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spctools-discuss
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spctools-discuss
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sudarshan kumar
Jan 2
killjob
Dear friends, I am trying to kill a job which was taking too much time. I even uninstalled the
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killjob
Dear friends, I am trying to kill a job which was taking too much time. I even uninstalled the
Jan 2
Xiao
, …
Luis Mendoza
4
12/24/20
Is there a threshold of min. peptide probability that ProteinProphet uses to pick the peptides?
Hello James, Yes, these values are still hard-coded. If you wish to test alternative values, you can
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Is there a threshold of min. peptide probability that ProteinProphet uses to pick the peptides?
Hello James, Yes, these values are still hard-coded. If you wish to test alternative values, you can
12/24/20
sudarshan kumar
,
Phillip Wilmarth
5
12/21/20
comet search parameters for TMT labeled tryptic peptides
Hi Sudarshan, I don't use the TPP much. It looks like InteractParser is trying to read a file it
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comet search parameters for TMT labeled tryptic peptides
Hi Sudarshan, I don't use the TPP much. It looks like InteractParser is trying to read a file it
12/21/20
Mehar Un Nissa
, …
Jason Winget
4
12/17/20
Related to St Peter tool in TPP
You would put 1 in that box, since you know you injected 1 ug. On Thursday, December 17, 2020 at 7:14
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Related to St Peter tool in TPP
You would put 1 in that box, since you know you injected 1 ug. On Thursday, December 17, 2020 at 7:14
12/17/20
sudarshan kumar
,
AZIZ ALNAKLI
2
12/15/20
Peptide sequence column in result contains modification mass
Hi Sud, I think you can do that with excel. Select the cells that have the modified peptides. Use the
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Peptide sequence column in result contains modification mass
Hi Sud, I think you can do that with excel. Select the cells that have the modified peptides. Use the
12/15/20
sudarshan kumar
,
David Shteynberg
3
12/15/20
iprophet is search showing blank page
Thank you David, I tried with another file. It worked. But can you please tell me about the
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iprophet is search showing blank page
Thank you David, I tried with another file. It worked. But can you please tell me about the
12/15/20
rita maria de Almeida
,
sudarshan kumar
3
12/15/20
Problems in search
Thank you. I will try that. Em ter., 15 de dez. de 2020 às 01:52, sudarshan kumar <kumarsudershan@
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Problems in search
Thank you. I will try that. Em ter., 15 de dez. de 2020 às 01:52, sudarshan kumar <kumarsudershan@
12/15/20
sudarshan kumar
,
Eric Deutsch
3
12/11/20
Endogenous peptide identification
Thank you so much Eric, I will use this.... Regards On Fri, Dec 11, 2020, 05:06 'Eric Deutsch
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Endogenous peptide identification
Thank you so much Eric, I will use this.... Regards On Fri, Dec 11, 2020, 05:06 'Eric Deutsch
12/11/20
Asif Ahmed
12/8/20
combine fractions, replicates and different parameters
Hi, I have two treatment groups and want to identify (& quantify) the peptides. 1. Metabolic
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combine fractions, replicates and different parameters
Hi, I have two treatment groups and want to identify (& quantify) the peptides. 1. Metabolic
12/8/20
shubha...@gmail.com
,
David Shteynberg
3
12/8/20
Select only top matching protein in spectrast
Dear David, Thanks for explaining the principle of multiple match. I was asking if there is any flag
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Select only top matching protein in spectrast
Dear David, Thanks for explaining the principle of multiple match. I was asking if there is any flag
12/8/20
Mehar Un Nissa
,
David Shteynberg
2
12/8/20
Query about TPP analysis
Hello Mehar, I am looking at the message that says you have 0 PSM in the input to the iProphet. This
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Query about TPP analysis
Hello Mehar, I am looking at the message that says you have 0 PSM in the input to the iProphet. This
12/8/20
Asif Ahmed
, …
David Shteynberg
8
12/2/20
command "C:/TPP/bin/PeptideProphetParser" failed
The script works perfectly without any error! Thanks for your help. On Thu, Dec 3, 2020 at 6:43 AM
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command "C:/TPP/bin/PeptideProphetParser" failed
The script works perfectly without any error! Thanks for your help. On Thu, Dec 3, 2020 at 6:43 AM
12/2/20
na jiang
,
Luis Mendoza
4
11/20/20
TPP seems never stop in windows......
Hi, Thanks for your answer. -I can see that "tandem.exe" processes is running by opening
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TPP seems never stop in windows......
Hi, Thanks for your answer. -I can see that "tandem.exe" processes is running by opening
11/20/20
Soroush F
,
Luis Mendoza
4
11/18/20
Not all the proteins in PeptideProphet appear in ProteinProphet
Hello Soroush, Great! Good to verify that it is working as designed. And you will not miss those zero
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Not all the proteins in PeptideProphet appear in ProteinProphet
Hello Soroush, Great! Good to verify that it is working as designed. And you will not miss those zero
11/18/20
AZIZ ALNAKLI
,
Eric Deutsch
8
11/11/20
maximum fasta file size
Hi, Comet does have a parameter for generating an internal decoy database: http://comet-ms.
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maximum fasta file size
Hi, Comet does have a parameter for generating an internal decoy database: http://comet-ms.
11/11/20
Miguel Cosenza
,
Luis Mendoza
3
11/9/20
Initiating Petunia GUI after TPP installation Windows Server 2019
Hi Miguel, Glad that you were able to solve this, and sorry we could not help, as we do not have
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Initiating Petunia GUI after TPP installation Windows Server 2019
Hi Miguel, Glad that you were able to solve this, and sorry we could not help, as we do not have
11/9/20
Emily Kawaler
, …
David Shteynberg
15
11/6/20
ProteinProphet sticking in findDegenGroups3
Not a problem! In the end I decided just to remove all of the titins from my database - it shouldn
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ProteinProphet sticking in findDegenGroups3
Not a problem! In the end I decided just to remove all of the titins from my database - it shouldn
11/6/20
Nathan Wamsley
, …
Luis Mendoza
3
11/6/20
Linux Build Error
Hi Nathan, In case you want to build something that closely resembles 5.2.0, you can follow the steps
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Linux Build Error
Hi Nathan, In case you want to build something that closely resembles 5.2.0, you can follow the steps
11/6/20
jane n
, …
Mark Athanason
7
10/22/20
DIA to mzML question
Thanks! On Thu, 22 Oct 2020 at 17:11, Mark Athanason <mark.athanason@gmail.com> wrote: If you
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DIA to mzML question
Thanks! On Thu, 22 Oct 2020 at 17:11, Mark Athanason <mark.athanason@gmail.com> wrote: If you
10/22/20
Jieyi Xiong
10/21/20
Run TPP on linux without root
Hi I want to run TPP on a Linux server of our institute. However, I'm not a super user so I
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Run TPP on linux without root
Hi I want to run TPP on a Linux server of our institute. However, I'm not a super user so I
10/21/20
Juergen Bartel
,
Eric Deutsch
3
10/20/20
SpectraST LibraryBuilding Decoys
Hi Eric, Thank you for the answer. I will try whether I could build such a fasta from the log file.
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SpectraST LibraryBuilding Decoys
Hi Eric, Thank you for the answer. I will try whether I could build such a fasta from the log file.
10/20/20
Wenhao
, …
Eric Deutsch
4
10/13/20
TPP 5.2.0 installation error CentOS 7.8
You can get a recipe for using TPP with Docker here: http://tools.proteomecenter.org/wiki/index.php?
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TPP 5.2.0 installation error CentOS 7.8
You can get a recipe for using TPP with Docker here: http://tools.proteomecenter.org/wiki/index.php?
10/13/20
vipulb...@gmail.com
, …
Robert Winkler
6
10/5/20
X!Tandem- Help please
Hi, eg I used X!Tandem in the past when searching for point mutations in proteins. For most tasks, I
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X!Tandem- Help please
Hi, eg I used X!Tandem in the past when searching for point mutations in proteins. For most tasks, I
10/5/20
vipulb...@gmail.com
, …
Robert Winkler
3
10/5/20
LFQ
For LFQ and sample comparison, you also could try ProtyQuant, which uses TPP pepXML (PeptideProphet
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LFQ
For LFQ and sample comparison, you also could try ProtyQuant, which uses TPP pepXML (PeptideProphet
10/5/20
Laura Muehlbauer
, …
Jason Winget
4
10/2/20
Converting Orbitrap Eclipse files to mzML
Both worked! Thanks so much! On Thursday, October 1, 2020 at 10:55:24 AM UTC-5 jwi...@gmail.com wrote
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Converting Orbitrap Eclipse files to mzML
Both worked! Thanks so much! On Thursday, October 1, 2020 at 10:55:24 AM UTC-5 jwi...@gmail.com wrote
10/2/20
AZIZ ALNAKLI
,
Luis Mendoza
6
9/28/20
TPP tutorial issue
Hello Aziz, X!Tandem parameters are in XML format. You can learn about them at their website: https:/
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TPP tutorial issue
Hello Aziz, X!Tandem parameters are in XML format. You can learn about them at their website: https:/
9/28/20
Robert
,
Luis Mendoza
2
9/25/20
ProtyQuant for comparing TPP samples (.pepXML)
This looks great! Thank you. Robert! --Luis On Fri, Sep 25, 2020 at 1:34 PM Robert <robert.winkler
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ProtyQuant for comparing TPP samples (.pepXML)
This looks great! Thank you. Robert! --Luis On Fri, Sep 25, 2020 at 1:34 PM Robert <robert.winkler
9/25/20
David Shteynberg
,
Lindsey Ulmer
2
9/16/20
Re: [spctools-discuss] Crosslink FDR from PeptideProphet
Thanks! I do have less error tables than I would expect. When I ran PeptideProphet, I received the
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Re: [spctools-discuss] Crosslink FDR from PeptideProphet
Thanks! I do have less error tables than I would expect. When I ran PeptideProphet, I received the
9/16/20
Annie Ha
9/15/20
Consensus spectral library with split RT
Hi, I have generated spectral libraries following the Nature Protocols paper in 2015. There are
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Consensus spectral library with split RT
Hi, I have generated spectral libraries following the Nature Protocols paper in 2015. There are
9/15/20
Francesco Demetrio Lofaro
,
Jimmy Eng
2
9/14/20
Comet fixed and variable modifications
Carbamidomethylation has a modification mass of 57.021464. To apply it to each peptide's n-
unread,
Comet fixed and variable modifications
Carbamidomethylation has a modification mass of 57.021464. To apply it to each peptide's n-
9/14/20