Hi,

You could try doing a Mascot search: http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=MIS, but the free version is limited with respect to the number of queries that can be submitted in a single run, so you probably have to divide your list of peptide data into smaller bits that can be searched.

Good luck!

Hi Poorna,

You cannot BLAST if you do not know the peptide identification.  Are you trying to identify or use BLAST to see what the peptide ID is?

Thanks, Hediye

Hi Hediye, 

I have obtained some 3200 peptide sequences from the MS/MS analysis of the tryptic digested protein(not pure, ingel digested) . Now I want to check these peptides for any hits to the protein of my interest.  

Thank you

Mrs./Miss Bhamidimarri,

Please pay attention to:

http://www.matrixscience.com/search_form_select.html

Hi Poorna

You can try Comet or Crux. Comet is an open source version of the Sequest algorithm which is widely used but you will need to able to use the command line interface in Windows or UNIX. Crux is a more complete toolkit to analyse MS/MS data with more options including the Tide algorithm (another fast implementation of Sequest) and Percolator for post-processing:

http://comet-ms.sourceforge.net/

http://cruxtoolkit.sourceforge.net/

Dear Poorna,

I would agree with Eef above.  If you only have ~1000 queries, the online version of Mascot should be able to identify these and give you a list of protein IDs.

Take the mass spec file and generate a Mascot Generic File (.mgf) by using some of the free conversion softwares such as "Proteowizard":

http://proteowizard.sourceforge.net/

Then, you can use Mascot search algorithm to search your mass spec data in order to identify your peptides.  Mascot will give you peptide IDs, as well as protein ID lists that are compiled from the individual peptide IDs.

Keep us posted.

Best,

Hediye

Hi Poorna

You do not specify how you collected the data or what the format of the peptide data is.

There are a number of software packages out there but a freely available shareware software called PeptideShaker ( http://compomics.github.io/projects/peptide-shaker.html ) that is platform independent and will be able to give identities is easy to use and has a very good tutorial on the use and requirements to make protein inferences. It has many other functions available for performing further proteomic analysis. Try it.

Good luck

Duncan