Manual MS2 spectra annotation tool

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viktori...@fh-hagenberg.at

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Jan 11, 2018, 10:41:38 AM1/11/18
to ProteomicsQA
Hi guys,

is anybody of you aware of a tool, which I could use to manually (and visually) annotate MS2 spectra? So, like I load a spectrum file (or also just a single spectrum) and then be able to click on a peak and attach a label (and even a color) to it? Anything that comes close to such a functionality would be highly appreciated!

Thanks in advance!
Cheers,
viktoria

David Bouyssié

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Jan 12, 2018, 11:29:58 AM1/12/18
to ProteomicsQA
Hi Viki,

Marc and Harald may give a better input than me, but I think it should not be too complicated to update PeptideShaker for such a kind of use case.

On my side I have successfully integrated the Lorikeet Javascript library (https://github.com/jmchilton/lorikeet) in my web application.
It may also be a good option but it would require to change some lines of javascript code.

It of course depends on the usage you want to do.
Do you want just to use it for personal purpose or do you want to integrate this tool in an existing one?

Cheers ;-)

David

Marc Vaudel

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Jan 12, 2018, 12:00:07 PM1/12/18
to David Bouyssié, ProteomicsQA
Hello!

Yes we have been thinking about making such a viewer for a long time. But it would cost us some time (which is sparse) for no publication (which we currently need to get a job). But if you know a student who could work on it we would be very happy to show him/her the modules that can be put together for such purposes :-)

Hope this helps,

Marc



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Eric Deutsch

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Jan 14, 2018, 12:46:55 AM1/14/18
to Marc Vaudel, David Bouyssié, ProteomicsQA, Eric Deutsch

Hi everyone, one minor update, the current code for Lorikeet should be obtained from here:

 

https://github.com/UWPR/Lorikeet

 

Viktoria, is your need just for browser display or for PDF output for publication?

 

Regards,

Eric

 

 

From: proteo...@googlegroups.com [mailto:proteo...@googlegroups.com] On Behalf Of Marc Vaudel
Sent: Friday, January 12, 2018 9:00 AM
To: David Bouyssié <david.b...@ipbs.fr>
Cc: ProteomicsQA <proteo...@googlegroups.com>
Subject: Re: [Proteomics Q&A] Re: Manual MS2 spectra annotation tool

 

Hello!

Yes we have been thinking about making such a viewer for a long time. But it would cost us some time (which is sparse) for no publication (which we currently need to get a job). But if you know a student who could work on it we would be very happy to show him/her the modules that can be put together for such purposes :-)

 

Hope this helps,

 

Marc

 

 

2018-01-12 17:29 GMT+01:00 David Bouyssié <david.b...@ipbs.fr>:

Hi Viki,

 

Marc and Harald may give a better input than me, but I think it should not be too complicated to update PeptideShaker for such a kind of use case.

 

On my side I have successfully integrated the Lorikeet Javascript library (https://github.com/jmchilton/lorikeet) in my web application.

It may also be a good option but it would require to change some lines of javascript code.

 

It of course depends on the usage you want to do.

Do you want just to use it for personal purpose or do you want to integrate this tool in an existing one?

 

Cheers ;-)

 

David

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David Bouyssié

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Jan 14, 2018, 4:46:23 AM1/14/18
to ProteomicsQA
Hi Eric,

Thanks for the project updates!

Are you still working on Lorikeet improvements?
I have to say this is a really handy tool.

On my side I'm currently trying to figure out if I could use the canvas2svg library (https://github.com/gliffy/canvas2svg) to enable conversion of the displayed canvas to SVG.
It could be nice if it was a builtin feature!

I can try to make a fork and then a pull request.
One thing that could also be nice is to move from Javascript to something like Typescript. It might be then easier to maintain and update the project.

Cheers,

David

Eric Deutsch

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Jan 14, 2018, 11:52:03 PM1/14/18
to David Bouyssié, ProteomicsQA, Eric Deutsch

Hi David, just so I didn’t leave the wrong impression, Lorikeet isn’t mine. The GitHub repo I sent for Lorikeet is the work of Vagisha Sharma at UW here in Seattle. I have made a few very minor contributions. I can say that I am still dreaming of improvements to Lorikeet, but can’t really say I am really working on them. In general Vagisha is very welcoming of contributions.

 

Regards,

Eric

 

 

From: proteo...@googlegroups.com [mailto:proteo...@googlegroups.com] On Behalf Of David Bouyssié
Sent: Sunday, January 14, 2018 1:46 AM
To: ProteomicsQA <proteo...@googlegroups.com>
Subject: Re: [Proteomics Q&A] Re: Manual MS2 spectra annotation tool

 

Hi Eric,

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Dorfer Viktoria

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Jan 15, 2018, 2:39:56 AM1/15/18
to ProteomicsQA

Dear all,

 

thanks a lot for the suggestions, I will check them out! I would indeed need it for a publication, so no time to get a student working on this (but maybe we can do something about that in the future).

 

Best regards,

Viktoria

Marc Vaudel

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Jan 15, 2018, 5:11:31 AM1/15/18
to Dorfer Viktoria, ProteomicsQA
Hi Viki,

If it is just for a publication it might be an idea to do it programatically. Writing a small script that does it takes few minutes in R and will look much better :) I can help you with this, just drop a message on Slack.

Best regards,

Marc

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Timo Sachsenberg

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Jan 15, 2018, 5:15:36 AM1/15/18
to Dorfer Viktoria, ProteomicsQA
Hi Viki,
you can also check out TOPPView in OpenMS. You can annotate peaks and peak distances.
The output in TOPPView does can easily be export as svg.
You can get some nice and polished results with minor editing in inkscape or illustrator.
Best,
Timo
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Dorfer Viktoria

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Jan 15, 2018, 6:03:13 AM1/15/18
to ProteomicsQA

Hi Marc & Timo,

 

yes, I am definitely considering writing a short script, I just wondered whether something is already out there…

Thanks, Timo, I will have a look at it!

 

Best regards,

Viki

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Julian Uszkoreit

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Jan 15, 2018, 6:13:14 AM1/15/18
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Hej Viki,


Also PIA (in KNIME) and PrideInspector allow for viewing and some annotation of MS/MS spectra. At least adding the distances of peaks is supported.


Cheers,

Julian

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