Hi,

Would you like to analyze a peptide mass fingerprinting result? What kind of data do you have?

The Mascot page is quite self-explanatory, it also contains a tutorial: http://www.matrixscience.com/help/pmf_help.html.

Good luck!

Dear Dr. Eef Dirksen,

Thank you very much for your reply. Yes, I would like to analyze a peptide mass fingerprinting result. Initially, I performed the MALDI-TOF for the full molecular mass of protein, then I did the trypsin digestion method. so now I have the data of MS data on the small fragment peptide molecular masses of protein.

Could please help me how to analyse it? I go through the above site. Its so much length process ....Do you have any videos....please send me.

Thank you so much 

with regards,

vikky rajulapati

Hi Vicky,

It is actually not that complicated.

If you click the link:

http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=PMF

Start by filling in your name, email addres and -if required- a title for your search.

Then select a database to search against, SwissProt is perfectly fine at

first.

You mention that you used trypsin to generate peptides, so that's already entered and you can leave the number of missed cleavages at '1'. Then select the organism from which your protein of interest originates.

Did you use iodoacetamide, or something else, to alkylate your reduced cysteine residues? You will have to enter that under 'Fixed modifications'.

The variable modifications on the right hand side include things like methionine

oxidation that is likely to happen on some methionine residues, but not all.

Protein mass doesn't need to be added.

What is the mass accuracy of your measurement (did you use (internal) calibration)?

Your data is probably [M+H]+ based and average mass data (or what type of MALDI did you use?

The list of ions that you extracted from your MALDI spectrum can be copy-pasted into the 'Data input' field

Don't tick the 'Decoy' box and leave the 'Report top' at 'AUTO'.

Hit 'Start Search...' and wait for the result :)

If this doesn't work for you, send me your data file, I'll do it for you.

Dear Eef Dirksen,

Am so sorry for troubling you..... but I don't have any option. Eef, In our institute we have the Brucker company MALDI-TOF so I have to upload.XML file during the analysis they gave to me, PDF file. I am unable to do this, will you suggest me....

Thank you,

With regards

vikky

Dear Dr. Eef Dirksen,

when I hit 'Start Search...' it show the following error:

Mascot terminated with error 26

Peptide mass of 1 is too small. The minimum mass allowed is 100. (Or incorrect data format) [M00133]

Peptide mass of 1 is too small. The minimum mass allowed is 100. (Or incorrect data format) [M00133]

Peptide mass of 1 is too small. The minimum mass allowed is 100. (Or incorrect data format) [M00133]

You have not entered any mass data, or the data file does not exist [M00026]

The 'QUE' field is empty, or does not contain any masses. Alternatively, a filename was specified in the file upload box that is empty, or does not exist

I don't know why it is so.