Our Download page explains how to install and run MassChroQ on your platform. What kind of isotopic labellings are handled in MassChroQ?

The quantification process in MassChroQ is based on MS level one continued data, thus only isotopic labeling techniques that can be analysed in MS level one are handled (for example Nter, Cter, SILAC, ICAT, …). This means that the ITRAQ isotopic labeling types (based on MS level 2) are not handled in MassChroQ. What isotopic labellings are not handled in MassChroQ?

ITRAQ isotopic labeling types, based on MS level 2 information, are not handled in MassChroQ. What LC-MS/MS data file formats does MassChroQ accept?

MassChroQ accepts mzXML and mzML data file formats. Due to the complicated and yet not secured nature of the mzML format, we strongly recommend you the use of the mzXML format, which is simple, secure and complete. Does MassChroQ perform protein identification?

No, MassChroQ is not an identification software. You have to perform identification before quantifying your identified peptides with MassChroQ. There are two possibilities for making MassChroQ automatically take into account the identification information of your data:

  • If you use the X!Tandem software as we do, things are quite easy: you can freely install our X!Tandempipeline which performs identification using X!Tandem, filtering and validation, and also offers a direct export of the results into a complete, ready-to-use, masschroqML input file to MassChroQ.
  • If you are using another identification engine (like Mascot, or other), you will have to export your results into spreadsheet files, then rearrange the columns in these files in the MassChroQ order. MassChroQ will automatically parse these files and extract the information they contain during quantification. For precise information on how to do this, see the dedicated chapter of the MassChroQ manual available on our Documentation page.