I have done analysis of LC-MS/MS using band of SDS PAGE result, I have got the data..but there are some data I don't yet understand how to read, ie : total, % cov, % cov (50) and % cov (95).
What do they mean?
Hi Rike, which software package are the results coming from? Looks like ProteinPilot to me :-) Your values are referring to the sequence coverage in %, which is calculated as (number of amino acid residues in all peptides that were identified)/(number of amino acid residues in your protein sequence).
The "total" value takes into account all identified peptides no matter what the confidence; the "50" only considers peptides which individually are identified at confidence 50% or better; and the "95" consequently only peptides with individual confidence of 95% or better.
yes absolutely right, I used protein pilot software. Ok thank you very much for your explanation. Thus score of total protein not indicates the amount of peptide in that band.. so if the total protein are high it doesnt mean that content of protein in that band is high as well.
The score is somewhat related to the number of peptide sequences that have been identified for a protein. The better indicator is actually "Peptides (95%)", this number reflects to a degree the relative abundance of a protein in the samples. Unfortunately ProteinPilot does not support per se the concept of Spectral Counts or its modifications, e.g. NSAF. Btw: work with the "Unused Score" rather than the "Total Score" for proteins - the total score can be high but does not reflect uniqueness of peptide assignments, so most or all of the peptides might be shared with other protein entries from the database
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