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Farshad AbdollahNia
,
David Shteynberg
12
Feb 29
PeptideProphet with X!Tandem
Hi David, Today I got a chance to update to 6.3.3 and now I am able to reproduce your results --
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PeptideProphet with X!Tandem
Hi David, Today I got a chance to update to 6.3.3 and now I am able to reproduce your results --
Feb 29
Sam Whedon
, …
Jimmy Eng
4
Feb 20
PepXML > spectrum > top hits viewer issue - Comet
Hi all, Thanks for the helpful suggestions. Fortunately, if the filepath for the mzML data is
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PepXML > spectrum > top hits viewer issue - Comet
Hi all, Thanks for the helpful suggestions. Fortunately, if the filepath for the mzML data is
Feb 20
Max Brazhnikov
,
Luis Mendoza
2
Feb 20
PepXML Schema v1.23
Hello Max, Thank you for bringing this to our attention. I have added the file and updated the wiki.
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PepXML Schema v1.23
Hello Max, Thank you for bringing this to our attention. I have added the file and updated the wiki.
Feb 20
Tuan Anh Nguyen Van
,
Eric Deutsch
2
Feb 5
How to assess quality of assembly of unmapped reads ?
Hi, it sounds like you question is related to DNA sequencing, not proteomics. The TPP tools are
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How to assess quality of assembly of unmapped reads ?
Hi, it sounds like you question is related to DNA sequencing, not proteomics. The TPP tools are
Feb 5
David Shteynberg
Jan 30
Bug Discovery in decoyFastaGenerator.pl
Dear TPP Users, We have recently discovered and patched a bug in the TPP tool decoyFastaGenerator.pl.
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Bug Discovery in decoyFastaGenerator.pl
Dear TPP Users, We have recently discovered and patched a bug in the TPP tool decoyFastaGenerator.pl.
Jan 30
2kl...@gmail.com
Jan 30
Xpress-related Discrepancy between pepXML and XPressPeptideUpdateParser.
Hi everybody,In reference to my report from 2022 (https://groups.google.com/g/spctools-discuss/c/
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Xpress-related Discrepancy between pepXML and XPressPeptideUpdateParser.
Hi everybody,In reference to my report from 2022 (https://groups.google.com/g/spctools-discuss/c/
Jan 30
Alex Gao
, …
Luis Mendoza
8
Jan 24
Trouble converting Waters.RAW with TPP msconvert
Hello Alex, Glad that you were able to get to the bottom of this issue and hope you have been able to
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Trouble converting Waters.RAW with TPP msconvert
Hello Alex, Glad that you were able to get to the bottom of this issue and hope you have been able to
Jan 24
Juergen Bartel
Jan 22
Lib2HTML truncates peptide sequences after modification
Dear all, I have recently generated an in-silico spectral library for several peptides which may
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Lib2HTML truncates peptide sequences after modification
Dear all, I have recently generated an in-silico spectral library for several peptides which may
Jan 22
Will Comstock
,
Luis Mendoza
4
Jan 12
TPP installation tutorials 404 errors?
Hi Will, Thanks for the reply and extra info. This strange redirects may be connected to IT changes
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TPP installation tutorials 404 errors?
Hi Will, Thanks for the reply and extra info. This strange redirects may be connected to IT changes
Jan 12
Aarthie Senathirajah
, …
David Shteynberg
8
12/5/23
Hi I cannot access the gui anymore is there something I'm missing
Thank you for that. Normally you would know the version installed based on the filename of the
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Hi I cannot access the gui anymore is there something I'm missing
Thank you for that. Normally you would know the version installed based on the filename of the
12/5/23
sudarshan kumar
, …
David Shteynberg
16
12/4/23
running ASAPratio for SILAC data
Of course, I am glad to help. The old and the new versions should run faster on the centroided data.
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running ASAPratio for SILAC data
Of course, I am glad to help. The old and the new versions should run faster on the centroided data.
12/4/23
sudarshan kumar
,
Jimmy Eng
5
11/30/23
EXpress in SILAC
I thought I did. Here's what I wrote regarding XPRESS: It simply reports light area to heavy area
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EXpress in SILAC
I thought I did. Here's what I wrote regarding XPRESS: It simply reports light area to heavy area
11/30/23
sudarshan kumar
,
David Shteynberg
3
11/22/23
sud silac asapratio
110623_Silac_TEST_01.mzML 110623_Sud_LH_TEST_01.raw 110623_Sud_LH_TEST_02.mzML 110623_Sud_LH_TEST_02.
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sud silac asapratio
110623_Silac_TEST_01.mzML 110623_Sud_LH_TEST_01.raw 110623_Sud_LH_TEST_02.mzML 110623_Sud_LH_TEST_02.
11/22/23
Longping Fu
, …
David Shteynberg
5
11/18/23
Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization
Dear David, Thank you for providing your suggestions. I implemented your advice by including all
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Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization
Dear David, Thank you for providing your suggestions. I implemented your advice by including all
11/18/23
Iryna Abramchuk
, …
sudarshan kumar
10
11/16/23
XPRESS peak intensity value
Do we have any dedicated discussion group for SILAC using aspartio and express? On Tuesday, November
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XPRESS peak intensity value
Do we have any dedicated discussion group for SILAC using aspartio and express? On Tuesday, November
11/16/23
sudarshan kumar
2
11/15/23
I need help with silac search using a a combined file from xtandem and comet
in the tutorial page, In ASPARatioit shows- a. In the “XPRESS Options” pane select “RUN XPRESS”. i.
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I need help with silac search using a a combined file from xtandem and comet
in the tutorial page, In ASPARatioit shows- a. In the “XPRESS Options” pane select “RUN XPRESS”. i.
11/15/23
sudarshan kumar
11/2/23
workflow for SILAC analysis
Hi, Can anyone please share with me the simple step by step workflow of SILAC data analysis. I have a
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workflow for SILAC analysis
Hi, Can anyone please share with me the simple step by step workflow of SILAC data analysis. I have a
11/2/23
Debojyoti Pal
,
Eric Deutsch
3
10/7/23
Feature request for LIBRA
Dear Eric Yes, I have considered that. I am using iTRAQ though and hence I was hoping the features
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Feature request for LIBRA
Dear Eric Yes, I have considered that. I am using iTRAQ though and hence I was hoping the features
10/7/23
Will Comstock
,
Eric Deutsch
3
10/6/23
Optimal hardware for TPP server?
Thank you Eric, this is very good to know! We'll probably stick with something similar to our
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Optimal hardware for TPP server?
Thank you Eric, this is very good to know! We'll probably stick with something similar to our
10/6/23
sudarshan kumar
9/25/23
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
9/25/23
sudarshan kumar
,
mhoo...@systemsbiology.org
6
9/25/23
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
9/25/23
Sanclayver Araújo
9/19/23
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
9/19/23
Jason Winget
,
David Shteynberg
2
9/1/23
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
9/1/23
sudarshan kumar
,
mhoo...@systemsbiology.org
2
8/16/23
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
8/16/23
Emma Whittington
,
Luis Mendoza
3
8/7/23
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
8/7/23
Debojyoti Pal
2
8/4/23
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
8/4/23
sophie culos
, …
David Shteynberg
7
8/1/23
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
8/1/23
Tanmay Singh
,
Luis Mendoza
2
8/1/23
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
8/1/23
Debojyoti Pal
,
Luis Mendoza
5
8/1/23
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
8/1/23
Debojyoti Pal
2
8/1/23
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
8/1/23