FragPipe for middle-down search

[Apirog9]

Hello, I wonder if FragPipe could be tuned to work as a middle-down search engine. It is a very fast tool, I can handle a nonspecific search of peptides in range 7-60 on full Uniprot database in reasonable time (<24h). Maybe there is some things that may make Fragpipe more capable for this kind of analyses:

• some kind of integrated deconvolution, I had some luck with FlashDeconv, I ve got some reasonably looking hits up to 100AA. However I am not quite sure about the overall search quality. Deconvolution also enabled to overcome 7+ charge limit.
• kind of tag-based search to reduce the search space size?

[danielgeiszler]

Hi @piroman999

1. This is something we will discuss internally
2. This would probably require a fundamental reworking of the search engine and is not possible

[anesvi]

Maybe you can contract us directly, and send mzML from FlashDeconv (and without) We can see how the search results look compared to no deconvolution.

Best Alexey

From: piroman999 @.> Sent: Tuesday, November 30, 2021 10:37 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: [Nesvilab/FragPipe] FragPipe for middle-down search (Issue #542)

External Email - Use Caution

Hello, I wonder if FragPipe could be tuned to work as a middle-down search engine. It is a very fast tool, I can handle a nonspecific search of peptides in range 7-60 on full Uniprot database in reasonable time (<24h). Maybe there is some things that may make Fragpipe more capable for this kind of analyses:

• some kind of integrated deconvolution, I had some luck with FlashDeconv, I ve got some reasonably looking hits up to 100AA. However I am not quite sure about the overall search quality. Deconvolution also enabled to overcome 7+ charge limit.
• kind of tag-based search to reduce the search space size?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/542, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM64RZ6VHHP3F4W6DL5TUOTVSTANCNFSM5JCD726Q. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[Apirog9]

Hi, have you recieved files?

[danielgeiszler]

Hi,

I’m downloading them today. Not sure when we’ll have the chance to look at them.