Proteome Discoverer's .msf to TPP input files (pepXML)

[Christine Vogel]

Hi All,

Reposting Thomas' question from earlier -- what is a good converter
from Thermo's .msf to TPP suitable files (i.e. pepXML)?

I tried to find it on the list, and the discussion let me to here:

https://github.com/itmat/thermo_msf/blob/master/README.rdoc#readme

But I am unable to successfully install/use this. Any help on this
converter/installation?

Thanks a lot,

Christine


-----

From: Thomas DV <Thomas.devijl...@ua.ac.be>
Date: Sun, 5 Dec 2010 08:43:28 -0800 (PST)
Local: Sun, Dec 5 2010 12:43 pm
Subject: proteome discoverer 1.1 to pepXML
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Hello everybody,

I'm new to this group and in fact rather new to proteome data analysis
as a whole.

We are using Thermo's proteome discoverer at the lab, which gives .msf
output files.
I wanted to try the Ascore program to see whether this could help in
localizing the phosphorylation site in peptides we measured.
but this requires pepXML input. I've tried to find a converter
for .msf into pepXML but it doesn't seem to exist, is that right?

is there any possibility to extract a SEQUEST .out file from within
proteome discoverer or any work-around to create pepXML from proteome
discoverer results through other data output formats?

thanks kindly for any help!
Thomas

student, University of Antwerp, Belgium

[Jimmy Eng]

Christine,

As far as I know, such a converter does not exist at this point.
Hopefully someone can chime in if that's not the case.

- Jimmy

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[gcrynen]

Hi
I have the same problem, I cant even use TPP since I cant even sequest
that is now under proteome discoverer. Thermo is not supporting
Bioworks anymore so we definitely need a converter for msf files
g

[Eric Deutsch]

Hi Angel, have you been able to transform MSF files to pepXML with your
library, or have ideas about how we might easily accomplish that?

Thanks,
Eric

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[tgreco]

While I also have not come across such as tool, I would like to add my
name to the list of those interested in having an open-source option
for Proteome Discoverer msf files. I do know that Scaffold by
ProteomeSoftware can accept msf files as input, so their team must
have developed some flavor of parsing tool. Though I seem to recall
when talking to Proteome Software support that achieving this
compatibility between msf and Scaffold was not trivial.
-Todd

On Apr 6, 12:15 pm, Eric Deutsch <Eric.Deut...@systemsbiology.org>
wrote:

[Taejoon Kwon]

Here's my simple, crude python code to convert MSF to SQT format, and
I confirm that it can be converted to pepxml with TPP Sqt2XML script.

Few things to mention:

* Sqt2XML script truncate terminal AA at both ends, but MSF does not
have that info. So I put a dummy AA 'X' at both end.
* I still cannot find the AA modification info in MSF, so calculated
mass in ''Match' record can be incorrect depending on modification.
* deltaCn has various definitions (I didn't know that).
http://mspire.rubyforge.org/spec_id/srf.html
I took the original definition for this script.

http://www.marcottelab.org/users/taejoon/MS/msf-to-sqt.py.txt

You can run this with the following simple command (after changing
filename & permission, of course):

./msf-to-sqt.py my_file.msf

I think there is an expert for this kind of task (inside TPP project).
I post this to save his/her time to dig MSF schema (that's what I did
yesterday). Of course I am happy to see him/her to take my code, and
make a single script to convert MSF to pepxml directly. :-)

Cheers,

Taejoon

[Christine Vogel]

Thanks, Taejoon. You're awesome!

Christine

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Christine Vogel, PhD

NYU-Biology

Center for Genomics & Systems Biology

12 Waverly Place, #403 (office) or 8th floor (mail)

New York, NY 10003

phone: +1-212-998-3976

fax:     +1-212-995-4015

http://www.nyu.edu/projects/vogel/

[Eric Deutsch]

Thank you all for posting this. Since there seems to be quite a bit of interest in this, we will try to get this working seamlessly in the TPP. However, we don’t have MSF results. Can someone provide an example dataset that we could test with? Some raw data, a FASTA file, and the resulting MSF?

 

Thanks,

Eric

[Jimmy Eng]

Eric,

I can do a couple of quick searches and get you sample files.

- Jimmy

[Eric Deutsch]

Hi Jimmy, that'd be great. If you could just do the tutorial dataset for
starters, that would likely be enough.

Thanks,
Eric

> -----Original Message-----
> From: Jimmy Eng [mailto:jke...@gmail.com]
> Sent: Thursday, April 07, 2011 12:32 PM
> To: spctools...@googlegroups.com
> Cc: Eric Deutsch
> Subject: Re: [spctools-discuss] Re: Proteome Discoverer's .msf to TPP
> input files (pepXML)
>

[gcrynen]

Hi Eric,
I also have msf data files, just let me know how to get them to you
cheers
gogce

[Eric Deutsch]

Thanks, I've already gotten a couple sets of msf files, thanks everyone!
We'll contact you if we need more.

Thanks,
Eric

> -----Original Message-----
> From: spctools...@googlegroups.com [mailto:spctools-
> dis...@googlegroups.com] On Behalf Of gcrynen

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[Angel]

woops, should pay closer attention to the list. Debugging the gem now.
-angel

[Suzanne]

Hello. I am sorry if I missed the solution to the original question about converting "*.msf to *.pepXML" and using it in TPP. Was there a workaround to using *.msf files in TPP?

 

Thank you.

 

Suzanne

 

 

On Wednesday, 8 August 2012 11:45:33 UTC-4, patrick Halvey wrote:

Hello. I came across this post while doing a google search for "conversion of msf files to pepXML". I am trying to use Proteome Discoverer output with a protein assembly tool called "IDpicker", but of course it is impossible to export pepXML format from Proteome Discoverer. Has there been a consensus reached on how to make the conversion to pepXML? Thanks   

Patrick

[shygza]

perhaps you can try scaffold
Chengpin

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[Suzanne]

Will do. Thank you.

[HFaz]

I am not sure if Eric or anybody in ISB/SPC has fixed this issue. TPP doesn't seem to read the pep.xml files generated from Proteome Discoverer. I appreciate any advice or suggestion. 

Thanks

Hfaz