i want to analyse the peptide isolated from 1D PAGE and the peptide was digested with trypsin and then subjected to lc pda ms. the data obtained in peak list or pdf format. which software i use to analyse this proteomic analysis.
Hi there
You can use MASCOT to perform peptide mass fingerprint
It is free and you just need to provide an email address
You need to go to the matrixscience website, then mascot database search and then PMF to perform a search
You can introduce the mass list directly by copy and paste or in a suitable file
There are many guides on how to interpret the results and perform searches online
A good starting point is here:
http://www.matrixscience.com/help/pmf_help.html
Hope this helps
Hi there
I would need to see the mascot report to be able to comment more.
Are you doing MS or MS/MS seach?
However I never look at the mascot score
What you need to be looking at is the "expected" value. This value is directly proportional to the p-value or the probability of the peptide being a true value, this value has to be less than 0.05, or 95% confidence value.
You also need to tick the decoy option, this option is needed for most publications because is a way to eliminate any positive results that occur randomly , what you expect is a low percentage of false discovery rate FRD
I hope this helps
- Badges
- Science topic
- Similar topics
- Mathematical Sciences
- Graphs