While analyzing data with FindPept, I am uploading my file in ppw format and matching it by copying and pasting my protein sequence from NCBI database. I am getting good sequence coverage. However, when I am putting other protein sequences (other proteins not having similarity with my protein), I am still getting substantial sequence coverage! Please let me know if anybody has any idea why this is happening ...
There are several possibilities. False positives can emerge from peptide fingerprinting as the sequence of amino acids can shuffle with each other in such a way that a single mass can correspond to several peptides. Also, check your errors in ppm if they differ much. You may also have two masses corresponding to a single peptide, from which the other one contains oxidation, for example. This might pop up also as a false positive and appear as it covers a sequence from another protein that is not even present.
Of course, it's possible to have contaminating peptides emerging from your protease (trypsin most often) or keratin (from skin, nails, hair...). It's good to rule out those peptides from the spectrum before doing peptide fingerprinting.
It's also good to measure MS/MS (if available) from major peptides to get more specific coverage on the amino acid level.
Hope this helps.
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