peptide mass fingerprint query

[mass spec novice]

Can anyone explain what exactly the following mass spec result means - i have an unknown protein that was subject to MALDI TOF MS and the result from mascot was this 'PREDICTED:Similar to X', i am not sure what exactly this means - does it mean that my protein is similar to a predicted protein X sequence in the database? Is there the possibility that my protein is protein X but that cannot be confirmed? or does it mean that my protein is definitely not protein X but something very similar?

thanks in advance

[danfive]

All of the possibilities you mention are plausible. Including more info on source of protein, modification, digestion, and P-values of database search hit are routine when describing spec results. Good luck!

[mass spec novice]

Hi thanks for your reply, i know a bit about MS as i've done it before but i have never got this 'predicted:similar to' before that's why i'm confused - the protein match is from the same species, same molecular weight, same isoelectric point and a good ststistically significant mowse score - so, does 'predicted' mean that the protein it is matching to is actually not in the database but its predicted sequence (from cDNA) is there, and, my protein is similar to that? my protein might be that protein?

sorry for going on! really need to understand this! thanks again

[danfive]

Originally Posted by mass spec novice

... the protein match is from the same species, same molecular weight, same isoelectric point and a good ststistically significant mowse score -

All of these things point to you isolating the right protein, do you have various (3-5) m/z values that are selected as matched peptides for the same protein ID; i.e., various peptide matches for that protein. You can also do an antibody-based assay like ELISA or Western to back up your protein isolation. And as always, if all else fails you can REPEAT, REPEAT, REPEAT the experiment.