Proteomics

Frequently Asked Questions

What is the GPS MASCOT report?

The excel report has a list of each spot labeled by the spot index. Under each spot is a list of the top protein hits based on MOWSE score, a number assigned by number of fragments submitted and search parameters assigned including size of database. You can find the math theory behind the score at www.matrixscience.com.  The report also lists name of protein, accession number from the database, protein score, confidence interval, and ion score.

How do I know which spot is which on this report?

The Well position names have not been conserved from the MTP to the MALDI target.  The PDQuest spot numbers can be found at the far left under each gray header bar. 

What is the additional excel file for?

The other excel file we attach lists what the digestion spectrum looked like i.e. good, low peptide signal.  These should help you determine if your mascot score is low because it didn’t find a match in the database or if there was not enough raw data available for a high score (these would be the low peptide signal samples).

I have looked at the report now I want to know more.

We can also send other varieties of the mascot report.  If you would like to see the matching peptide list for any or all of your spots please let us know.  Our goal is to not overwhelm you with data if you don’t know what you are looking at.

What do all of these scores mean?

Matrix Science has a detailed explanation of the scoring on their website.  It can be found at http://www.matrixscience.com/help/interpretation_help.html  

Why do my results look different than if I had submitted them directly to MASCOT online?

The Applied Biosystems software package has its own interface for viewing the MASCOT results.  At this time, the content of the data exported as excel reports cannot be modified.  Not satisfied with that answer?  Ask us about viewing your data on IDQuest.

I am writing up my results, what do I need to include in my manuscript?

A short description of the protein digestion/MALDI analysis can be found on our website:

http://www.unr.edu/inbre/cores/proteomics/documents/MassSpecMaterialsandMethods.pdf

If you want a more detailed protocol or if your samples were analyzed by a different method, please let us know and we will be happy to send you the required information.