Dear All
I have three peptides sequences from MALDI TOF/TOF MS analysis, now i am confused where to blast in MASCOT database and the second confusion is that i have to separately blast each one or combine all of the with no space inbetween them. Please send me a detail ansewer thanks.
sehroon
The MASCOT is"a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases" a search engine based on scoring .The online version have online protein database.You shoud install a local version if you have your favorite sequence.The local version MASCOT's database is a ".fasta"file includ your three peptides sequences .The database shoud be Browser-based configured.Online version'link attached.
Thanks for your reply Dear Wang
Could you please tell me, forexample i have
KMHGVDS, QWESAFHG, and YTHGFRDM
These three peptides, how will i search for these three peptides the identicle proteins or peptides online on mascot. What i mean is that i have to combine all these three OR search separately for each one or how???
Please add a detailed reply thanks..
sehroon
Oh,you just want to usepeptide to identify proteins .The balst tools on NCBI could be competent.link:https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
you can enter your sequence and click "blast"and wait a few seconds,the result will be shown.Maybe you shouldn't combine all the three ,because the three peptides might not be in the same protein.And the sequence you entered must be consecutive.
Dear Wang Once again thanks for your reply,
I know on NCBI how to find the identicle proteins and where to Blast, thanks for that also.
I have the above three peptides from MALDI TOF/TOF results, now i am wondering about the how to find the whole peptide or proteins sequence from these three peptides. I do not know where i have to search for each one on MASCOT or combile all togather and Blast at MASCOT database. Please also send me the link where i have to b;ast on MASCOT database, thanks.
sejhoom
Thanks dear
But still i am not able to find the results, show the below error
Mascot Search
Mascot terminated with error 88
Invalid command/mass at line 2 of your query. Line is HMGDIYK. [M00088]
The query does not conform to the required format. The first item on the line should be a mass value. See the online user help for details.
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