Forum: MassChroQ now accepts mzML input files
Until now MassChroQ only worked with mzXML input data. But recently we have implemented the mzML input data format too. So, MassChroQ is now able to work with mzXML and mzML data. You can even combine them, quantify some samples in mzXML and others in mzML format.
Our mzML implementation has been so far tested successfully with several mzML files obtained using the msconvert tool. But given the heterogeneity of the mzML files we have seen, we strongly recommend the use of the mzXML data format. However, do not hesitate to report to us possible problems you encounter with the mzML parsing in MassChroQ.