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sudarshan kumar
Sep 25
I need to acquisition settings for running silac samples (only heavy lysine (13 C6 and 15N2 and no argininge)
Hi can anyone please share or refer to me the aquisition settings and search settings/script for
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I need to acquisition settings for running silac samples (only heavy lysine (13 C6 and 15N2 and no argininge)
Hi can anyone please share or refer to me the aquisition settings and search settings/script for
Sep 25
sudarshan kumar
,
mhoo...@systemsbiology.org
6
Sep 25
Stpeter negative SIn value?
Ok Thank you. that makes sense. I should filter the list first before Stpeter quantitation. On
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Stpeter negative SIn value?
Ok Thank you. that makes sense. I should filter the list first before Stpeter quantitation. On
Sep 25
Sanclayver Araújo
Sep 19
MASH explorer
Good Morning! Does anyone know the link to download MASH explorer software? -- Sanclayver Corrêa
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MASH explorer
Good Morning! Does anyone know the link to download MASH explorer software? -- Sanclayver Corrêa
Sep 19
Jason Winget
,
David Shteynberg
2
Sep 1
StPeter error - Could not read spectra
Hey Jason, If you are able to compress the dataset directory and share it I would be happy to
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StPeter error - Could not read spectra
Hey Jason, If you are able to compress the dataset directory and share it I would be happy to
Sep 1
sudarshan kumar
,
mhoo...@systemsbiology.org
2
Aug 16
Stpeter
1. No - see your other thread (https://groups.google.com/g/spctools-discuss/c/yDBVf5nHxmM) for a
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Stpeter
1. No - see your other thread (https://groups.google.com/g/spctools-discuss/c/yDBVf5nHxmM) for a
Aug 16
Emma Whittington
,
Luis Mendoza
3
Aug 7
converting prot.xml to tsv/something else
Thank you. A co-worker with a windows machine tried the ProtXMLViewer with the GUI. However, I'm
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converting prot.xml to tsv/something else
Thank you. A co-worker with a windows machine tried the ProtXMLViewer with the GUI. However, I'm
Aug 7
Debojyoti Pal
2
Aug 4
Regarding protein prophet input - what difference does it make if I use PTM prophet file or not
And should I tick the "input is from iProphet" if I am using the PTM Prophet file generated
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Regarding protein prophet input - what difference does it make if I use PTM prophet file or not
And should I tick the "input is from iProphet" if I am using the PTM Prophet file generated
Aug 4
sophie culos
, …
David Shteynberg
7
Aug 1
Navigating peptideSieve Tips/Tricks?
Yes! I am doing everything in the bin directory for the test to make it easier to specify paths. My
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Navigating peptideSieve Tips/Tricks?
Yes! I am doing everything in the bin directory for the test to make it easier to specify paths. My
Aug 1
Tanmay Singh
,
Luis Mendoza
2
Aug 1
Problem with PeptideProphet
Hello Tanmay, How did you generate the input pepXML files? Which search engine did you use? Are you
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Problem with PeptideProphet
Hello Tanmay, How did you generate the input pepXML files? Which search engine did you use? Are you
Aug 1
Debojyoti Pal
,
Luis Mendoza
5
Aug 1
Variable mod query in COMET
I meant that they would come up with something to get it done with only variable modifications. By
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Variable mod query in COMET
I meant that they would come up with something to get it done with only variable modifications. By
Aug 1
Debojyoti Pal
2
Aug 1
Regarding total intensity normalization in LIBRA
Can anyone help me with this, please? On Monday, July 31, 2023 at 11:39:47 PM UTC+5:30 Debojyoti Pal
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Regarding total intensity normalization in LIBRA
Can anyone help me with this, please? On Monday, July 31, 2023 at 11:39:47 PM UTC+5:30 Debojyoti Pal
Aug 1
Carlo de Oliveira Martins
,
Luis Mendoza
3
Jul 26
Access to Mascot file results
These are valuable tips. I will check if our Admin can open this port. Definitely, if I am able to
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Access to Mascot file results
These are valuable tips. I will check if our Admin can open this port. Definitely, if I am able to
Jul 26
Luis Mendoza
, …
Luis
9
Jul 21
Upcoming Trans-Proteomic Pipeline (TPP) course
Hello Sud, You can find some info and links to the download instructions and release notes at our
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Upcoming Trans-Proteomic Pipeline (TPP) course
Hello Sud, You can find some info and links to the download instructions and release notes at our
Jul 21
suzmcde...@gmail.com
, …
Luis Mendoza
8
Jul 18
Next proteomics informatics course?
Hi Don, We'll look into setting up a Zoom option and get back to you soon. Thank you for your
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Next proteomics informatics course?
Hi Don, We'll look into setting up a Zoom option and get back to you soon. Thank you for your
Jul 18
muriell...@gmail.com
, …
David Shteynberg
10
Jun 28
ProteinProphet output number of unique peptides vs total number of peptides
Hi Brian, I just confirmed in the code that it is counted here when the weight of the peptide is
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ProteinProphet output number of unique peptides vs total number of peptides
Hi Brian, I just confirmed in the code that it is counted here when the weight of the peptide is
Jun 28
Emma Whittington
,
Luis Mendoza
2
Jun 19
TPP Tandem input files
Hello Emma, According to this, X!Tandem is indeed able to process MGF files: https://www.thegpm.org/
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TPP Tandem input files
Hello Emma, According to this, X!Tandem is indeed able to process MGF files: https://www.thegpm.org/
Jun 19
Luis Mendoza
Jun 2
TPP @ ASMS 2023 -- Posters, Tuesday Workshop, and Bioinformatics Hub
Hello everyone, Next week the TPP software tools team will be attending and giving several
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TPP @ ASMS 2023 -- Posters, Tuesday Workshop, and Bioinformatics Hub
Hello everyone, Next week the TPP software tools team will be attending and giving several
Jun 2
Sanclayver Araújo
, …
Jimmy Eng
4
May 25
Proteome discoverer users guide
Thank you very much to all On Thu, 25 May 2023 at 14:07 Jimmy Eng <jke...@gmail.com> wrote: I
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Proteome discoverer users guide
Thank you very much to all On Thu, 25 May 2023 at 14:07 Jimmy Eng <jke...@gmail.com> wrote: I
May 25
felipe velasquez
, …
Jimmy Eng
5
May 5
protein validation
Dear Jimmy Thanks for your reply. I will use the correct database. Felipe El jue, 4 may 2023 a las 15
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protein validation
Dear Jimmy Thanks for your reply. I will use the correct database. Felipe El jue, 4 may 2023 a las 15
May 5
Scott Starry
,
David Shteynberg
2
May 5
Installer for TPP 6.3.0 does not recognize existence of MS VC++ 2015-2022
Hello Scott, You should be able to get around this issue by unchecking the option to download and
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Installer for TPP 6.3.0 does not recognize existence of MS VC++ 2015-2022
Hello Scott, You should be able to get around this issue by unchecking the option to download and
May 5
Luis Mendoza
May 4
TPP 6.3.0 Release is now available
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.3.0 "Arcus" We are
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TPP 6.3.0 Release is now available
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.3.0 "Arcus" We are
May 4
felipe velasquez
,
Luis Mendoza
5
Apr 29
Problem with PTMprophet
Thanks Luis for your quick response. Finally, I could resolve the problem. As a beginner user, I made
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Problem with PTMprophet
Thanks Luis for your quick response. Finally, I could resolve the problem. As a beginner user, I made
Apr 29
Will Comstock
, …
Luis Mendoza
5
Apr 7
SILAC quantification with targeted SIM
Hi Will, Glad you got this to work! A potentially quicker solution is to enter those extra flags in
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SILAC quantification with targeted SIM
Hi Will, Glad you got this to work! A potentially quicker solution is to enter those extra flags in
Apr 7
Yasir Ahmed
,
Luis Mendoza
6
Mar 28
Output sequence coverage info
Sure thing. And to answer your original question: there is a command-line tool in TPP called
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Output sequence coverage info
Sure thing. And to answer your original question: there is a command-line tool in TPP called
Mar 28
felipe velasquez
, …
Eric Deutsch
7
Mar 28
SSL problem
Hi Felipe, great! Yes, if you have questions, please post them to the list here. I may not always be
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SSL problem
Hi Felipe, great! Yes, if you have questions, please post them to the list here. I may not always be
Mar 28
Aarthie Senathirajah
Mar 23
How does RT train work?
Hi I was wondering if there was a tutorial on how to use RT Train? I'm not sure what kind of
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How does RT train work?
Hi I was wondering if there was a tutorial on how to use RT Train? I'm not sure what kind of
Mar 23
Priti Panchal
,
Eric Deutsch
4
Feb 22
MSFragger param
ah, I see, okay, sure, I put one here: http://www.tppms.org/tmp/msfragger.params On Tue, Feb 21, 2023
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MSFragger param
ah, I see, okay, sure, I put one here: http://www.tppms.org/tmp/msfragger.params On Tue, Feb 21, 2023
Feb 22
Luis Mendoza
Feb 17
TPP 6.2.0 Release is now available
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.2.0 "Nacreous" We are
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TPP 6.2.0 Release is now available
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.2.0 "Nacreous" We are
Feb 17
Aarthie Senathirajah
,
Luis Mendoza
2
Feb 14
Analyzing Metaproteomic Data
Hello, The version of msconvert that is shipped with TPP is a couple of years old and does not know
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Analyzing Metaproteomic Data
Hello, The version of msconvert that is shipped with TPP is a couple of years old and does not know
Feb 14
reeju
Jan 27
not getting significant hits while analyzing .raw file
Hi all, I have been trying to analyze .raw file generated on waters synapt of standard protein BSA
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not getting significant hits while analyzing .raw file
Hi all, I have been trying to analyze .raw file generated on waters synapt of standard protein BSA
Jan 27