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database search for MALDI peptide peaks - Protein identification....help needed (Apr/22/2006 )

dear all,

I am analysing peptide mass fingerprint data(to identify proteins) obtained by MALDI-TOF using matrix science search programme......

I need to know which database (MSDB/NCBInr/Swissprot) is preffered for search....

I have seen people reporting in journal papers only NCBInr database when using matrixscience search programme....though the protein gets identified by using both MSDB and NCBInr databases.....any suggestions will be of huge help to me......

Thanks in advance..... smile.gif

-transposon9-

QUOTE (transposon9 @ Apr 22 2006, 07:11 AM)
dear all,

I am analysing peptide mass fingerprint data(to identify proteins) obtained by MALDI-TOF using matrix science search programme......

I need to know which database (MSDB/NCBInr/Swissprot) is preffered for search....

I have seen people reporting in journal papers only NCBInr database when using matrixscience search programme....though the protein gets identified by using both MSDB and NCBInr databases.....any suggestions will be of huge help to me......

Thanks in advance..... smile.gif

Perhaps youy should have a look at the macot search tool - just type that into google and see what you get. Iy I was trying to identify a protein from a mass finger print I would use the largest databases available regardless of redundancy. MSDB and swissprot would be fine I guess - and I assume a first pass is done on the NR database.

-DPK-

hello,

the NCBInr database is a very rich resource for mass fingerprint analysis, as is MSDB...either will work fine. the fact that you are getting the same IDs from both databases is what you would hope for. as long as this occurs consistently with each protein you analyse, you might as well keep using both databases, and just include that in the methods of your manuscript...no one will punish you for that kind of redundancy...it might even be a plus.

QUOTE (transposon9 @ Apr 22 2006, 11:01 AM)
dear all,

I am analysing peptide mass fingerprint data(to identify proteins) obtained by MALDI-TOF using matrix science search programme......

I need to know which database (MSDB/NCBInr/Swissprot) is preffered for search....

I have seen people reporting in journal papers only NCBInr database when using matrixscience search programme....though the protein gets identified by using both MSDB and NCBInr databases.....any suggestions will be of huge help to me......

Thanks in advance..... smile.gif

-johanski-

hai johanski
thanks for your timely suggestion... smile.gif

-transposon9-

hai perlmunky
thanks for your suggestion... smile.gif

-transposon9-