1D, 2D, HPLC, SDS PAGE, etc. Talk about it here.
Proton Member
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Postby Dania.Awad » Mon Mar 04, 2013 12:36 pm

I am running a nanoflow LC followed by MSMS using MALDI TOF TOF. I am still optimizing my method using a BSA digest.
Luckily everything went well (so far), but I still need to identify the BSA by the mascot server search. I am not sure which options to choose in the mascot website. I would appreciate any help in guiding me through my next step.

Thank you

Phosphoserine Member
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Postby achimt » Thu Mar 07, 2013 2:31 am

Dear Dania,

have a look at the following:

You might need your own licensed server to search your LCMSMS data. If you want to try a free search engine, there are several around, such as X!Tandem (, OMSSA ( or others.

Hope this helps,

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Postby aky » Mon Mar 11, 2013 10:02 am

Choose trypsin, missed cleavage 1, Contaminants (or cRAP) as database (or swissprot) , Carbamidomethylation as fixed mod and Methioinine Oxidation as variable mod. Rest can be left default, though a tolerance of 0.2-0.5 Da should be fine for both precursor and fragments (neither too strict, nor too loose).

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