Comet ms/ms db search support

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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 Pal6

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.

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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.

Jun 8

Shadi Nayeri, Jimmy Eng2

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

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 Eng4

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 Eng2

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 Eng2

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 Eng2

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 Eng3

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 Eng10

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 Eng2

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).

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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).

Feb 22

Jannik Schneider, Jimmy Eng3

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

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 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

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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

8/1/23

Dear Comet users, the OpenMS team is currently conducting a survey to better understand the needs of

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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

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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 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

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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 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

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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

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/

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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

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/

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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

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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 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

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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

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/

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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 Eng2

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

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 "

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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 Eng2

10/31/22

Additional var mods added?

Roger, The first parameter entry for the variable_mod0X parameters is the modification mass

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Additional var mods added?

Roger, The first parameter entry for the variable_mod0X parameters is the modification mass

10/31/22

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 Eng5

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

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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

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 Eng5

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 Eng3

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

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*** 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

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