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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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FragMethod not correct? #53

Open leiwang-me opened 5 years ago

leiwang-me commented 5 years ago

Hi there,

I ran MSGF+ on the PXD004452 dataset, and according to the dataset description, it should be a Q Exactive instrument type. However, in the final tsv file after running MSGF+, the values for the FragMethod column are all CID. Is it because I forgot to set the fragment method? This is my script: 

java -Xmx${mem}g -jar $msgf/MSGFPlus.jar -s $mgf_location/$mgf.mgf -o $out_location/$mgf.carbonate.uniprot.mzid -d $database -inst 1 -t 50ppm -ti -1,2 -mod $msgf/Mods_normal.txt -ntt 2 -tda 1 -maxCharge 7 -minCharge 1 -addFeatures 1 -n 1

Thanks, Lei

FarmGeek4Life commented 5 years ago

Does the MGF file contain the fragmentation methods? If it doesn't, you will need to add "-m 3" to the command line to specify HCD.

You can see the full list of command line options here.