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Welcome to the Comet ms/ms database search Google group. You can find the Comet project at
https://uwpr.github.io/
Comet
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Yang Qianying
,
Jimmy Eng
2
Mar 25
Comet Search Error (Code 256) with TimsTof Flex MALDI Data
Hi. Comet identifies peptides by comparing tandem mass spectra (or MS3 spectra) against sequences in
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Comet Search Error (Code 256) with TimsTof Flex MALDI Data
Hi. Comet identifies peptides by comparing tandem mass spectra (or MS3 spectra) against sequences in
Mar 25
Jimmy Eng
Mar 16
Comet 2025.01 rev.1 is now available
Comet 2025.01 rev. 1 is now available. Release notes: https://uwpr.github.io/Comet/releases/
unread,
Comet 2025.01 rev.1 is now available
Comet 2025.01 rev. 1 is now available. Release notes: https://uwpr.github.io/Comet/releases/
Mar 16
Jimmy Eng
Feb 19
Comet 2025.01 rev. 0 is now available
Comet 2025.01 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/
unread,
Comet 2025.01 rev. 0 is now available
Comet 2025.01 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/
Feb 19
Marina Carrera i Dulsat
,
Jimmy Eng
2
12/12/24
Comet ran out of memory
Marina, Sorry you're experiencing this issue. A spectrum batch size of 500 should use well under
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Comet ran out of memory
Marina, Sorry you're experiencing this issue. A spectrum batch size of 500 should use well under
12/12/24
Erik Johnson
,
Jimmy Eng
4
11/12/24
Interpretation help
Hi Erik. Regarding #1, the processed "spectrum" that Comet uses internally is a binned
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Interpretation help
Hi Erik. Regarding #1, the processed "spectrum" that Comet uses internally is a binned
11/12/24
Erik Johnson
, …
Suresh Poudel
3
11/1/24
Running Comet on one spectrum
You can always make .ms2 file and comet works great. Best, Suresh Poudel Lead Bioinformatics Research
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Running Comet on one spectrum
You can always make .ms2 file and comet works great. Best, Suresh Poudel Lead Bioinformatics Research
11/1/24
Jimmy Eng
10/15/24
Comet 2024.02 rev. 0 is now available.
Comet 2024.02 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/
unread,
Comet 2024.02 rev. 0 is now available.
Comet 2024.02 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/
10/15/24
Jimmy Eng
7/17/24
Comet 2024.01 rev. 1 is now available
Comet 2024.01 rev. 1 is now available. Release notes: https://uwpr.github.io/Comet/releases/
unread,
Comet 2024.01 rev. 1 is now available
Comet 2024.01 rev. 1 is now available. Release notes: https://uwpr.github.io/Comet/releases/
7/17/24
Jimmy Eng
,
Debojyoti Pal
6
6/8/24
Re: Regarding peptide mass type and isotope error
Yes, this thread had very valuable information (atleast for a novice). Thank you for posting it back.
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Re: Regarding peptide mass type and isotope error
Yes, this thread had very valuable information (atleast for a novice). Thank you for posting it back.
6/8/24
Shadi Nayeri
,
Jimmy Eng
2
5/31/24
Example file for testing Comet
Shadi, You can find an example yeast test.mzML, comet.params, and yeast.fasta at the URL below. There
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Example file for testing Comet
Shadi, You can find an example yeast test.mzML, comet.params, and yeast.fasta at the URL below. There
5/31/24
Jimmy Eng
4
5/31/24
Comet 2024.01 rev 0 is now available
I just re-tagged the 2024.01.0 release to address Windows searches failing. Addressed with commit
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Comet 2024.01 rev 0 is now available
I just re-tagged the 2024.01.0 release to address Windows searches failing. Addressed with commit
5/31/24
Nate Camp
,
Jimmy Eng
4
5/22/24
Error code 139 when searching with "No enzyme"
Just to give some closure to this thread if anyone comes across this issue in the future, this issue
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Error code 139 when searching with "No enzyme"
Just to give some closure to this thread if anyone comes across this issue in the future, this issue
5/22/24
Debojyoti Pal
,
Jimmy Eng
2
5/6/24
Will the decoy file be generated by Comet or will I have to generate it externally?
I replied to this post and your other one via the google group website but my replies did not show up
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Will the decoy file be generated by Comet or will I have to generate it externally?
I replied to this post and your other one via the google group website but my replies did not show up
5/6/24
Christian Treitz
,
Jimmy Eng
2
5/2/24
Comet search with peff database in proteome discoverer
Sorry for the late response and this unhelpful answer which is I don't know but I would guess
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Comet search with peff database in proteome discoverer
Sorry for the late response and this unhelpful answer which is I don't know but I would guess
5/2/24
Jannik Schneider
,
Jimmy Eng
2
2/26/24
Question about "add_C_cysteine" Parameter and output format
Alkylation by iodoacetamide of free cysteines is pretty common in mass spec experiments. That being
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Question about "add_C_cysteine" Parameter and output format
Alkylation by iodoacetamide of free cysteines is pretty common in mass spec experiments. That being
2/26/24
Jannik Schneider
,
Jimmy Eng
3
2/26/24
Question about scannr extraction from input
Alright, thank you for the explanation Jimmy Eng schrieb am Donnerstag, 22. Februar 2024 um 23:44:38
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Question about scannr extraction from input
Alright, thank you for the explanation Jimmy Eng schrieb am Donnerstag, 22. Februar 2024 um 23:44:38
2/26/24
Farshad Abdollah-Nia
,
Jimmy Eng
10
2/23/24
15N metabolic labeling -- mods output
As you likely have seen already, I sent you an email with an initial implementation of this. We can
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15N metabolic labeling -- mods output
As you likely have seen already, I sent you an email with an initial implementation of this. We can
2/23/24
wille...@gmail.com
,
Jimmy Eng
2
2/22/24
Small question fragment_bin_tol
Sorry for the late response (as I didn't get notification of posts to this group since January).
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Small question fragment_bin_tol
Sorry for the late response (as I didn't get notification of posts to this group since January).
2/22/24
Jannik Schneider
,
Jimmy Eng
3
2/22/24
Met-loss and Met-loss+Acetyl modifications
Sorry I wasn't aware of this post as I never got notification of it (as well as others since
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Met-loss and Met-loss+Acetyl modifications
Sorry I wasn't aware of this post as I never got notification of it (as well as others since
2/22/24
yu sun
1/26/24
Question About Ion Injection Time
Hello everyone, I have been using SEQUEST for my research and its results have one column named '
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Question About Ion Injection Time
Hello everyone, I have been using SEQUEST for my research and its results have one column named '
1/26/24
Sam Whedon
,
Jimmy Eng
2
9/13/23
Precursor and Fragment charge values
Hi Sam. Yes, changing those two defines and re-compiling would lift those limits. There's also
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Precursor and Fragment charge values
Hi Sam. Yes, changing those two defines and re-compiling would lift those limits. There's also
9/13/23
Chris Bielow
8/1/23
OpenMS survey
Dear Comet users, the OpenMS team is currently conducting a survey to better understand the needs of
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OpenMS survey
Dear Comet users, the OpenMS team is currently conducting a survey to better understand the needs of
8/1/23
Debojyoti Pal
,
Jimmy Eng
6
7/31/23
Variable mod query in COMET
I am on windows On Tuesday, August 1, 2023 at 8:19:03 AM UTC+5:30 Debojyoti Pal wrote: Hi Jimmy That
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Variable mod query in COMET
I am on windows On Tuesday, August 1, 2023 at 8:19:03 AM UTC+5:30 Debojyoti Pal wrote: Hi Jimmy That
7/31/23
Rantwon Jaylen Domazsa
, …
Jimmy Eng
6
7/10/23
Parameters for MS2 TMT11Plx Thermo Orbitrap
This is one of those posts/threads that I didn't get any notifications of until Phil's
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Parameters for MS2 TMT11Plx Thermo Orbitrap
This is one of those posts/threads that I didn't get any notifications of until Phil's
7/10/23
June Wang
,
Jimmy Eng
4
3/30/23
Comet V2023.01 does not work with mzML files converted from Thermo raw files.
June, this issue is addressed in the 2023.01.2 release available now. On Tuesday, March 21, 2023 at
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Comet V2023.01 does not work with mzML files converted from Thermo raw files.
June, this issue is addressed in the 2023.01.2 release available now. On Tuesday, March 21, 2023 at
3/30/23
Jimmy Eng
3/30/23
Comet 2023.01 rev 2 is now available
Comet 2023.01 rev. 2 is now available. Release notes: https://uwpr.github.io/Comet/releases/
unread,
Comet 2023.01 rev 2 is now available
Comet 2023.01 rev. 2 is now available. Release notes: https://uwpr.github.io/Comet/releases/
3/30/23
Jimmy Eng
3/15/23
Comet 2023.01 rev 1 is now available
Comet 2023.01 rev. 1 is now available. Release notes: https://uwpr.github.io/Comet/releases/
unread,
Comet 2023.01 rev 1 is now available
Comet 2023.01 rev. 1 is now available. Release notes: https://uwpr.github.io/Comet/releases/
3/15/23
Florian Prodinger
, …
Jimmy Eng
4
3/1/23
running comet on linux (fedora)
Florian, I'm not sure why but your replies to this conversion (that you have since deleted
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running comet on linux (fedora)
Florian, I'm not sure why but your replies to this conversion (that you have since deleted
3/1/23
David Tabb
,
Jimmy Eng
3
2/21/23
A PTM that can happen on any residue?
Hi, Jimmy. Thank you for your kind note and making a rapid fix to handle the "any AA" PTM
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A PTM that can happen on any residue?
Hi, Jimmy. Thank you for your kind note and making a rapid fix to handle the "any AA" PTM
2/21/23
Jimmy Eng
1/31/23
Comet 2023.01 rev. 0 is now available
Comet 2023.01 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/
unread,
Comet 2023.01 rev. 0 is now available
Comet 2023.01 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/
1/31/23