I've obtained the mascot protein list in mgf file
And I need to carry out further identification and validation steps
My data comprises of treated, untreated and control and I need to determine the fold change as well the molecular mechanism using LC ms ms
Hello dear Anjali Patni,
1. You can make an overlap to know which proteins were only found in each of the groups.
2. With the lists generated in each group you can make the functional enrichment of them using the http://amp.pharm.mssm.edu/Enrichr/.
3. And to determine the fold change, you need to have at least two replicates of each sample and you can do this using the mascot label-free option.
Other software I recommend to do this:
MaxQuant (Free)
http://www.biochem.mpg.de/5111795/maxquant
Peaks (Free key 15 days)
http://www.bioinfor.com/peaks-studio/
Best regards,
Leite
Hi
you can check for Scaffold4 Software, it allows to inspect parallel several samples, you can do statistical test and perform data filtering using the implemented Protein and Peptide Prophet algorithm. You can also load GO-terms with this software and it is easy to generate the files necessary for upload on ProteomeXchange (some journals rewuire that for publication).
The only disadvantage is the software is not for free... But it is very good for inspecting Mascot results.
Cheers
Sir, what if I go with David Annotation tool?
And the data validation can be proceeded with Protein Prophet only.
I´m not very familiar with DAVID but that should also work.
Cheers
Hallo, please how can you determine results as a fold change by using Mascot? Is it possible by spectral counting method via Matches values in Mascot???
Hello Miroslav Ferko,
It is not possible to determine results as a fold change by using Mascot.
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