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nicky bright
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Erik Johnson
,
jke...@gmail.com
7
Jan 22
Comet returning PSM with unexpected m/z PPM differences
Erik, Here's an explanation of the "isotope_error" parameter in Comet. Your search was
unread,
Comet returning PSM with unexpected m/z PPM differences
Erik, Here's an explanation of the "isotope_error" parameter in Comet. Your search was
Jan 22
Erik Johnson
, …
Attila Kertesz-Farkas
4
10/22/25
"Could not convert string '-nan'" error
Hi Erik, Im glad you found the issue. But nan is still not accepted in the search results. Could you
unread,
"Could not convert string '-nan'" error
Hi Erik, Im glad you found the issue. But nan is still not accepted in the search results. Could you
10/22/25
Erik Johnson
,
William Stafford Noble
2
10/21/25
Trouble replicating assign-confidence results
Hi Erik, The method used in assign-confidence is different from the ones in the papers you are
unread,
Trouble replicating assign-confidence results
Hi Erik, The method used in assign-confidence is different from the ones in the papers you are
10/21/25
Erik Johnson
,
jke...@gmail.com
3
10/21/25
Trouble reimplementing xcorr calculation in Python
Thanks Jimmy. Those are very helpful! On Thursday, October 16, 2025 at 11:39:17 PM UTC+2 jke...@gmail
unread,
Trouble reimplementing xcorr calculation in Python
Thanks Jimmy. Those are very helpful! On Thursday, October 16, 2025 at 11:39:17 PM UTC+2 jke...@gmail
10/21/25
Erik Johnson
,
William Stafford Noble
3
6/13/25
Which PSMs does assign-confidence return?
Ahhh! You're absolutely right. Thank you, Bill! On Fri, Jun 13, 2025 at 1:51 PM William Stafford
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Which PSMs does assign-confidence return?
Ahhh! You're absolutely right. Thank you, Bill! On Fri, Jun 13, 2025 at 1:51 PM William Stafford
6/13/25
Erik Johnson
, …
Jimmy Eng
4
6/13/25
Seeming error in delta_cn in Comet output via crux
Thanks Jimmy and Mike! Makes sense. I've got another question that I'll open another thread
unread,
Seeming error in delta_cn in Comet output via crux
Thanks Jimmy and Mike! Makes sense. I've got another question that I'll open another thread
6/13/25
Charles E Grant
4/9/24
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
4/9/24
Tang888
,
William Stafford Noble
3
4/1/24
Error when creating index
By the way, I noticed that you tried to specify three different types of mods like this: --mods-spec
unread,
Error when creating index
By the way, I noticed that you tried to specify three different types of mods like this: --mods-spec
4/1/24
agus rungkad
,
Charles E Grant
2
1/16/24
hacked domain
Hi Agus, Thanks for bringing this to our attention. We were indeed the victims of subdomain “
unread,
hacked domain
Hi Agus, Thanks for bringing this to our attention. We were indeed the victims of subdomain “
1/16/24
Nina Wliilam
,
Charles E Grant
2
1/16/24
Crux got hacked by illegal Gambling Site
Hi Nina, Thanks for bringing this to our attention. We were indeed the victims of subdomain “
unread,
Crux got hacked by illegal Gambling Site
Hi Nina, Thanks for bringing this to our attention. We were indeed the victims of subdomain “
1/16/24
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/
unread,
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
unread,
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
unread,
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