[spctools-discuss] Installer for TPP 6.3.0 does not recognize existence of MS VC++ 2015-2022

[Scott Starry]

Due to security restrictions, my company does not allow redirected calls, 
which the TPP 6.3.0 installer uses to obtain the Microsoft Visual C++ 
redistributables.  This is usually not a problem as I simply install the MS 
VC++ 2010 and 2015-2022 redistributables beforehand.

v5.2.0 found the two redistributables and did not attempt to install them.  
However, TPP v6.3.0 only recognizes that the 2010 redistributable is 
already installed; the installer tries to install the 2015-2022 
redistributable causing the the Windows installer to crash in my 
environment.

Would be good if the v6.3.0 installer would recognize that both 
prerequisites are already installed.

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[spctools-discuss] TPP 6.3.0 Release is now available

['Luis Mendoza' via spctools-discuss]

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.3.0
"Arcus"

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 6.3.0.  The software is available for Windows as well as
Linux from all the usual locations (please see the section below, "Getting
the TPP Software").  Most users are recommended to use the Windows
installer, which installs and configures TPP and other required software,
such as a web server.  For advanced users who need to customize TPP, or for
those who run on Linux or OS X, the source code can be downloaded.


*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:6.3.0_Release_Notes


*Getting the TPP Software*
Download the TPP version 6.3.0 native windows installer from the Sashimi
SourceForge project file release page:
  https://sourceforge.net/

projects/sashimi/files/Trans-
Proteomic
Pipeline (TPP)/


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 6.3.0 source
code .zip package
or, check out the code directly from svn:
  svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_6-3-0

For building from source, please refer to the README and INSTALL files in
src/ directory of TPP 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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Re: [spctools-discuss] protein validation

[Jimmy Eng]

Felipe,

You should not search sequence databases composed of just a single protein
or even tens of proteins and hope to process them through downstream
validation tools like the Prophets.  When you do this, you break lots of
assumptions that the tools expect which makes the results, like
probability of 1 for many peptides, meaningless.  Ideally you search the
full organism protein sequence database.  But if you feel you understand
the analysis and tools well enough that you need to search a smaller
database, minimally use 500 or 1000 protein sequences and include your
protein of interest.

Jimmy

On Wed, May 3, 2023 at 9:41 PM felipe velasquez  wrote:

> Hello Luis
>
> Thanks for your request. Yes, I performed TPP/Prophets, and their
> probability is high as 0.9 or 1, in many peptides. The database I used
> only contains my protein of interest in FASTA. I do not know how to use
> decoys.
>
> Kind regards,
>
> Felipe
>
> El mar, 2 may 2023 a las 22:53, 'Luis Mendoza' via spctools-discuss (<
> spctools-discuss@googlegroups.com>) escribió:
>
>> Hello Felipe,
>>
>> There may be several reasons why you see the viral protein in your
>> analysis, e.g.
>>
>>- Did you only run Comet, or did you validate using the
>>TPP/Prophets?  If the latter, what was the probability of the protein(s) 
>> in
>>question?
>>- What were the contents of the database that you used to search?
>>Did they contain only "the sequence of my protein of interest"/virus
>>protein, or did you use a full proteome database?  Did you use decoys?
>>Contaminants?
>>- Does the virus protein contain peptides that may be shared with
>>proteins in the sample itself?   Do you observe unique/proteotypic 
>> peptides
>>from that protein?
>>
>> Cheers,
>> --Luis
>>
>>
>>
>> On Sun, Apr 30, 2023 at 7:13 PM felipe velasquez 
>> wrote:
>>
>>> Hello
>>>
>>> I have a question about protein validation. I am trying to use TPP to
>>> identify post-translational modifications of certain proteins. I performed
>>> a Comet search using the sequence of my protein of interest. However, while
>>> exploring another database, I performed a search using a protein that is
>>> not in the experimental design, as it comes from a virus. Surprisingly,
>>> this protein appeared in my analysis. Is this normal?
>>>
>>> thanks,
>>>
>>> Felipe Ignacio Velásquez Salinas
>>> Bioquímico
>>> Doctor en Microbiología
>>>
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>>> .
>>>
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