Groups keyboard shortcuts have been updated

Dismiss

See shortcuts

Comet ms/ms db search support

Contact owners and managers

1–30 of 312

Welcome to the Comet ms/ms database search Google group. You can find the Comet project at https://uwpr.github.io/Comet

0 selected

Yang Qianying, Jimmy Eng2

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

unread,

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 Eng2

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

unread,

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 Eng4

11/12/24

Interpretation help

Hi Erik. Regarding #1, the processed "spectrum" that Comet uses internally is a binned

unread,

Interpretation help

Hi Erik. Regarding #1, the processed "spectrum" that Comet uses internally is a binned

11/12/24

Erik Johnson, … Suresh Poudel3

11/1/24

Running Comet on one spectrum

You can always make .ms2 file and comet works great. Best, Suresh Poudel Lead Bioinformatics Research

unread,

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 Pal6

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.

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.

6/8/24

Shadi Nayeri, Jimmy Eng2

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

unread,

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 Eng4

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

unread,

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 Eng4

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

unread,

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 Eng2

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

unread,

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 Eng2

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

unread,

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 Eng2

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

unread,

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 Eng3

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

unread,

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 Eng10

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

unread,

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 Eng2

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).

unread,

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 Eng3

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

unread,

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 '

unread,

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 Eng2

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

unread,

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 Eng6

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

unread,

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 Eng6

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

unread,

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 Eng4

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

unread,

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 Eng4

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

unread,

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 Eng3

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

unread,

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