Re: First steps for MS-GF+ and PeptideShaker integration within Galaxy-P.

[Pratik Jagtap]

Hello Harald,

This is great to hear !

We would be very keen on trying MS-GF+ with PeptideShaker in Galaxy whenever it is available. I am sure Ira and Bjoern have taken notes about the SearchGUI option. 

I am copying this message to gal...@umn.edu (the google group) so that it gets recorded as exciting progress that we are making !

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

On Fri, Mar 7, 2014 at 7:59 AM, <Harald....@biomed.uib.no> wrote:

Hi Pratik,

Sounds good. But as mentioned before I'd very much recommend having
a combined SearchGUI wrapper instead of just an MS-GF+ wrapper. In
other words a wrapper that can be used to run X!Tandem, OMSSA and
MS-GF+ with the same input parameters.

This would also simplify the integration with the PeptideShaker wrapper,
as the input needed for PeptideShaker will directly be available.

But I would assume that a wrapper for MS-GF+ can easily be extended
or merged with the current SearchGUI wrapper?

Some progress to report from our side as well. We've already added
MS-GF+ support in SearchGUI, meaning that we now can run X!Tandem,
OMSSA and MS-GF+ with the same search parameters. Our MS-GF+ support
has also been validated by Sangtae (the MS-GF+ developer), and it
produces identical results as for the command line version. (Note
that the version with MS-GF+ support has not yet been released, but
if someone wants to try it I can always make a version available.)

Next on our list is the import of the mzIdentML output from MS-GF+
into PeptideShaker. This work has already begun and we aim for a
first beta version with MS-GF+ support within the next two weeks.

We've also been in contact with the developers of MS Amanda, and
will also work towards integrating this search engine into SearchGUI.
(Only available for Windows at the moment, but support for other
platforms is in development.) Which again means that a general
SearchGUI wrapper will be a lot more powerful than single search
engine wrappers.

Best regards,
Harald

Quoting Pratik Jagtap <pja...@umn.edu>:

Hello Lennart, Marc and Harald,

Just an update - Ira Cooke along with Bjoern Gruening (copied on this mail)
is working on developing the MS-GF+ wrapper. I am anticipating that they
will communicate with your group for PeptideShaker integration.

We have not yet heard from ASMS but I am anticipating a poster for the
abstract that we submitted.

We would be interested in your thoughts on moving forward. I am looking
forward to adding users and testing the tools !

With Regards,

Pratik

[Pratik Jagtap]

Hello Harald,

I discussed about SearchGUI with Ira and read your paper.

The question that we have going forward on this project is - do you already have a SearchGUI developed for MS-GF+? If so is the next step to develop a Galaxy wrapper for the same? Would you our your group be interested in doing so? Ira and other Galaxy developers will be happy to provide you instructions or help if needed. 

Let us plan on next steps so that we have a good poster / talk in Baltimore in three months !

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

On Sun, Mar 9, 2014 at 6:41 PM, Ira Cooke <irac...@gmail.com> wrote:

Hi Harald,

Sounds great … I think we will still put the separate ms-gf+ wrapper on the toolshed .. for people with alternate pipelines.

But .. as you say I think the SearchGUI option will clearly be superior for most people.

Cheers
Ira

[Pratik Jagtap]

Thanks Harald,

This is great progress - thanks so much !

I spoke with Ira recently - and he (along with Bjoern - as indicated in his mail) will also be able to help Gerben in implementation of Galaxy wrappers.

We are three months away from ASMS - and this development and beta-testing on usegalaxyp.org should give us sufficient iterations to make it work in Galaxy-P and its workflows.

I have copied this mail to gal...@umn.edu - so that we have this as a record in our Galaxy-P user group.

Thanks again !

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

On Wed, Mar 19, 2014 at 11:01 AM, Björn Grüning <bjoern....@gmail.com> wrote:

Hi,

that sounds fantastic!

@Gerben: if you need any help with the Galaxy wrappers feel free to contact me.

Cheers,
Bjoern

Am 19.03.2014 16:58, schrieb Harald....@biomed.uib.no:

Hi all,

We've now completed the first beta versions of SearchGUI and
PeptideShaker with MS-GF+ support. You can download them here:
https://www.dropbox.com/s/f958r27tvgw7wc8/SearchGUI-1.16.5-beta-windows.zip
https://www.dropbox.com/s/1u0was6s4f8crrx/SearchGUI-1.16.5-beta-mac_and_linux.tar.gz

https://www.dropbox.com/s/te4jpm8yqaghqzx/PeptideShaker-0.26.3-beta.zip

We have not yet updated the command line wiki pages, so to see
the complete list of parameters available use:
java -cp SearchGUI-X.Y.Z.jar eu.isas.searchgui.cmd.SearchCLI
java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI
java -cp SearchGUI-X.Y.Z.jar
eu.isas.searchgui.cmd.IdentificationParametersCLI
java -cp PeptideShaker-X.Y.Z.jar
eu.isas.peptideshaker.cmd.IdentificationParametersCLI

Note that our MS-GF+ support is still in development and that
the results achieved will most likely improve in future versions.
We are in contact with Sangtae (the MS-GF+ developer), and hope
that he can help us further improve the results.

And being beta versions there will probably be some bugs we haven't
yet detected. So if you find any, please let us now.

But in any case, we should now have all we need to support SearchGUI
and PeptideShaker with MS-GF+ (and X!Tandem and OMSSA) in Galaxy right?

Finally, note that I added a new person in the CC: Gerben Menschaert.
He's a postdoc at Ghent University, and has showed an interest in
helping out with the implementation of the Galaxy wrappers for SearchGUI
and PeptideShaker. So instead of developing the same wrappers twice,
I thought I'd include him on our development. :)

Best regards,
Harald