spctools-discuss

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Will Comstock, David Shteynberg6

Apr 15

PTMProphet command failure (for larger datasets?)

Will, Thanks for the update! Cheers, David On Thu, Apr 15, 2021, 6:22 AM Will Comstock <wc622@

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PTMProphet command failure (for larger datasets?)

Will, Thanks for the update! Cheers, David On Thu, Apr 15, 2021, 6:22 AM Will Comstock <wc622@

Apr 15

Oded, David Shteynberg11

Apr 14

Changes in number of peptides identifications in TPP 6.0 RC

Hi Oded, I ran the Decoy Peptide Validation tool on both of the file you sent, using DECOY1 as decoy

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Changes in number of peptides identifications in TPP 6.0 RC

Hi Oded, I ran the Decoy Peptide Validation tool on both of the file you sent, using DECOY1 as decoy

Apr 14

Benoit Kunath, … Eric Deutsch3

Apr 13

You can convert the sptxt format to msp with: rename mylibrary.sptxt mylibrary.msp sptxt and msp are

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You can convert the sptxt format to msp with: rename mylibrary.sptxt mylibrary.msp sptxt and msp are

Apr 13

Hugo Amedei, David Shteynberg2

Apr 13

SpectraST fail to open my files in windows and in Linux as well

Hello Hugo, It appears from the error message that SpectraST is unable to find any PSMs having

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SpectraST fail to open my files in windows and in Linux as well

Hello Hugo, It appears from the error message that SpectraST is unable to find any PSMs having

Apr 13

Apr 2

Add Additional fields in spectrast-generated spectral libraries

Hello, I am currently using SpectraST to generate spectral libraries from a TSV and I am aware that

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Add Additional fields in spectrast-generated spectral libraries

Hello, I am currently using SpectraST to generate spectral libraries from a TSV and I am aware that

Apr 2

AZIZ ALNAKLI, … Jimmy Eng14

Mar 25

maximum fasta file size

Yes, the two parameters I specified in my post. On Thu, Mar 25, 2021 at 3:17 PM AZIZ ALNAKLI <aziz

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maximum fasta file size

Yes, the two parameters I specified in my post. On Thu, Mar 25, 2021 at 3:17 PM AZIZ ALNAKLI <aziz

Mar 25

Panyue Chen, David Shteynberg9

Mar 10

job end with error when following PTMprophet tutorial

Hi Panyue, Thanks for confirming that it works. I think after you run that code from the commandline

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job end with error when following PTMprophet tutorial

Hi Panyue, Thanks for confirming that it works. I think after you run that code from the commandline

Mar 10

Mar 9

end with error when follow PTMprophet tutorial

Hi there, I was following the PTMprophet tutorial v0.4.0 on my windows system, which analyzes a

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end with error when follow PTMprophet tutorial

Hi there, I was following the PTMprophet tutorial v0.4.0 on my windows system, which analyzes a

Mar 9

Juergen Bartel, Eric Deutsch4

Feb 24

SpectraST LibraryBuilding Decoys

Dear all, if someone else needs mapping of the shuffled decoy spectra to proteins (eg for downstream

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SpectraST LibraryBuilding Decoys

Dear all, if someone else needs mapping of the shuffled decoy spectra to proteins (eg for downstream

Feb 24

Matthew Russell, Juergen Bartel2

Feb 22

propogating retention time from .ms2 to .sptxt with spectrast

Dear Matthew, did you find a solution for this? I have the exact same question as I also try use a

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propogating retention time from .ms2 to .sptxt with spectrast

Dear Matthew, did you find a solution for this? I have the exact same question as I also try use a

Feb 22

Asif Ahmed, David Shteynberg10

Feb 12

Error in fitted models for MSgf+ search

I combined fractions on peptide-prophet stage, and subsequently run i-prophet and protein prophet.

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Error in fitted models for MSgf+ search

I combined fractions on peptide-prophet stage, and subsequently run i-prophet and protein prophet.

Feb 12

Ladislav Cséfalvay, Luis Mendoza3

Feb 11

TPP working directory - how to change

Hi Luis, Thank you so much! Laco Dne úterý 9. února 2021 v 23:13:00 UTC+1 uživatel Luis napsal: Hello

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TPP working directory - how to change

Hi Luis, Thank you so much! Laco Dne úterý 9. února 2021 v 23:13:00 UTC+1 uživatel Luis napsal: Hello

Feb 11

Cethgar XXX, David Shteynberg2

Jan 25

Tutorial DIA Analysis

Dear Cethgar, Thanks for pointing that out, we have updated the link. Please try again and let us

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Tutorial DIA Analysis

Dear Cethgar, Thanks for pointing that out, we have updated the link. Please try again and let us

Jan 25

giangiacomo beretta, … Luis Mendoza6

Jan 24

Error generation while converting raw files

Hello Giangiacomo, You can use the Lib2html tool to convert an splib into a webpage with clickable

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Error generation while converting raw files

Hello Giangiacomo, You can use the Lib2html tool to convert an splib into a webpage with clickable

Jan 24

Soroush F, David Shteynberg5

Jan 21

When to use "Decoy hits to pin down negative distribution" in PeptideProphet

Thanks so much David for your response. It makes sense. All the best, Soroush On Wednesday, January

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When to use "Decoy hits to pin down negative distribution" in PeptideProphet

Thanks so much David for your response. It makes sense. All the best, Soroush On Wednesday, January

Jan 21

JWang Lu, David Shteynberg2

Jan 20

How could I run PTMProphet correctly?

Dear JWangLu, This message would come up when the software tool attempts to read the mzML file that

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How could I run PTMProphet correctly?

Dear JWangLu, This message would come up when the software tool attempts to read the mzML file that

Jan 20

sudarshan kumar

Jan 2

Dear friends, I am trying to kill a job which was taking too much time. I even uninstalled the

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Dear friends, I am trying to kill a job which was taking too much time. I even uninstalled the

Jan 2

Xiao, … Luis Mendoza4

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 Wilmarth5

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 Winget4

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 ALNAKLI2

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 Shteynberg3

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 kumar3

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 Deutsch3

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

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 Shteynberg3

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 Shteynberg2

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 Shteynberg8

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 Mendoza4

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 Mendoza4

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

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