MsFragger vs Comet

[David Zhao]

Hi there,

We've started to evaluate MsFragger tool, has anybody done a comparison between Comet and MsFragger? Is it complementary to Comet? We've run a couple of MsFragger searches, using parameters converted from comet parameters, it seems MsFragger is focusing more on finding more PTMs, which results in many long peptide hits, and overriding charge option doesn't seem to be working...

Any inputs or comments is greatly appreciated!

Thanks,

David

[Alexey Nesvizhskii]

David,

We have done many comparisons. You should be getting very similar results when performing closed searches.

You can post questions on MSFragger here:

https://github.com/chhh/MSFragger-GUI/issues

Also, are you using the latest version?

You can get the latest version of MSFragger here:

http://msfragger.arsci.com/upgrader/

Best,

Alexey Nesvizhskii

[David Zhao]

Thanks for reply, Alexey. I am using the latest version, and I've posted my question on git.https://github.com/chhh/MSFragger-GUI/issues/63

David