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Charles E Grant
Apr 9
Crux 4.2 released
Crux version 4.2 has been released. This release includes all the fixes and improvements included in
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Crux 4.2 released
Crux version 4.2 has been released. This release includes all the fixes and improvements included in
Apr 9
Tang888
,
William Stafford Noble
3
Apr 1
Error when creating index
By the way, I noticed that you tried to specify three different types of mods like this: --mods-spec
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Error when creating index
By the way, I noticed that you tried to specify three different types of mods like this: --mods-spec
Apr 1
agus rungkad
,
Charles E Grant
2
Jan 16
hacked domain
Hi Agus, Thanks for bringing this to our attention. We were indeed the victims of subdomain “
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hacked domain
Hi Agus, Thanks for bringing this to our attention. We were indeed the victims of subdomain “
Jan 16
Nina Wliilam
,
Charles E Grant
2
Jan 16
Crux got hacked by illegal Gambling Site
Hi Nina, Thanks for bringing this to our attention. We were indeed the victims of subdomain “
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Crux got hacked by illegal Gambling Site
Hi Nina, Thanks for bringing this to our attention. We were indeed the victims of subdomain “
Jan 16
Malcolm Cook
,
lin...@uw.edu
3
9/19/23
crux spectral-counts input formats not including mzML and mzXML.
Hi again - sorry I just realized that I missed something in my explanation above. The input into
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crux spectral-counts input formats not including mzML and mzXML.
Hi again - sorry I just realized that I missed something in my explanation above. The input into
9/19/23
Vyacheslav Tretyachenko
,
Yang Lu
4
9/6/23
MS1 intensity from DIAmeter output
...and just to be sure, you are suggesting to replace https://github.com/crux-toolkit/crux-toolkit/
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MS1 intensity from DIAmeter output
...and just to be sure, you are suggesting to replace https://github.com/crux-toolkit/crux-toolkit/
9/6/23
Michael Pique
,
William S Noble
3
1/19/23
Tide-search Xcorr values seem wildly different from Thermo "PSMS" software values
Bill, thanks for looking at this so fast. I sent Andy Lin a description of what I did to extract the
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Tide-search Xcorr values seem wildly different from Thermo "PSMS" software values
Bill, thanks for looking at this so fast. I sent Andy Lin a description of what I did to extract the
1/19/23
Michael Pique
11/15/22
Can Crux identify peptides in Waters “MSe” files?
I've searched the support group in vain, and had no success with Bullseye (or Tide/comet): is it
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Can Crux identify peptides in Waters “MSe” files?
I've searched the support group in vain, and had no success with Bullseye (or Tide/comet): is it
11/15/22
Michael Pique
,
William S Noble
3
7/3/22
Tide-search "peptide-centric-search" output is missing "xcorr score" values.
Hi Michael, This bug has been fixed in the latest release of Crux. Thanks for pointing it out. Bill
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Tide-search "peptide-centric-search" output is missing "xcorr score" values.
Hi Michael, This bug has been fixed in the latest release of Crux. Thanks for pointing it out. Bill
7/3/22
Stanislav Felshtyn
,
Charles E Grant
2
5/25/22
Tutorials
Hi Stanislav, The URL in the screen shot you provided is incorrect. It reads crux.ms/tutorials/
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Tutorials
Hi Stanislav, The URL in the screen shot you provided is incorrect. It reads crux.ms/tutorials/
5/25/22
Caroline Labelle
,
William Stafford Noble
2
3/22/22
Using Crux toolkit on SILAC data
Hi Caroline, I am glad to hear that the Crux software is working for you. The example from the FAQ
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Using Crux toolkit on SILAC data
Hi Caroline, I am glad to hear that the Crux software is working for you. The example from the FAQ
3/22/22
Sami Pietilä
,
William Stafford Noble
2
3/22/22
FAIMS Support
No, sorry, we do not have FAIMS support at this time. If you want to tell us what that would entail,
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FAIMS Support
No, sorry, we do not have FAIMS support at this time. If you want to tell us what that would entail,
3/22/22
Shiri Tsour
,
William S Noble
3
1/24/22
PSM p-value error
Hi Bill, Thanks for your response. I was able to get it working properly with num-threads=1. I ran
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PSM p-value error
Hi Bill, Thanks for your response. I was able to get it working properly with num-threads=1. I ran
1/24/22
Jiali Yu
,
William S Noble
3
11/9/21
percolator source code link
Thank you for the quick fix! Jiali On Tue, Nov 9, 2021 at 1:54 PM William S Noble <thabangh@gmail.
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percolator source code link
Thank you for the quick fix! Jiali On Tue, Nov 9, 2021 at 1:54 PM William S Noble <thabangh@gmail.
11/9/21
William S Noble
,
William Stafford Noble
2
10/15/21
Announcing Crux v4.1
The Crux development team is pleased to announce the release of version 4.1 of the Crux tandem mass
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Announcing Crux v4.1
The Crux development team is pleased to announce the release of version 4.1 of the Crux tandem mass
10/15/21
Jiali Yu
,
William Stafford Noble
3
9/13/21
tide-search low retained rates
Hi Bill, Thank you for your suggestions, it was really helpful! I tried the param-medic and found my
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tide-search low retained rates
Hi Bill, Thank you for your suggestions, it was really helpful! I tried the param-medic and found my
9/13/21
Le Tung
,
William Stafford Noble
2
9/11/21
tide-index --mods-spec & extract matched b/y ions
Hi Tung, Yes, this behavior for a static mod on C is normal: --mods-spec <string> – The general
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tide-index --mods-spec & extract matched b/y ions
Hi Tung, Yes, this behavior for a static mod on C is normal: --mods-spec <string> – The general
9/11/21
Daryl W-M
,
Rita Chupalov
7
6/22/21
spectral-counts fails to process percolator output
Hi Rita. Thank you for the workaround; much appreciated. On Wed, Jun 23, 2021 at 7:42 AM Rita
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spectral-counts fails to process percolator output
Hi Rita. Thank you for the workaround; much appreciated. On Wed, Jun 23, 2021 at 7:42 AM Rita
6/22/21
Peppe
,
William S Noble
2
6/7/21
fasta database not found in tide-search
I also answered this on the issue tracker, where this issue was also raised: https://github.com/crux-
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fasta database not found in tide-search
I also answered this on the issue tracker, where this issue was also raised: https://github.com/crux-
6/7/21
William S Noble
4/8/21
Announcing Crux version 4.0 Inbox
The Crux development team is pleased to announce the release of version 4.0 of the Crux tandem mass
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Announcing Crux version 4.0 Inbox
The Crux development team is pleased to announce the release of version 4.0 of the Crux tandem mass
4/8/21
Alex Saltzman
,
William S Noble
7
2/22/21
Invalid cvParam accession "1003028"
Yes, alas, threading bugs in general are very hard to track down. This one has eluded us for a while.
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Invalid cvParam accession "1003028"
Yes, alas, threading bugs in general are very hard to track down. This one has eluded us for a while.
2/22/21
Joseph Harrison
, …
Rita Chupalov
3
2/11/21
Tide index unable to specify a modification that prevents cleavage
Hi Joseph, the problem is in the :T:T flags in 2K+114.0429:T:T modspec. These cleavage prevention
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Tide index unable to specify a modification that prevents cleavage
Hi Joseph, the problem is in the :T:T flags in 2K+114.0429:T:T modspec. These cleavage prevention
2/11/21
esv...@gmail.com
,
William S Noble
7
2/4/21
spectral-count issues regarding decoy database and protein quantification
Thanks for your work, Bill! Also, I didn't realize comet was using reversed decoys. You should
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spectral-count issues regarding decoy database and protein quantification
Thanks for your work, Bill! Also, I didn't realize comet was using reversed decoys. You should
2/4/21
abhishekdub...@gmail.com
,
William S Noble
2
1/11/21
Question on experimental aspect of Mass Spectrometry
Hi Ahbishek, My attempted answers are interleaved below. On Sun, Jan 10, 2021 at 3:06 AM abhishekdub.
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Question on experimental aspect of Mass Spectrometry
Hi Ahbishek, My attempted answers are interleaved below. On Sun, Jan 10, 2021 at 3:06 AM abhishekdub.
1/11/21
abhishekdub...@gmail.com
,
William S Noble
3
1/9/21
tide-index of Mus Musculus database
Hi Bill Thank you very much for your response. Indeed, I was able to get indexing done without using
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tide-index of Mus Musculus database
Hi Bill Thank you very much for your response. Indeed, I was able to get indexing done without using
1/9/21
Robot mantou
,
William Fondrie
5
12/11/20
How to understand the weight values in percolator.weights.txt
Hi Song, I'm glad to hear that using param-medic seems to have fixed things. I forgot to ask, but
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How to understand the weight values in percolator.weights.txt
Hi Song, I'm glad to hear that using param-medic seems to have fixed things. I forgot to ask, but
12/11/20
Robot mantou
,
William Fondrie
2
12/7/20
The CalcMass in make-pin.pin is not equal to theory mass
Thank you for your question and using crux. The "CalcMass" column in the make-pin.pin file
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The CalcMass in make-pin.pin is not equal to theory mass
Thank you for your question and using crux. The "CalcMass" column in the make-pin.pin file
12/7/20
Brian Connolly
, …
Charles E Grant
4
11/19/20
Crux comet does not write output files to the --output-dir
Please find attached the params file that was used. Brian On Thu, Nov 19, 2020 at 10:31 AM Charles E
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Crux comet does not write output files to the --output-dir
Please find attached the params file that was used. Brian On Thu, Nov 19, 2020 at 10:31 AM Charles E
11/19/20
William S Noble
,
Sangeetha R
7
9/20/20
Re: [crux-users] Crux PSM search identify very few PSM with q<=0.01
That really helped me. Thanks a lot for the response. The issue got solved now. On Sunday, September
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Re: [crux-users] Crux PSM search identify very few PSM with q<=0.01
That really helped me. Thanks a lot for the response. The issue got solved now. On Sunday, September
9/20/20
Sangeetha R
9/18/20
Crux PSM search identifies very few PSM with q<=0.01
Dear Team, I am a beginner in using the crux software. I have tried running the tide- search to
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Crux PSM search identifies very few PSM with q<=0.01
Dear Team, I am a beginner in using the crux software. I have tried running the tide- search to
9/18/20