How is the rate of protein sequence coverage calculated in MS/MS Ions Search in Mascot database?

01 January 2018 1 2K Report

As shown in this picture, if the rate of protein sequence coverage is a result that the number of matched amino acids among MS/MS peptides is divided by the total number of amino acids in searched protein sequence, the result is 8.566666.

protein sequence coverage should be 9%, but here is 8%, I don't know why? Or this is the fixed algorithm in scoring system of Mascot database?

Hediye Erdjument-Bromage

Hi Wei,

The percentage sequence coverage is calculated as you have figured it out. It is the number of amino acids identified compared with the amino acid sequence of the full length protein.

I am also not sure why the sequence coverage is showing to be 8% when it is, as you calculated, closer to 9%.

Hediye.

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