Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization

2023-11-18 Thread Longping Fu 
Dear David, 

Thank you for providing your suggestions. I implemented your advice by 
including all variable modifications in the search, and the warning 
messages did not appear. 

I appreciate your assistance.

Sincerely,
Longping

在2023年11月17日星期五 UTC-5 20:49:25 写道：

> Thanks Longping, I got your files.
>
> On Nov 17, 2023, at 5:21 PM, Longping Fu  wrote:
>
> Dear David,
>
> I appreciate your swift response. I've compressed the pepXML and mzML 
> files and uploaded them to Google Drive. You can access them through the 
> following link: 
> https://drive.google.com/file/d/1P463uxdvw67ZI7axiZO1OZOIlEZZg5qh/view?usp=sharing
>
> Kindly confirm if you can successfully open the files.
>
> Additionally, I'll be following your suggestion to include all variable 
> modifications and check for any remaining warning messages.
>
> Thank you for your assistance.
>
> Sincerely,
> Longping
>
> 在2023年11月17日星期五 UTC-5 16:20:11 写道：
>
> Dear Longping,
>
> Maybe you can compress your analysis pepXML and mzML files and post them 
> somewhere so I can replicate the issue locally?
>
> Meanwhile, you can try the specifying all variable mods used in the 
> search, when you run PTMProphet by changing the modification string as 
> follows:
>  M:15.9949,n:42.1016,STC:299.123,C:57.02146
>
>
> Cheers!
>
> -David
>
>
>
>
> On Fri, Nov 17, 2023 at 1:02 PM Longping Fu  wrote:
>
> I am currently working with PTMProphet in TPP version 6.3.3 for PTM 
> localization. While PTMProphet successfully completes the task, I am 
> encountering a significant number of warning messages in the console.
>
> To provide some context, my workflow involves utilizing MSFragger as the 
> search engine to convert raw files to mzML files and then searching against 
> a database. For the modification parameters, I have set M 15.9949, N-term 
> 42.1016, STC 299.123, and C 57.02146 as variable modifications, with no 
> fixed modifications specified.
>
> Upon obtaining the pepXML file from MSFragger, I employed Percolator for 
> PSM validation using the following settings: *--only-psms --no-terminate 
> --post-processing-tdc*. The resulting pepxml file was then processed with 
> PTMProphet using the command: *STC:299.123 MINPROB=0.5 MODPREC=0 
> FRAGPPMTOL=15 NOSTACK MAXTHREADS=1*. 
>
> However, during the PTMProphet processing, I encountered warning messages 
> similar to the following:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
> S[386]CNGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD 
> (SpectraST::Peptide) = S[386]CNGGSHPR Neutral Computed Mass for Evaluation 
> = 1212.51 PPM difference = 33487.5[INFO:] please check your specified 
> modification masses for precision or adjust MODPREC= parameter 
> ...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
> SC[402]NGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD 
> (SpectraST::Peptide) = SC[402]NGGSHPR Neutral Computed Mass for Evaluation 
> = 1212.51 PPM difference = 33487.5[INFO:] please check your specified 
> modification masses for precision or adjust MODPREC= parameter 
> ...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
> SCNGGS[386]HPR Neutral Mass (from pepXML) = 1254.52 BAD 
> (SpectraST::Peptide) = SCNGGS[386]HPR Neutral Computed Mass for Evaluation 
> = 1212.51 PPM difference = 33487.5[INFO:] please check your specified 
> modification masses for precision or adjust MODPREC= parameter ...*
>
> This pattern repeats for various peptides, indicating that PTMProphet is 
> struggling to localize modifications on S, T, or C. The tool suggests 
> adjusting parameters, specifically the MODPREC= parameter.
>
> Has anyone encountered a similar issue with PTMProphet and successfully 
> addressed it? I would greatly appreciate any insights, advice, or 
> suggestions regarding this matter.
>
> -- 
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> "spctools-discuss" group.
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>  
> 
> .
>
>
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>  
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> .
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>
>

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Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization

2023-11-17 Thread David Shteynberg 
Thanks Longping, I got your files.

> On Nov 17, 2023, at 5:21 PM, Longping Fu  wrote:
> 
> Dear David,
> 
> I appreciate your swift response. I've compressed the pepXML and mzML files 
> and uploaded them to Google Drive. You can access them through the following 
> link: 
> https://drive.google.com/file/d/1P463uxdvw67ZI7axiZO1OZOIlEZZg5qh/view?usp=sharing
> 
> Kindly confirm if you can successfully open the files.
> 
> Additionally, I'll be following your suggestion to include all variable 
> modifications and check for any remaining warning messages.
> 
> Thank you for your assistance.
> 
> Sincerely,
> Longping
> 
> 在2023年11月17日星期五 UTC-5 16:20:11 写道：
> Dear Longping,
> 
> Maybe you can compress your analysis pepXML and mzML files and post them 
> somewhere so I can replicate the issue locally?
> 
> Meanwhile, you can try the specifying all variable mods used in the search, 
> when you run PTMProphet by changing the modification string as follows:
>  M:15.9949,n:42.1016,STC:299.123,C:57.02146
> 
> 
> Cheers!
> 
> -David
> 
> 
> 
> 
> On Fri, Nov 17, 2023 at 1:02 PM Longping Fu > wrote:
> I am currently working with PTMProphet in TPP version 6.3.3 for PTM 
> localization. While PTMProphet successfully completes the task, I am 
> encountering a significant number of warning messages in the console.
> 
> To provide some context, my workflow involves utilizing MSFragger as the 
> search engine to convert raw files to mzML files and then searching against a 
> database. For the modification parameters, I have set M 15.9949, N-term 
> 42.1016, STC 299.123, and C 57.02146 as variable modifications, with no fixed 
> modifications specified.
> 
> Upon obtaining the pepXML file from MSFragger, I employed Percolator for PSM 
> validation using the following settings: --only-psms --no-terminate 
> --post-processing-tdc. The resulting pepxml file was then processed with 
> PTMProphet using the command: STC:299.123 MINPROB=0.5 MODPREC=0 FRAGPPMTOL=15 
> NOSTACK MAXTHREADS=1. 
> 
> However, during the PTMProphet processing, I encountered warning messages 
> similar to the following:
> 
> [WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
> S[386]CNGGSHPR
>   Neutral Mass (from pepXML) = 1254.52
>   BAD (SpectraST::Peptide) = S[386]CNGGSHPR
>   Neutral Computed Mass for Evaluation = 1212.51
>   PPM difference = 33487.5
> [INFO:] please check your specified modification masses for precision or 
> adjust MODPREC= parameter ...
> [WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
> SC[402]NGGSHPR
>   Neutral Mass (from pepXML) = 1254.52
>   BAD (SpectraST::Peptide) = SC[402]NGGSHPR
>   Neutral Computed Mass for Evaluation = 1212.51
>   PPM difference = 33487.5
> [INFO:] please check your specified modification masses for precision or 
> adjust MODPREC= parameter ...
> [WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
> SCNGGS[386]HPR
>   Neutral Mass (from pepXML) = 1254.52
>   BAD (SpectraST::Peptide) = SCNGGS[386]HPR
>   Neutral Computed Mass for Evaluation = 1212.51
>   PPM difference = 33487.5
> [INFO:] please check your specified modification masses for precision or 
> adjust MODPREC= parameter ...
> 
> This pattern repeats for various peptides, indicating that PTMProphet is 
> struggling to localize modifications on S, T, or C. The tool suggests 
> adjusting parameters, specifically the MODPREC= parameter.
> 
> Has anyone encountered a similar issue with PTMProphet and successfully 
> addressed it? I would greatly appreciate any insights, advice, or suggestions 
> regarding this matter.
> 
> -- 
> You received this message because you are subscribed to the Google Groups 
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
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>  
> .
> 
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>  
> .

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Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization

2023-11-17 Thread Longping Fu 
Dear David,

I appreciate your swift response. I've compressed the pepXML and mzML files 
and uploaded them to Google Drive. You can access them through the 
following link: 
https://drive.google.com/file/d/1P463uxdvw67ZI7axiZO1OZOIlEZZg5qh/view?usp=sharing

Kindly confirm if you can successfully open the files.

Additionally, I'll be following your suggestion to include all variable 
modifications and check for any remaining warning messages.

Thank you for your assistance.

Sincerely,
Longping

在2023年11月17日星期五 UTC-5 16:20:11 写道：

Dear Longping,

Maybe you can compress your analysis pepXML and mzML files and post them 
somewhere so I can replicate the issue locally?

Meanwhile, you can try the specifying all variable mods used in the search, 
when you run PTMProphet by changing the modification string as follows:
 M:15.9949,n:42.1016,STC:299.123,C:57.02146


Cheers!

-David




On Fri, Nov 17, 2023 at 1:02 PM Longping Fu  wrote:

I am currently working with PTMProphet in TPP version 6.3.3 for PTM 
localization. While PTMProphet successfully completes the task, I am 
encountering a significant number of warning messages in the console.

To provide some context, my workflow involves utilizing MSFragger as the 
search engine to convert raw files to mzML files and then searching against 
a database. For the modification parameters, I have set M 15.9949, N-term 
42.1016, STC 299.123, and C 57.02146 as variable modifications, with no 
fixed modifications specified.

Upon obtaining the pepXML file from MSFragger, I employed Percolator for 
PSM validation using the following settings: *--only-psms --no-terminate 
--post-processing-tdc*. The resulting pepxml file was then processed with 
PTMProphet using the command: *STC:299.123 MINPROB=0.5 MODPREC=0 
FRAGPPMTOL=15 NOSTACK MAXTHREADS=1*. 

However, during the PTMProphet processing, I encountered warning messages 
similar to the following:


















*[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
S[386]CNGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD 
(SpectraST::Peptide) = S[386]CNGGSHPR Neutral Computed Mass for Evaluation 
= 1212.51 PPM difference = 33487.5[INFO:] please check your specified 
modification masses for precision or adjust MODPREC= parameter 
...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
SC[402]NGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD 
(SpectraST::Peptide) = SC[402]NGGSHPR Neutral Computed Mass for Evaluation 
= 1212.51 PPM difference = 33487.5[INFO:] please check your specified 
modification masses for precision or adjust MODPREC= parameter 
...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
SCNGGS[386]HPR Neutral Mass (from pepXML) = 1254.52 BAD 
(SpectraST::Peptide) = SCNGGS[386]HPR Neutral Computed Mass for Evaluation 
= 1212.51 PPM difference = 33487.5[INFO:] please check your specified 
modification masses for precision or adjust MODPREC= parameter ...*

This pattern repeats for various peptides, indicating that PTMProphet is 
struggling to localize modifications on S, T, or C. The tool suggests 
adjusting parameters, specifically the MODPREC= parameter.

Has anyone encountered a similar issue with PTMProphet and successfully 
addressed it? I would greatly appreciate any insights, advice, or 
suggestions regarding this matter.

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.

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Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization

2023-11-17 Thread 'David Shteynberg' via spctools-discuss 
Dear Longping,

Maybe you can compress your analysis pepXML and mzML files and post them
somewhere so I can replicate the issue locally?

Meanwhile, you can try the specifying all variable mods used in the search,
when you run PTMProphet by changing the modification string as follows:
 M:15.9949,n:42.1016,STC:299.123,C:57.02146


Cheers!

-David




On Fri, Nov 17, 2023 at 1:02 PM Longping Fu  wrote:

> I am currently working with PTMProphet in TPP version 6.3.3 for PTM
> localization. While PTMProphet successfully completes the task, I am
> encountering a significant number of warning messages in the console.
>
> To provide some context, my workflow involves utilizing MSFragger as the
> search engine to convert raw files to mzML files and then searching against
> a database. For the modification parameters, I have set M 15.9949, N-term
> 42.1016, STC 299.123, and C 57.02146 as variable modifications, with no
> fixed modifications specified.
>
> Upon obtaining the pepXML file from MSFragger, I employed Percolator for
> PSM validation using the following settings: *--only-psms --no-terminate
> --post-processing-tdc*. The resulting pepxml file was then processed with
> PTMProphet using the command: *STC:299.123 MINPROB=0.5 MODPREC=0
> FRAGPPMTOL=15 NOSTACK MAXTHREADS=1*.
>
> However, during the PTMProphet processing, I encountered warning messages
> similar to the following:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass:
> S[386]CNGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD
> (SpectraST::Peptide) = S[386]CNGGSHPR Neutral Computed Mass for Evaluation
> = 1212.51 PPM difference = 33487.5[INFO:] please check your specified
> modification masses for precision or adjust MODPREC= parameter
> ...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass:
> SC[402]NGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD
> (SpectraST::Peptide) = SC[402]NGGSHPR Neutral Computed Mass for Evaluation
> = 1212.51 PPM difference = 33487.5[INFO:] please check your specified
> modification masses for precision or adjust MODPREC= parameter
> ...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass:
> SCNGGS[386]HPR Neutral Mass (from pepXML) = 1254.52 BAD
> (SpectraST::Peptide) = SCNGGS[386]HPR Neutral Computed Mass for Evaluation
> = 1212.51 PPM difference = 33487.5[INFO:] please check your specified
> modification masses for precision or adjust MODPREC= parameter ...*
>
> This pattern repeats for various peptides, indicating that PTMProphet is
> struggling to localize modifications on S, T, or C. The tool suggests
> adjusting parameters, specifically the MODPREC= parameter.
>
> Has anyone encountered a similar issue with PTMProphet and successfully
> addressed it? I would greatly appreciate any insights, advice, or
> suggestions regarding this matter.
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
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> 
> .
>

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[spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization

2023-11-17 Thread Longping Fu 
I am currently working with PTMProphet in TPP version 6.3.3 for PTM 
localization. While PTMProphet successfully completes the task, I am 
encountering a significant number of warning messages in the console.

To provide some context, my workflow involves utilizing MSFragger as the 
search engine to convert raw files to mzML files and then searching against 
a database. For the modification parameters, I have set M 15.9949, N-term 
42.1016, STC 299.123, and C 57.02146 as variable modifications, with no 
fixed modifications specified.

Upon obtaining the pepXML file from MSFragger, I employed Percolator for 
PSM validation using the following settings: *--only-psms --no-terminate 
--post-processing-tdc*. The resulting pepxml file was then processed with 
PTMProphet using the command: *STC:299.123 MINPROB=0.5 MODPREC=0 
FRAGPPMTOL=15 NOSTACK MAXTHREADS=1*. 

However, during the PTMProphet processing, I encountered warning messages 
similar to the following:


















*[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
S[386]CNGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD 
(SpectraST::Peptide) = S[386]CNGGSHPR Neutral Computed Mass for Evaluation 
= 1212.51 PPM difference = 33487.5[INFO:] please check your specified 
modification masses for precision or adjust MODPREC= parameter 
...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
SC[402]NGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD 
(SpectraST::Peptide) = SC[402]NGGSHPR Neutral Computed Mass for Evaluation 
= 1212.51 PPM difference = 33487.5[INFO:] please check your specified 
modification masses for precision or adjust MODPREC= parameter 
...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
SCNGGS[386]HPR Neutral Mass (from pepXML) = 1254.52 BAD 
(SpectraST::Peptide) = SCNGGS[386]HPR Neutral Computed Mass for Evaluation 
= 1212.51 PPM difference = 33487.5[INFO:] please check your specified 
modification masses for precision or adjust MODPREC= parameter ...*

This pattern repeats for various peptides, indicating that PTMProphet is 
struggling to localize modifications on S, T, or C. The tool suggests 
adjusting parameters, specifically the MODPREC= parameter.

Has anyone encountered a similar issue with PTMProphet and successfully 
addressed it? I would greatly appreciate any insights, advice, or 
suggestions regarding this matter.

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