Peptide Matches!

[Alejandro Cohen]

Hi DeNovoGui...

I'm back to denovo sequencing. I run a NOVOR search and now want to EXPORT>PeptideMatches (Beta) to map the peptides to proteins. Everything works fine BUT the Protein column on the Excel spreadsheet appear empty. I know for sure some of the peptides belong to proteins which ARE in the selected DB (I manually checked this).

I've done the EXPORT>PeptideMatches (Beta) before and it seemed to work, on another verion of DenovoGui. Can you help me out?

Alex

[Harald Barsnes]

Hi Alex,

Thanks for telling us about this. The same happens on our end as well. We'll look into it and get back to you.

Best regards,

Harald

[Harald Barsnes]

Hi Alex,

DeNovoGUI v1.9.10 has just been released which should fix the problem of exporting the peptide matches for Novor results. Please let us know if you still experience any issues.

Best regards,

Harald

[Alejandro Cohen]

Thanks Harald, 

I will take a look at this.

Cheers

Alex

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[Alejandro Cohen]

Harald, Marc

Just a heads up, I'm using PepExplorer (in PatternLab) for mapping the results of Novor. My understanding is that it does something similar as to PeptideMatches, but goes one step further by doing some peptide aggregation into protein IDs.

I should compare same dataset with PeptideShaker and see if results are similar.

Also, I tried downloading the latest DenovoGui, but I got an error in my computer. Its says: "Could not create the folder 'C:ProgramFiles\DeNvovoGui-1-9-10' to download the file to'

Could this be a permission issue? I think before it tried to Download to the Download folder. Any ideas?

Cheers

Alex

[Harald Barsnes]

Hi Alex,

You can aggregate the peptides at the protein level by loading the Novor output in PeptideShaker (the Novor output file itself, not the peptide matches export). The feature is still on beta test state though and the statistics are not yet to be trusted, but it should be able to give you an idea about the protein detection. You might want to wait until next week though, as I just tested it an came across a couple of minor issues that I'm now looking into fixing.

As for the "Could not create the folder 'C:ProgramFiles\DeNvovoGui-1-9-10'" error the problem seems to be that you put DeNovoGUI in the ProgramFiles folder, and most setups will require administrator privileges to write to this folder. I would recommend unzipping DeNovoGUI in a sub folder of your user home folder.

Best regards,

Harald

On Wednesday, March 2, 2016 at 10:24:40 PM UTC+1, Alejandro Cohen wrote:

Harald, Marc

Just a heads up, I'm using PepExplorer (in PatternLab) for mapping the results of Novor. My understanding is that it does something similar as to PeptideMatches, but goes one step further by doing some peptide aggregation into protein IDs.

I should compare same dataset with PeptideShaker and see if results are similar.

Also, I tried downloading the latest DenovoGui, but I got an error in my computer. Its says: "Could not create the folder 'C:ProgramFiles\DeNvovoGui-1-9-10' to download the file to'

Could this be a permission issue? I think before it tried to Download to the Download folder. Any ideas?

Cheers

Alex

On Tue, 1 Mar 2016 at 09:14 Alejandro Cohen wrote:

Thanks Harald, 

I will take a look at this.

Cheers

Alex

On Mon, 29 Feb 2016 at 16:26 Harald Barsnes wrote:

Hi Alex,

DeNovoGUI v1.9.10 has just been released which should fix the problem of exporting the peptide matches for Novor results. Please let us know if you still experience any issues.

Best regards,

Harald

On Friday, February 26, 2016 at 8:26:30 PM UTC+1, Harald Barsnes wrote:

Hi Alex,

Thanks for telling us about this. The same happens on our end as well. We'll look into it and get back to you.

Best regards,

Harald

On Friday, February 26, 2016 at 4:56:12 PM UTC+1, Alejandro Cohen wrote:

Hi DeNovoGui...

I'm back to denovo sequencing. I run a NOVOR search and now want to EXPORT>PeptideMatches (Beta) to map the peptides to proteins. Everything works fine BUT the Protein column on the Excel spreadsheet appear empty. I know for sure some of the peptides belong to proteins which ARE in the selected DB (I manually checked this).

I've done the EXPORT>PeptideMatches (Beta) before and it seemed to work, on another verion of DenovoGui. Can you help me out?

Alex

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[Alejandro Cohen]

Harald,

Once I run the old version, it tells me whether I want to update, and it automatically tries downloading into that folder (It doesn't give me the option to which folder to download)... I guess I'll dowload it from the website.

ALSO, the Peptide Search option (Top right of screen) doesn't seem to be working on my system, does it on yours??

Best

Alex

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[Harald Barsnes]

Hi Alex,

The update will always try to download the new version into a folder next to the current DeNovoGUI installation. So for the auto update to work you have to move the current installation to a folder where you don't need admin privileges to create folders. Or you can simply download a new version from the website and put it in an appropriate folder. Then the auto update should then be ok next time a new version becomes available.

Regarding the search, you are correct, it's not working the way it should. I'll look into it and get back to you.

BTW, it's easier for us if you report bugs like this via the DeNovoGUI issue tracker (https://github.com/compomics/denovogui/issues), as this makes it easier for us to keep track of all the issues.

Best regards,

Harald

On Thursday, March 3, 2016 at 9:39:59 PM UTC+1, Alejandro Cohen wrote:

Harald,

Once I run the old version, it tells me whether I want to update, and it automatically tries downloading into that folder (It doesn't give me the option to which folder to download)... I guess I'll dowload it from the website.

ALSO, the Peptide Search option (Top right of screen) doesn't seem to be working on my system, does it on yours??

Best

Alex

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[Harald Barsnes]

Hi Alex,

We've just released new versions of both DeNovoGUI and PeptideShaker which should allow you to load the Novor results in PeptideShaker. The Find feature in DeNovoGUI should also now work again.

If you come across any other issues please let us know.

Best regards,

Harald