The CalcMass in is not equal to theory mass

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Robot mantou

Dec 7, 2020, 10:49:38 AM12/7/20
to crux-users
Dear Cruxers,

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

In file:
CalcMass of 'SSTAFGK' is '697.3515',

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.


William Fondrie

Dec 7, 2020, 12:50:14 PM12/7/20
to crux-users
Thank you for your question and using crux.

The "CalcMass" column in the 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 (, the "spectrum neutral mass" column should be the neutral mass of the peptide, 696.3443.

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