Comet ms/ms db search support

1–30 of 288

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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June Wang, Jimmy Eng4

Mar 30

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

Mar 30

Mar 30

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/

Mar 30

Mar 15

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/

Mar 15

Florian Prodinger, … Jimmy Eng4

Mar 1

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

Mar 1

David Tabb, Jimmy Eng3

Feb 21

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

Feb 21

Jan 31

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/

Jan 31

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/

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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

Shagun Gupta, … Jimmy Eng3

6/23/22

Something like isolation interference (%) calculation

Comet doesn't provide this information and nor does anything in the Trans-Proteomics Pipeline as

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Something like isolation interference (%) calculation

Comet doesn't provide this information and nor does anything in the Trans-Proteomics Pipeline as

6/23/22

MT S, … Paulo C Carvalho3

6/4/22

A new Comet user

I make myself available should you have any questions running comet with PatternLab. Please let me

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A new Comet user

I make myself available should you have any questions running comet with PatternLab. Please let me

6/4/22

Yiyang Liu, … Jimmy Eng7

5/29/22

Search of fractionated mzML, merge or separately?

Good to know that you are seeing the same score produced. Just as an FYI: the "expect"

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Search of fractionated mzML, merge or separately?

Good to know that you are seeing the same score produced. Just as an FYI: the "expect"

5/29/22

anon anon, Jimmy Eng4

5/3/22

direct search of thermo raw with msfile reader

* I should say; i installed both the 32 and 64 bit versions in that archive. On Tuesday, 3 May 2022

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direct search of thermo raw with msfile reader

* I should say; i installed both the 32 and 64 bit versions in that archive. On Tuesday, 3 May 2022

5/3/22

5/2/22

Comet 2022.01 rev. 0 is now available.

Comet 2022.01 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/

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Comet 2022.01 rev. 0 is now available.

Comet 2022.01 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/

5/2/22

3/26/22

is there a way to parse the comet output .mzID file?

Hi, It looks like the current version of comet search outputs version 1.2 mzID file, and I cannot

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is there a way to parse the comet output .mzID file?

Hi, It looks like the current version of comet search outputs version 1.2 mzID file, and I cannot

3/26/22

Jeff Jones, Jimmy Eng2

2/28/22

Precursor mass v Target Mass

Jeff, I apologize for the delayed response. I had no notification of this month old post and only

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Precursor mass v Target Mass

Jeff, I apologize for the delayed response. I had no notification of this month old post and only

2/28/22

12/11/21

Comet 2021.02 rev. 0 is now available

Comet 2021.02 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/

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Comet 2021.02 rev. 0 is now available

Comet 2021.02 rev. 0 is now available. Release notes: https://uwpr.github.io/Comet/releases/

12/11/21

盛睿, Jimmy Eng2

9/15/21

A new Comet user

Hi. That libid error indicated that you do not have Thermo's MSFileReader installed (and are

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A new Comet user

Hi. That libid error indicated that you do not have Thermo's MSFileReader installed (and are

9/15/21

Paulo C Carvalho, … Jimmy Eng5

9/3/21

Question on DeltaCN and robustness in regards to search space size

I typed out, then re-typed my reply a number of times before hitting send and now I see I left

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Question on DeltaCN and robustness in regards to search space size

I typed out, then re-typed my reply a number of times before hitting send and now I see I left

9/3/21

Shagun Gupta, … Suresh Poudel4

8/30/21

Comet search - Precursor Intensity column empty

I think you can easily use something like Pyteomics to get all the information from mzml or mzXml

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Comet search - Precursor Intensity column empty

I think you can easily use something like Pyteomics to get all the information from mzml or mzXml

8/30/21

natt...@gmail.com

7/13/21

Anyone have a download link for the program Preview?

Hi, Firstly, I apologise as this isn't related to comet. However, I need some help and couldn

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Anyone have a download link for the program Preview?

Hi, Firstly, I apologise as this isn't related to comet. However, I need some help and couldn

7/13/21

Daniel Nebauer, Jimmy Eng2

7/6/21

Hi Daniel. If you're new to Comet, you probably don't want to attempt to binaries I release

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Hi Daniel. If you're new to Comet, you probably don't want to attempt to binaries I release

7/6/21

Jimmy Eng, Harald Barsnes4

6/24/21

Comet 2021.01 rev. 0 is now available

Hi Jimmy, I can confirm that the progress display is now back to normal. Thanks for the quick fix!

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Comet 2021.01 rev. 0 is now available

Hi Jimmy, I can confirm that the progress display is now back to normal. Thanks for the quick fix!

6/24/21

Jimmy Eng, ros...@gene.com3

5/11/21

Comet 2020.01 rev. 4 is now available

Chris, this minor release should have no impact whatsoever with the real time search. If you are just

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Comet 2020.01 rev. 4 is now available

Chris, this minor release should have no impact whatsoever with the real time search. If you are just

5/11/21

Dennis Goldfarb, … Jimmy Eng4

4/10/21

delta mass calculation for percolator .pin file

Only the .pin output. On Sat, Apr 10, 2021 at 7:21 AM Manuel Belmadani <manuel.b...@gmail.com

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delta mass calculation for percolator .pin file

Only the .pin output. On Sat, Apr 10, 2021 at 7:21 AM Manuel Belmadani <manuel.b...@gmail.com

4/10/21

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