I wish to run an iTRAQ labeled data in the Protein Pilot. The peptides
have been labeled with the iTRAQ 4-plex (114-117). The data was
acquired on a Waters Synapt using DDA mode.
I have converted the .raw data to the .mgf files using the MSConvert.
However, when running the files on the Protein Pilot, the peak lists
were no correct- a label resulted in 3 peaks which we checked and it
results from the data conversion.
Which settings on the MSConvert do you recommend to convert the .raw
data to the .mgf one?
Laboratory for Protein Biochemistry and Biomolecular Engineering
Department for Biochemistry and Microbiology
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