Re: [spctools-discuss] TPP 7.0.0 Release is now available

['Juergen Bartel' via spctools-discuss]

Dear David,

Thank you for your reply and the offer to help!

I will answer in my original post to avoid spaming this announcement too 
much.

Best regards,
Juergen



David Shteynberg schrieb am Donnerstag, 4. April 2024 um 17:15:02 UTC+2:

> Now that I have also read your original message... sorry, I somehow missed 
> that message originally.  I have used Lib2HTML to successfully convert a 
> spectral library to an HTML page, although I do remember having some issues 
> with unrecognized modifications when I first tried.  Lib2HTML is a 
> completely separate tool from Seq2MS and uses a different code base.  The 
> version of the Seq2MS software in the TPP is somewhat different from the 
> original version and includes more PTMs encoded.  So this is still a bit of 
> a work in progress with the PTMs and I would be happy to help you further 
> if you can share your input files so I can reproduce the problem.   Seq2MS 
> in the TPP distribution currently supports the subset of proforma mods 
> pasted below.
>
> Cheers!
>
> Oxidation Phospho TMT Silac Carbamyl Carbamidomethyl Acetyl Methyl 
> Hydroxylation GlyGly Biotinylation Crotonyl Dimethyl Malonyl Nitro 
> Butyryl Formyl Gluratylation hydroxyisobutyryl Propionyl Succinyl 
> Trimethyl Deamidated Gln->pyro-Glu Glu->pyro-Glu
>
>
>
> On Apr 4, 2024, at 6:59 AM, David Shteynberg  
> wrote:
>
> Hello Juergen,
>
> Thank you for your question and use of TPP! Seq2MS's support in TPP is 
> brand new. Truncation at the PTM usually indicates that the modification 
> was not recognized or encoded in the model you applied.  Can you tell me 
> the model you applied and the modification you were searching?
>
> Thanks!
> David
>
> On Thu, Apr 4, 2024, 2:19 AM 'Juergen Bartel' via spctools-discuss <
> spctools...@googlegroups.com> wrote:
>
>> Dear TPP Team,
>>
>> Thanks for generating the new TPP version. Just a question concerning the 
>> release notes: These state that Seq2MS was added. Does that also mean that 
>> the issue I mentioned some time ago with Lib2HTML ([This topic] 
>> ; 
>> when peptides with multiple different modification variants are present on 
>> the same residue, it did truncate the peptides after the modified residue) 
>> was solved?
>>
>> Best regards,
>> Juergen
>>
>>
>>
>> David Shteynberg schrieb am Samstag, 30. März 2024 um 02:47:30 UTC+1:
>>
>>> Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.0.0 
>>>
>> Arafel
>>>
>>
>>> We are proud to offer a major update to the Trans-Proteomic Pipeline 
>>> (TPP) software, release 7.0.0.  The software is available for MacOS, 
>>> Windows, Linux, as well as Android from all the usual locations (please see 
>>> the section below, 
>>>
>> Getting the TPP Software
>>>
>> ).  We recommend for most users to use the Windows or MacOS installer, 
>>> which installs and configures TPP and other required software, such as the 
>>> Apache web server, perl, and python.  For advanced users, who need to 
>>> customize TPP, or for those users who run on Linux or Android, the source 
>>> code should be downloaded and the software configured and compiled.  If 
>>> building from source, please add your site specific configuration to 
>>> site.mk in the top level directory after unpacking the source-code.
>>>
>>> == Highlights ==
>>> + MacOS two-click install!
>>> + Python Support and addition of Seq2MS for Generative AI of Peptide 
>>> Fragment Spectra
>>> + Native Support of Kojak for Cross-linked Peptide Search
>>> + Native Support of Magnum for Open-mass Peptide Search
>>> + StPeter Quantification 
>>>
>> by run
>>>
>> or 
>>>
>> by experiment
>>>
>> + Easy to access PeptideProphet VMC model for rare-PTMs
>>>
>>>
>>> == Release Notes ==
>>> Release notes on the most important new features, changes, and known 
>>> issues are available at:
>>>  
>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.0.0_Release_Notes
>>>
>>>
>>> == Getting the TPP Software ==
>>> Download the TPP version 7.0.0 native windows installer from the Sashimi 
>>> SourceForge project file release page:
>>> https://sourceforge.net/projects/sashimi/files/latest/download
>>>
>>> Everyone is encouraged to read and contribute to our wiki, at
>>>   http://tools.proteomecenter.org/wiki/
>>>
>>> For guides to installing and using our software, please see our wiki:
>>>   http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
>>>
>>> For downloading the source code, please go to the following link:
>>>   http://sourceforge.net/projects/sashimi/files/  and find the 7.0.0 
>>> source code  package
>>> or, check out the code directly from svn:
>>>   svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_7-0-0
>>>
>>> For building from source, please refer to the README and INSTALL files 
>>> in top level source directory of the TPP code tree as well as the wiki.
>>>
>>>
>>> == Acknowledgements ==
>>> The TPP Team: David, Luis, Mike, Eric, Jim

Re: [spctools-discuss] TPP 7.0.0 Release is now available

[David Shteynberg]

Now that I have also read your original message... sorry, I somehow missed that 
message originally.  I have used Lib2HTML to successfully convert a spectral 
library to an HTML page, although I do remember having some issues with 
unrecognized modifications when I first tried.  Lib2HTML is a completely 
separate tool from Seq2MS and uses a different code base.  The version of the 
Seq2MS software in the TPP is somewhat different from the original version and 
includes more PTMs encoded.  So this is still a bit of a work in progress with 
the PTMs and I would be happy to help you further if you can share your input 
files so I can reproduce the problem.   Seq2MS in the TPP distribution 
currently supports the subset of proforma mods pasted below.

Cheers!

Oxidation Phospho TMT Silac Carbamyl Carbamidomethyl Acetyl Methyl 
Hydroxylation GlyGly Biotinylation Crotonyl Dimethyl Malonyl Nitro 
Butyryl Formyl Gluratylation hydroxyisobutyryl Propionyl Succinyl 
Trimethyl Deamidated Gln->pyro-Glu Glu->pyro-Glu



> On Apr 4, 2024, at 6:59 AM, David Shteynberg 
>  wrote:
> 
> Hello Juergen,
> 
> Thank you for your question and use of TPP! Seq2MS's support in TPP is brand 
> new. Truncation at the PTM usually indicates that the modification was not 
> recognized or encoded in the model you applied.  Can you tell me the model 
> you applied and the modification you were searching?
> 
> Thanks!
> David
> 
> On Thu, Apr 4, 2024, 2:19 AM 'Juergen Bartel' via spctools-discuss 
>  > wrote:
>> Dear TPP Team,
>> 
>> Thanks for generating the new TPP version. Just a question concerning the 
>> release notes: These state that Seq2MS was added. Does that also mean that 
>> the issue I mentioned some time ago with Lib2HTML ([This topic] 
>> ; 
>> when peptides with multiple different modification variants are present on 
>> the same residue, it did truncate the peptides after the modified residue) 
>> was solved?
>> 
>> Best regards,
>> Juergen
>> 
>> 
>> 
>> David Shteynberg schrieb am Samstag, 30. März 2024 um 02:47:30 UTC+1:
>>> Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.0.0
>>> Arafel
>>> 
>>> We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) 
>>> software, release 7.0.0.  The software is available for MacOS, Windows, 
>>> Linux, as well as Android from all the usual locations (please see the 
>>> section below,
>>> Getting the TPP Software
>>> ).  We recommend for most users to use the Windows or MacOS installer, 
>>> which installs and configures TPP and other required software, such as the 
>>> Apache web server, perl, and python.  For advanced users, who need to 
>>> customize TPP, or for those users who run on Linux or Android, the source 
>>> code should be downloaded and the software configured and compiled.  If 
>>> building from source, please add your site specific configuration to 
>>> site.mk  in the top level directory after unpacking the 
>>> source-code.
>>> 
>>> == Highlights ==
>>> + MacOS two-click install!
>>> + Python Support and addition of Seq2MS for Generative AI of Peptide 
>>> Fragment Spectra
>>> + Native Support of Kojak for Cross-linked Peptide Search
>>> + Native Support of Magnum for Open-mass Peptide Search
>>> + StPeter Quantification
>>> by run
>>> or
>>> by experiment
>>> + Easy to access PeptideProphet VMC model for rare-PTMs
>>> 
>>> 
>>> == Release Notes ==
>>> Release notes on the most important new features, changes, and known issues 
>>> are available at:
>>>  
>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.0.0_Release_Notes
>>> 
>>> 
>>> == Getting the TPP Software ==
>>> Download the TPP version 7.0.0 native windows installer from the Sashimi 
>>> SourceForge project file release page:
>>> https://sourceforge.net/projects/sashimi/files/latest/download
>>> 
>>> Everyone is encouraged to read and contribute to our wiki, at
>>>   http://tools.proteomecenter.org/wiki/
>>> 
>>> For guides to installing and using our software, please see our wiki:
>>>   http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
>>> 
>>> For downloading the source code, please go to the following link:
>>>   http://sourceforge.net/projects/sashimi/files/  and find the 7.0.0 source 
>>> code  package
>>> or, check out the code directly from svn:
>>>   svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_7-0-0 
>>> 
>>> 
>>> For building from source, please refer to the README and INSTALL files in 
>>> top level source directory of the TPP code tree as well as the wiki.
>>> 
>>> 
>>> == Acknowledgements ==
>>> The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers who 
>>> contributed to this release from ISB.  Thanks to developers and users from 
>>> the TPP's user community who also provided feedback and code contributio

[spctools-discuss] TPP 7.0.0 Release is now available

['David Shteynberg' via spctools-discuss]

Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.0.0
"Arafel"

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 7.0.0.  The software is available for MacOS, Windows,
Linux, as well as Android from all the usual locations (please see the
section below, "Getting the TPP Software").  We recommend for most users to
use the Windows or MacOS installer, which installs and configures TPP and
other required software, such as the Apache web server, perl, and python.
For advanced users, who need to customize TPP, or for those users who run
on Linux or Android, the source code should be downloaded and the software
configured and compiled.  If building from source, please add your site
specific configuration to site.mk in the top level directory after
unpacking the source-code.

== Highlights ==
+ MacOS two-click install!
+ Python Support and addition of Seq2MS for Generative AI of Peptide
Fragment Spectra
+ Native Support of Kojak for Cross-linked Peptide Search
+ Native Support of Magnum for Open-mass Peptide Search
+ StPeter Quantification "by run" or "by experiment"
+ Easy to access PeptideProphet VMC model for rare-PTMs


== Release Notes ==
Release notes on the most important new features, changes, and known issues
are available at:

http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.0.0_Release_Notes


== Getting the TPP Software ==
Download the TPP version 7.0.0 native windows installer from the Sashimi
SourceForge project file release page:
https://sourceforge.net/projects/sashimi/files/latest/download

Everyone is encouraged to read and contribute to our wiki, at
  http://tools.proteomecenter.org/wiki/

For guides to installing and using our software, please see our wiki:
  http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

For downloading the source code, please go to the following link:
  http://sourceforge.net/projects/sashimi/files/  and find the 7.0.0 source
code  package
or, check out the code directly from svn:
  svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_7-0-0

For building from source, please refer to the README and INSTALL files in
top level source directory of the TPP code tree as well as the wiki.


== Acknowledgements ==
The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers who
contributed to this release from ISB.  Thanks to developers and users from
the TPP's user community who also provided feedback and code contributions.

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