DeNovoGUI

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Welcome to the DeNovoGUI user group!

DeNovoGUI is an open source graphical user interface for de novo sequencing of tandem mass spectra.

You can find complete information and downloads at http://compomics.github.io/projects/denovogui.html.

For reporting specific issues or bugs, please use the issue tracker at https://github.com/compomics/denovogui/issues.

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Fábio CS Nogueira, Harald Barsnes3

10/3/22

Different enzyme for the Novor's parameters

Dear Harald, Thanks for your quick reply. Kind Regards, Fábio On Mon, Oct 3, 2022 at 11:10 AM Harald

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Different enzyme for the Novor's parameters

Dear Harald, Thanks for your quick reply. Kind Regards, Fábio On Mon, Oct 3, 2022 at 11:10 AM Harald

10/3/22

Phuc nguyen minh Ho, Harald Barsnes2

7/4/22

BLAST tag sequence

Hi Phuc, The "Click to BLAST tag sequence" option seems to be working fine on my end.

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BLAST tag sequence

Hi Phuc, The "Click to BLAST tag sequence" option seems to be working fine on my end.

7/4/22

Nikko, Harald Barsnes2

9/24/21

Quant analysis after de novo

Hi Nikko, In DeNovoGUI you have some options on the Export menu that you can try out for exporting

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Quant analysis after de novo

Hi Nikko, In DeNovoGUI you have some options on the Export menu that you can try out for exporting

9/24/21

Irina Tarasova, Harald Barsnes6

9/2/21

using deNovoGUI from cmd LINUX

Done. Seems I found working combination ) Thanks! On Thursday, September 2, 2021 at 5:56:41 PM UTC+3

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using deNovoGUI from cmd LINUX

Done. Seems I found working combination ) Thanks! On Thursday, September 2, 2021 at 5:56:41 PM UTC+3

9/2/21

Qin Fu, Harald Barsnes5

2/26/21

Questions for deNovoGUI

Hi Harald, Thanks for your kind reply. I figure out the sequence I want. Thanks again. All the best.

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Questions for deNovoGUI

Hi Harald, Thanks for your kind reply. I figure out the sequence I want. Thanks again. All the best.

2/26/21

Ryan, Harald Barsnes2

5/8/20

Searching HCD data with pepNovo

Hi Ryan, I would recommend that you contact the PepNovo developers directly (see http://proteomics.

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Searching HCD data with pepNovo

Hi Ryan, I would recommend that you contact the PepNovo developers directly (see http://proteomics.

5/8/20

KATHERINE MURATORE, Thilo Muth2

1/21/20

Interpreting peptide sequence output

Dear Katherine, thanks for your interest in using our tool DeNovoGUI. Actually having no information

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Interpreting peptide sequence output

Dear Katherine, thanks for your interest in using our tool DeNovoGUI. Actually having no information

1/21/20

Andrew Ottens, Harald Barsnes2

8/10/18

Optimizing DirecTag Params via DeNovoGUI

Hi Andrew, I'm afraid we've been unable to locate documentation for the DirecTag parameters

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Optimizing DirecTag Params via DeNovoGUI

Hi Andrew, I'm afraid we've been unable to locate documentation for the DirecTag parameters

8/10/18

Catherine Heylings, Harald Barsnes6

5/2/18

CLI results

Hi Catherine, > I must not be getting the right output, I haven't got a tab text file out. For

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CLI results

Hi Catherine, > I must not be getting the right output, I haven't got a tab text file out. For

5/2/18

dcan...@uw.edu, Harald Barsnes2

5/1/18

Changing enzyme or no enzyme in the GUI

Hi, The enzyme does not have an impact on the de novo sequencing, as either the algorithm does not

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Changing enzyme or no enzyme in the GUI

Hi, The enzyme does not have an impact on the de novo sequencing, as either the algorithm does not

5/1/18

cha...@nanoprecisionmedical.com2

3/30/18

Can I add my sequence anywhere?

never mind...lol I guess I already asked that question On Friday, March 30, 2018 at 11:30:23 AM UTC-7

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Can I add my sequence anywhere?

never mind...lol I guess I already asked that question On Friday, March 30, 2018 at 11:30:23 AM UTC-7

3/30/18

cha...@nanoprecisionmedical.com, Marc Vaudel2

3/29/18

where is the program?

Hi, There is no dumb question, it is never easy to get started on a new tool :-) If you double-click

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where is the program?

Hi, There is no dumb question, it is never easy to get started on a new tool :-) If you double-click

3/29/18

bechtel...@gmail.com, … Harald Barsnes4

2/28/18

import peptide sequence?

Hi Charity, > Do u have a manual on this besides the one online? There is no manual besides what

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import peptide sequence?

Hi Charity, > Do u have a manual on this besides the one online? There is no manual besides what

2/28/18

cha...@nanoprecisionmedical.com, Harald Barsnes2

11/20/17

Trojan virus on download?

Hi, This looks like a false positive by the Gateway Anti-Virus. I've just rechecked both the

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Trojan virus on download?

Hi, This looks like a false positive by the Gateway Anti-Virus. I've just rechecked both the

11/20/17

Samuel Miller, Marc Vaudel2

9/14/17

mzML file format?

Hi Sam, Yes, we are working towards supporting more formats in our tools. However, to run the

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mzML file format?

Hi Sam, Yes, we are working towards supporting more formats in our tools. However, to run the

9/14/17

Marc Vaudel

7/17/17

Evolution of java requirements

Dear all, We are in the process of refactoring our code for better performance and integration with

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Evolution of java requirements

Dear all, We are in the process of refactoring our code for better performance and integration with

7/17/17

Samuel Miller, Harald Barsnes3

3/11/17

Error in IdentificationParametersCLI

Thank you, Harald. On Friday, March 10, 2017 at 4:26:53 PM UTC-6, Harald Barsnes wrote: Hi Samuel,

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Error in IdentificationParametersCLI

Thank you, Harald. On Friday, March 10, 2017 at 4:26:53 PM UTC-6, Harald Barsnes wrote: Hi Samuel,

3/11/17

Thys Potgieter, Marc Vaudel3

12/19/16

Understanding mass gaps

Thank you so much Marc! I will have a look at the new feature of PeptideShaker as well, Kind regards

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Understanding mass gaps

Thank you so much Marc! I will have a look at the new feature of PeptideShaker as well, Kind regards

12/19/16

Thys Potgieter, Harald Barsnes3

11/28/16

Precursor ion charge in blast_output.txt sometimes missing

Thank you Harald! I use Tag Match option instead. On Sunday, 27 November 2016 22:52:40 UTC+2, Harald

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Precursor ion charge in blast_output.txt sometimes missing

Thank you Harald! I use Tag Match option instead. On Sunday, 27 November 2016 22:52:40 UTC+2, Harald

11/28/16

Thys Potgieter, Harald Barsnes4

11/11/16

Parent ion mass

Hi Thys, > Does the BLAST export also include tag sequences, excluding the regions of uncertainty

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Parent ion mass

Hi Thys, > Does the BLAST export also include tag sequences, excluding the regions of uncertainty

11/11/16

mcamen...@gmail.com, Harald Barsnes2

10/23/16

Using DeNovoGUI for mass spectra obtained in negative ion mode

Hi Michelle, Thank you for your interest in DeNovoGUI. DeNovoGUI is simply a single user interface

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Using DeNovoGUI for mass spectra obtained in negative ion mode

Hi Michelle, Thank you for your interest in DeNovoGUI. DeNovoGUI is simply a single user interface

10/23/16

Lee S Parsons, … Harald Barsnes4

9/12/16

How to relate Spectrum Title to Retention Time?

Hi Lee, We've just released DeNovoGUI v1.12.4 which adds retention time to the exports. Hopefully

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How to relate Spectrum Title to Retention Time?

Hi Lee, We've just released DeNovoGUI v1.12.4 which adds retention time to the exports. Hopefully

9/12/16

Thys Potgieter, Marc Vaudel3

8/24/16

Command line result export

Thanks Marc, that is exciting news, please do keep me posted, and I will very much like to try the

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Command line result export

Thanks Marc, that is exciting news, please do keep me posted, and I will very much like to try the

8/24/16

Nyari, Harald Barsnes2

4/23/16

Error using CLI

Hi Nyari, What is the command line you are trying to run? The following command line works fine for

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Error using CLI

Hi Nyari, What is the command line you are trying to run? The following command line works fine for

4/23/16

Adriana Rizzo, Marc Vaudel2

4/7/16

Incorporating PepNovo RankScore?

Hi Adriana, Thank you for this suggestion, it is very helpful to know what is needed on your side. We

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Incorporating PepNovo RankScore?

Hi Adriana, Thank you for this suggestion, it is very helpful to know what is needed on your side. We

4/7/16

Darryl Davis, Marc Vaudel3

3/27/16

Where are the individual results for each algorithm stored? I would like to load them in PS

Hi DD, No worries :) These are indeed in the output folder. You can directly open the results in the

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Where are the individual results for each algorithm stored? I would like to load them in PS

Hi DD, No worries :) These are indeed in the output folder. You can directly open the results in the

3/27/16

Darryl Davis, Lennart Martens2

3/22/16

De Novo Gui Updates

Hello, We have some issues with the genesis server. We're resolving these right now (and are

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De Novo Gui Updates

Hello, We have some issues with the genesis server. We're resolving these right now (and are

3/22/16

Alejandro Cohen, Harald Barsnes9

3/4/16

Peptide Matches!

Hi Alex, We've just released new versions of both DeNovoGUI and PeptideShaker which should allow

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Peptide Matches!

Hi Alex, We've just released new versions of both DeNovoGUI and PeptideShaker which should allow

3/4/16

Teck Yew Low, Harald Barsnes2

12/3/15

New user of DeNovoGUI

Hi Teck, I've tried to answer your questions in-line below. Let me know if something is unclear.

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New user of DeNovoGUI

Hi Teck, I've tried to answer your questions in-line below. Let me know if something is unclear.

12/3/15

Teck Yew Low, Harald Barsnes2

12/3/15

pNovo+ stopped in the middle of a analysis

Hi Teck, If one of the algorithms fails to complete in this way we'd recommend contacting the

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pNovo+ stopped in the middle of a analysis

Hi Teck, If one of the algorithms fails to complete in this way we'd recommend contacting the

12/3/15