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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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Jimmy Eng
,
Debojyoti Pal
6
Jun 8
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.
unread,
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.
Jun 8
Shadi Nayeri
,
Jimmy Eng
2
May 31
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
May 31
Jimmy Eng
4
May 31
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
May 31
Nate Camp
,
Jimmy Eng
4
May 22
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
May 22
Debojyoti Pal
,
Jimmy Eng
2
May 6
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
May 6
Christian Treitz
,
Jimmy Eng
2
May 2
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
May 2
Jannik Schneider
,
Jimmy Eng
2
Feb 26
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
Feb 26
Jannik Schneider
,
Jimmy Eng
3
Feb 26
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
Feb 26
Farshad Abdollah-Nia
,
Jimmy Eng
10
Feb 23
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
Feb 23
wille...@gmail.com
,
Jimmy Eng
2
Feb 22
Small question fragment_bin_tol
Sorry for the late response (as I didn't get notification of posts to this group since January).
unread,
Small question fragment_bin_tol
Sorry for the late response (as I didn't get notification of posts to this group since January).
Feb 22
Jannik Schneider
,
Jimmy Eng
3
Feb 22
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
Feb 22
yu sun
Jan 26
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 '
Jan 26
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
unread,
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
Debojyoti Pal
,
Jimmy Eng
2
11/27/22
Libra results for individual peptides in ProteinProphet results page
Hi. I was just going to reply to suggest that you post this to the spctools-discuss google group for
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Libra results for individual peptides in ProteinProphet results page
Hi. I was just going to reply to suggest that you post this to the spctools-discuss google group for
11/27/22
Jimmy Eng
11/17/22
bug report with "mass_offsets" and "prec_NL_ions" parameters
The "mass_offsets" parameter was introduced in Comet version 2015.02.0 and the "
unread,
bug report with "mass_offsets" and "prec_NL_ions" parameters
The "mass_offsets" parameter was introduced in Comet version 2015.02.0 and the "
11/17/22
Roger Olivella
,
Jimmy Eng
2
10/31/22
Additional var mods added?
Roger, The first parameter entry for the variable_mod0X parameters is the modification mass
unread,
Additional var mods added?
Roger, The first parameter entry for the variable_mod0X parameters is the modification mass
10/31/22
Jimmy Eng
2
9/14/22
Comet 2022.01 rev. 2 is now available.
I just updated this release to address a new issue with MGF files. The TITLE line entries are
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Comet 2022.01 rev. 2 is now available.
I just updated this release to address a new issue with MGF files. The TITLE line entries are
9/14/22
Srdfr
,
Jimmy Eng
5
8/19/22
filter fragmentation method from output
Thank you! On Thursday, 18 August 2022 at 21:55:18 UTC+2 jke...@gmail.com wrote: I'll send you
unread,
filter fragmentation method from output
Thank you! On Thursday, 18 August 2022 at 21:55:18 UTC+2 jke...@gmail.com wrote: I'll send you
8/19/22
Jimmy Eng
7/25/22
Comet 2022.01 rev. 1 is now available
Comet 2022.01 rev. 1 is now available. Release notes: https://uwpr.github.io/Comet/releases/
unread,
Comet 2022.01 rev. 1 is now available
Comet 2022.01 rev. 1 is now available. Release notes: https://uwpr.github.io/Comet/releases/
7/25/22
Chris Bielow
, …
Jimmy Eng
5
7/25/22
Search speed for variable modifications -- internal optimization potential?
Hi Roger. This little optimization will be included in the next minor release likely today (version
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Search speed for variable modifications -- internal optimization potential?
Hi Roger. This little optimization will be included in the next minor release likely today (version
7/25/22
Animesh Sharma
,
Jimmy Eng
3
6/23/22
*** buffer overflow detected ***
Just to give an update to this for anyone who may come across this thread in the future, the buffer
unread,
*** buffer overflow detected ***
Just to give an update to this for anyone who may come across this thread in the future, the buffer
6/23/22