I've been using MSClustering (http://proteomics.ucsd.edu/Software/MSClustering.html) to cluster some MS/MS data. MSclustering can produce mgf files of the consensus spectra of these clusters. Now I want to use these consesus spectra to search MaxQuant. However, MaxQuant only accepts .raw and .mzXML files. I want to use MaxQuant because for the not-clustered files MaxQuant has also been used. I tried using MSConvert from Proteowizard to convert the data, and although this produces some results, MaxQuant does not recognize it. Opening the file with XCalibur's Qual Browser says that the files are corrupted (so the files aren't converted correctly)
Is it possible to convert .mgf files to a format so that MaxQuant can be used to search for peptide identities?