matching pass is based on the retention times (MS level) of the corresponding peaks matched during the first pass. This allows the matching of some previously unmatched peptides. The peak post-matching mode is recommended only in high resolution experiments, as it can lead to mismatched background noise peaks in low resolution ones. 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.

• Support for new identification results: Mascot result (.dat format). This compatibility uses mascotdatfile library . Processing, filtering and visualization of Mascot results are similar to XTandem ones, except for the information that need protein sequences like PAI, coverage, ...
• Correction and improvement of FDR calculation using reverse option of X!Tandem, or decoy option of Mascot.

Version 3.3.0 of X!TandemPipeline, called "Myosine Rachitique" is now released. This version correct problems of grouping on very large dataset and enhanced the quickness of this steps.

If you have very large dataset, we recommend to reload xtandem results to gain benefit of this patch.

This new release will be automatically updated, but it can also be retrieved at this address .

• MassChroQ Studio

This is the main novelty in MassChroQ. MassChroQ Studio is a graphical, user friendly tool, allowing to load runs or masschroqML files and to perform XIC extraction, filtering, detection and alignment on them. The results of these operations can be instantly visualized on graphical plots. The goal of the Studio is to help the user find the masschroqML parameters that best fit his data and experiment. The final parameters can be exported into masschroqML format, the user has only to integrate them in his masschroqML file.

• MassChroQ Graphical User Interface (GUI)

Another novelty in MassChroQ is the MassChroQ GUI , a simple graphical interface that allows the user to launch masschroq graphically, without having to do strange things on the command-line. A graphical console allows to see the runtime messages of MassChroQ.

• The .time and .trace alignment files

In the masschroq core module, we have added the possibility for the user to decide whether he wants to load previous .time files or not, and if yes to directly indicate the directory where to find these files. This way, one can use previous alignment results without having to repeat the alignment. In the same way, the user has to indicate in the alignment methods the directory on disk where to put the .time and .trace alignment files if he wants them. If no directory is specified, these files will not be written to disk by default. In previous versions of MassChroQ the .time files were always loaded from the current directory if any, and they were always written to disk in the current directory. This implicit behavior could easily induce errors. Indeed, the user had to be careful and to remember to delete the .time files that he did not wanted to be loaded. He does not have to delete anything now.

As a consequence, the masschroqML schema has changed in MassChroQ, the current schema version being 2.0 (the same version number as MassChroQ). Older masschroqML files stay functional with the new schema, but new masschroqML files containing the .time directories attributes, will not work with older schema versions.

• MassChroQ Studio

MassChroQ Studio now takes into account peptide isotopes from the MassChroqML file

• several bug fixed
• XML generation of the spike filter in MassChroQ studio fixed
• MS2 alignement don't crash when there is no common peptides between two runs