PeptideShaker v1.0.0 and SearchGUI v2.0.0

[Harald Barsnes]

 

Hi all,

 

We have just released new versions of both PeptideShaker (v1.0.0) and SearchGUI (v2.0.0).

 

The most important news are:
- Andromeda is now supported (beta).

- MS Amanda and Comet has been updated.

- The PTM list has been cleaned up and the PTMs renamed.

- PTM masses are now set via the atomic composition.

- File renaming: .cps to .cpsx and .parameters to .par.

 

For the complete release notes please see:
- http://compomics.github.io/searchgui/wiki/releasenotes.html
- http://compomics.github.io/peptide-shaker/wiki/releasenotes.html

 

Note that the changes required to support Andromeda has resulted in that old search settings files and old PeptideShaker projects cannot be open in this new release. (Old PeptideShaker projects can always be opened in PeptideShaker v0.41.1.) We're sorry for the inconvenience and hope to avoid such issues in the future. If you have any questions regarding these changes please don't hesitate to contact us. 

 

Also note that due to the closing of Google Code, the tools have new web pages:

- http://compomics.github.io/projects/peptide-shaker.html

- http://compomics.github.io/projects/searchgui.html

 

Here you can download the latest versions and find all the information from the old pages. Please let us know if something is missing or you find non-working links!

 

The easiest way to get the new versions is to simply start SearchGUI or PeptideShaker, say yes to the update question, and let the auto update take care of the rest.

 

And as always, any feedback, suggestions or bug reports are very welcome!

 

Best regards,
Harald and Marc

 

[Zhibin Ning]

Great news!

I have been following the updates, honestly, I am a big fan of search GUI and peptideshaker.

Not easy that these two guys have been taken good care to be better and better.
I have two suggestions, which may be considered for future development. 

One is the MS2 spectra export in batch mode, for example, I would like to select some proteins, or just mark some peptide/spectra to export all corresponding well-labeled spectra for publication.

The other is to take good advantage of the displaying function of peptideshaker, users are allowed to import a part of the already combined result (like protein list and corresponding peptide with scan number etc) to be able to display and label the MS2 spectra. 

This is based on that the importing is slow for peptideshaker for large scale dataset, and sometimes there is really no need to examine all proteins. 

Best!

[Marc Vaudel]

Dear Ning Zhibin,

Thank you very much for your positive feedback, and the clever suggestions. Concerning the export of spectra for multiple proteins it is something we can look into, but I cannot promise that it will happen in the near future so you will need to be patient :) 

Concerning the import time you are very correct that, unless you encounter memory problems or have heavily modified samples, most of the time is usually spent on mapping peptides to proteins and inspecting the PSMs/Peptides/Protein quality. And you are also correct that this is not always needed. You will be happy to know that we have already worked on your suggestion of making it up to the user to skip it whenever it is not needed. The release of this feature is expected in December this year!

Best regards,

Marc

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[Polina Drozdova]

Dear Harald and Marc,

Where can I find documentation for command line of PeptideShaker v1.0?

Or are there any plans to release a tutorial for command line usage of PeptideShaker? It would be great.

Thank you for your work. The new PeptideShaker looks great.

Best regards,

Polina

[Marc Vaudel]

Dear Polina,

Thank you for the kind words! The wiki pages on command line usage have been migrated with the tools to GitHub. You will find them to in the menu to the right of the webpages:

SeachGUI: http://compomics.github.io/searchgui/wiki/searchcli.html
PeptideShaker: http://compomics.github.io/peptide-shaker/wiki/peptideshakercli.html
DenovoGUI: http://compomics.github.io/denovogui/wiki/denovocli.html

If anything is unclear, don't hesitate to ask :)

Best regards,

Marc

2015-09-25 3:23 GMT+02:00 Polina Drozdova <drozd...@gmail.com>:

Dear Harald and Mark,

Where can I find documentation for command line of PeptideShaker v1.0?

Or are there any plans to release a tutorial for command line usage of PeptideShaker? It would be great.

Thank you for your work. The new PeptideShaker looks great.

Best regards,

Polina

On Thursday, August 27, 2015 at 3:24:50 PM UTC+3, Harald Barsnes wrote:

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