The CalcMass in make-pin.pin is not equal to theory mass

[Robot mantou]

Dear Cruxers,

I found that the CalcMass in make-pin.pin file is not equal to the theory mass of peptides:

In make-pin.pin file:

CalcMass of 'SSTAFGK' is '697.3515',

In http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet.html:

mass of 'SSTAFGK' is '696.3443' (mono weight without proton)

My commands of Crux is:

1. crux tide-index --overwrite T --max-length 30 --min-length 7 --mods-spec C+57.02146,1M+15.994915 --mod-precision 4 --max-mods 3 --missed-cleavages 1 x.fasta index/
2. crux tide-search --max-precursor-charge 4 --mod-precision 4 --num-threads 4 --overwrite T --top-match 1 --concat T --compute-sp T x.raw index/ 
3. crux percolator --output-weights T --overwrite T crux-output/tide-search.txt

Did I do something wrong?

Looking forward to your reply.

Best

[William Fondrie]

Thank you for your question and using crux.

The "CalcMass" column in the make-pin.pin file is actually the monoisotopic mass of the singly charged peptide (the [M+H]+), which in this case is 697.3515. However, if you look in your Percolator result files (percolator.target.psms.txt), the "spectrum neutral mass" column should be the neutral mass of the peptide, 696.3443.

Best,

Will