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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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How to customize house-made isobaric tags in FragPipe/MSFragger #1549

Closed Miqimiaomiaow closed 6 months ago

Miqimiaomiaow commented 6 months ago

Dear authors,

I am trying to edit our house-made isobaric tags (DiLeu) in MSFragger. However, I didn't find any place for customized tags. Could you please let me know if MSFragger allows customized tags and how to do so? Thank you very much for your help!

Best regards,

Fei

fcyu commented 6 months ago

I guess you meant FragPipe and isobaric quantification? Current version does not support customized the tags but we can add it for you if you send us the masses. And the new changes will be available in the next release.

Best,

Fengchao

Miqimiaomiaow commented 6 months ago

Hi Fengchao,

Thanks a lot for your reply. Please see the attached mass of reporter ions of DiLeu isobaric tags. The first page is the list of masses and the second is the format we used in Proteome Discover software for your reference.

Could you let me know about when the new release will be available so we can plan accordingly? Please free to reach out if you need further information. Thank you very much!

Best regards,

Feixuan Wu

Graduate Student, School of Pharmacy

Lingjun Li Lab

University of Wisconsin--Madison

From: Fengchao @.> Sent: Friday, April 19, 2024 10:25 AM To: Nesvilab/FragPipe @.> Cc: Feixuan Wu @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] How to customize house-made isobaric tags in FragPipe/MSFragger (Issue #1549)

I guess you meant FragPipe and isobaric quantification? Current version does not support customized the tags but we can add it for you if you send us the masses. And the new changes will be available in the next release.

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/Nesvilab/FragPipe/issues/1549*issuecomment-2066805655__;Iw!!Mak6IKo!M_YenmKS9OMy-Lf8tEH9Ym4hFZ1auCiBAqSsK8ecR3OjV8FLkutN8gIpQLzywyS94PidvfqKiHyZ6jwStEJ1yj10QQ$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BHT3CEKLKA2DTCABYSRW52LY6EZN7AVCNFSM6AAAAABGPMHNI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRWHAYDKNRVGU__;!!Mak6IKo!M_YenmKS9OMy-Lf8tEH9Ym4hFZ1auCiBAqSsK8ecR3OjV8FLkutN8gIpQLzywyS94PidvfqKiHyZ6jwStEJsPm1Amw$. You are receiving this because you authored the thread.Message ID: @.***>

fcyu commented 6 months ago

Hi Feixuan,

The attachment was truncated by GitHub. Could you go to https://github.com/Nesvilab/FragPipe/issues/1549 and do it again?

Thanks,

Fengchao

Miqimiaomiaow commented 5 months ago

DiLeu 12-plex.method.xlsx

Please let me know if it works for you. Thanks!

fcyu commented 5 months ago

Hi Feixuan,

Thanks for the file. It works.

May I ask if DiLeu-12's variable modification mass is 145.12801 (https://pubs.acs.org/doi/10.1021/ac503276z)?

Thanks,

Fengchao

Miqimiaomiaow commented 5 months ago

Hi Fengchao,

Yes, the static modifications consisted of DiLeu labels on peptide N termini is 145.12801 Da.

Best regards,

Fei

From: Fengchao @.> Sent: Tuesday, May 7, 2024 2:17 PM To: Nesvilab/FragPipe @.> Cc: Feixuan Wu @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] How to customize house-made isobaric tags in FragPipe/MSFragger (Issue #1549)

Hi Feixuan,

Thanks for the file. It works.

May I ask if DiLeu-12's variable modification mass is 145.12801 (https://pubs.acs.org/doi/10.1021/ac503276zhttps://urldefense.com/v3/__https://pubs.acs.org/doi/10.1021/ac503276z__;!!Mak6IKo!MMu5TQNBjUasCh8b-Gw6xwuxN7AxhG3uqjFhiau6iW5rSxNj_WR7w-LxgAhBYLZARwrn-N_6xxMgQZ2wN9Cwyg-HZw$)?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/Nesvilab/FragPipe/issues/1549*issuecomment-2099133899__;Iw!!Mak6IKo!MMu5TQNBjUasCh8b-Gw6xwuxN7AxhG3uqjFhiau6iW5rSxNj_WR7w-LxgAhBYLZARwrn-N_6xxMgQZ2wN9DpjkLymQ$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BHT3CEJWLB46KTDIHXGJCJ3ZBESELAVCNFSM6AAAAABGPMHNI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJZGEZTGOBZHE__;!!Mak6IKo!MMu5TQNBjUasCh8b-Gw6xwuxN7AxhG3uqjFhiau6iW5rSxNj_WR7w-LxgAhBYLZARwrn-N_6xxMgQZ2wN9ASDy-Ofg$. You are receiving this because you authored the thread.Message ID: @.***>

fcyu commented 5 months ago

Thanks for the prompt reply. I have pushed the changes regarding FragPipe (need to have the new IonQuant to make it work).

I think the new versions will be released this month.

Best,

Fengchao

Miqimiaomiaow commented 5 months ago

[like] Feixuan Wu reacted to your message:

From: Fengchao @.> Sent: Tuesday, May 7, 2024 7:27:45 PM To: Nesvilab/FragPipe @.> Cc: Feixuan Wu @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] How to customize house-made isobaric tags in FragPipe/MSFragger (Issue #1549)

Thanks for the prompt reply. I have pushed the changes regarding FragPipe (need to have the new IonQuant to make it work).

I think the new versions will be released this month.

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/Nesvilab/FragPipe/issues/1549*issuecomment-2099149003__;Iw!!Mak6IKo!Jyaa64DDWUoq6XKGaLmdfQPU3yI2g79xYT1ChzwqmF7ieISh1ZH6zSq7wPf_L2Dh0hZAVUWYD4mkvnhZXiK4H2KCxg$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BHT3CEOWBA4I4ACSBZEKKB3ZBETLDAVCNFSM6AAAAABGPMHNI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJZGE2DSMBQGM__;!!Mak6IKo!Jyaa64DDWUoq6XKGaLmdfQPU3yI2g79xYT1ChzwqmF7ieISh1ZH6zSq7wPf_L2Dh0hZAVUWYD4mkvnhZXiI4AkTl0A$. You are receiving this because you authored the thread.Message ID: @.***>