Upload a list of modifications

[nilitiko]

Hi, Is there a way to upload a list of ~90 modifications we want to look for in the search?

[jgriss]

Hi,

Unfortunately not. But most important searching for 90 modifications will not work with MSGF+ (the search engine used by the workflow).

If you need to characterise that many PTMs I suggest to use FragPipe. It also supports TMT/iTRAQ and users MSFragger as search engine.

Kind regards, Johannes

On 23 May 2021 08:19:44 CEST, nilitiko @.***> wrote:

Hi, Is there a way to upload a list of ~90 modifications we want to look for in the search?

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[nilitiko]

Thank you very much for your prompt answer!

בתאריך יום א׳, 23 במאי 2021, 09:24, מאת Johannes Griss ‏< @.***>:

Hi,

Unfortunately not. But most important searching for 90 modifications will not work with MSGF+ (the search engine used by the workflow).

If you need to characterise that many PTMs I suggest to use FragPipe. It also supports TMT/iTRAQ and users MSFragger as search engine.

Kind regards, Johannes

On 23 May 2021 08:19:44 CEST, nilitiko @.***> wrote:

Hi, Is there a way to upload a list of ~90 modifications we want to look for in the search?

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/ProtProtocols/IsoProt/issues/97

-- Sent from my Android device with K-9 Mail. Please excuse my brevity.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ProtProtocols/IsoProt/issues/97#issuecomment-846511472, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASWIMLDV4ZS4PD4Q6GWKNGTTPCNRRANCNFSM45LMEQ7Q .

[Dmorgen]

Hi, Unfortunately not. But most important searching for 90 modifications will not work with MSGF+ (the search engine used by the workflow). If you need to characterise that many PTMs I suggest to use FragPipe. It also supports TMT/iTRAQ and users MSFragger as search engine. Kind regards, Johannes … On 23 May 2021 08:19:44 CEST, nilitiko @.***> wrote: Hi, Is there a way to upload a list of ~90 modifications we want to look for in the search? -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: #97 -- Sent from my Android device with K-9 Mail. Please excuse my brevity.

is there any way to use the software just for quantification? without the search stage? we've got results from another search engine we'd like to use.

Thanks! David.

[jgriss]

Hi @Dmorgen,

"Officially" not, but it does work if you use PeptideShaker to validate your search results. If the pipeline detects the search results in PeptideShaker's format, it offers to start directly from the quantification step.

If you don't have the results in PeptideShaker's format, we'd need to see if we can implement this.

Kind regards, Johannes

[Dmorgen]

Thanks!

From: Johannes Griss @.> Sent: Sunday, May 23, 2021 11:57 AM To: ProtProtocols/IsoProt @.> Cc: David Morgenstern @.>; Mention @.> Subject: Re: [ProtProtocols/IsoProt] Upload a list of modifications (#97)

Hi @Dmorgenhttps://github.com/Dmorgen,

"Officially" not, but it does work if you use PeptideShaker to validate your search results. If the pipeline detects the search results in PeptideShaker's format, it offers to start directly from the quantification step.

If you don't have the results in PeptideShaker's format, we'd need to see if we can implement this.

Kind regards, Johannes

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ProtProtocols/IsoProt/issues/97#issuecomment-846528672, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIQ5VINGV64S23FRWQV2QQDTPC7O5ANCNFSM45LMEQ7Q.