How To Convert .Mgf (Mascot Generic File) To A Format (Mzxml?) So That They Can Be Used With Maxquant?
Entering edit mode
8.1 years ago
Niek De Klein ★ 2.6k

I've been using MSClustering ( 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?

mass-spec • 8.6k views
Entering edit mode
7.8 years ago
Bioinfo ▴ 30

Hi Niek,

You might have already discovered the reason for your mzXML file not working in MaxQuant.

I just now found your question as I do have similar issues. I am working with Bruker Amazon Analysis.yep files and trying to use MaxQuant for label-free quantitation. I converted the files using Bruker's CompassXport as well as msconvert from ProteoWizard (it also uses CompassXtract lib from Bruker). MaxQuant complains that the converted mzXML files are corrupt. So I opened them in a text editor and examined -everything looked fine. Also, I could open these supposedly corrupt files in MZmine (, which is a very good software for LC-MS data analysis.

After spending more than a day's work, I am wondering the reason for the mzXML files not opening with MaxQuant could be due to incompatibility in mzXML version. CompassXport / msconvert outputs in mzXML 2.1 version. I used a test data in mzXML 3.0 format and it opens in MaxQuant. By the way, I am trying to convert my files from 2.1 to 3.0 version, but I could not find any tools for that - probably I might write a script to do this.


Entering edit mode
6.8 years ago

Is there any way of convert to mascot to fasta file?


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