Change FDR for XTandem search

[EvgenyKanshin]

Hello, I was wondering if there is a way to change the FDR used by XTandem. I'd like to get numbers for peptides/proteins @ FDR<0.01 and now I think it is set at 5%. Thank you for this great tool, really useful and we are currently trying to implement it for all our QC samples.

[kevinkovalchik]

Hello,

Sorry for my slow response. Right now there is no way to set the FDR. I'm working on a new version of the tool which I hope will be more flexible in terms of experiment design and getting specific metrics of interest. I will definitely consider adding control of the FDR rate for the QC metrics.

Best, Kevin

On Tue, Oct 15, 2019 at 9:51 AM EvgenyKanshin notifications@github.com wrote:

Hello, I was wondering if there is a way to change the FDR used by XTandem. I'd like to get numbers for peptides/proteins @ FDR<0.01 and now I think it is set at 5%. Thank you for this great tool, really useful and we are currently trying to implement it for all our QC samples.

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[EvgenyKanshin]

Thank you,

and BTW it is really a great tool. It is within that tiny 1 % of all the tools that really work and useful.

Evgeny Kanshin, PhD Proteomics Laboratory Division of Advanced Research and Technology NYU Langone Medical Center Office: 646-501-4554 Cell: 862-220-6090

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From: Kevin Kovalchik notifications@github.com Sent: Monday, October 21, 2019 12:32:45 PM To: kevinkovalchik/RawTools Cc: Kanshin, Evgeny; Author Subject: Re: [kevinkovalchik/RawTools] Change FDR for XTandem search (#48)

Hello,

Sorry for my slow response. Right now there is no way to set the FDR. I'm working on a new version of the tool which I hope will be more flexible in terms of experiment design and getting specific metrics of interest. I will definitely consider adding control of the FDR rate for the QC metrics.

Best, Kevin

On Tue, Oct 15, 2019 at 9:51 AM EvgenyKanshin notifications@github.com wrote:

Hello, I was wondering if there is a way to change the FDR used by XTandem. I'd like to get numbers for peptides/proteins @ FDR<0.01 and now I think it is set at 5%. Thank you for this great tool, really useful and we are currently trying to implement it for all our QC samples.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kevinkovalchik/RawTools/issues/48?email_source=notifications&email_token=AD2PTUHBQ76THOUKJM5UQ6DQOXDF7A5CNFSM4JA455V2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HR4FKNA, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD2PTUB2NUUUCACFBP3LZV3QOXDF7ANCNFSM4JA455VQ .

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