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MS Amanda
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Mario Picciani
,
Viktoria Dorfer
3
May 26
Toubleshooting / Suggestions for current standalone development version
Hi Mario, thanks a lot for the detailed feedback and the suggestions, we highly appreciate that! The
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Toubleshooting / Suggestions for current standalone development version
Hi Mario, thanks a lot for the detailed feedback and the suggestions, we highly appreciate that! The
May 26
Danyl McLauchlan
,
Viktoria Dorfer
2
Mar 28
Install Error
Hi Danyl, can you please create a bug report in PD 2.4 (Tools -> Create Bug Report) and send that
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Install Error
Hi Danyl, can you please create a bug report in PD 2.4 (Tools -> Create Bug Report) and send that
Mar 28
jeanmarc...@gmail.com
,
Viktoria Dorfer
2
Feb 7
Acces to PD node download
Hi! this is not normal ;) We are unfortunately currently having issues with the webpage, but we are
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Acces to PD node download
Hi! this is not normal ;) We are unfortunately currently having issues with the webpage, but we are
Feb 7
Amadeus
,
Viktoria Dorfer
2
12/5/22
Could we set max rank to an infinity?
Hi! Great to hear, that you like MS Amanda :) The maximum number for the max rank property already is
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Could we set max rank to an infinity?
Hi! Great to hear, that you like MS Amanda :) The maximum number for the max rank property already is
12/5/22
Filippo GENOVESE
, …
Viktoria Dorfer
8
11/16/22
Virus in the PD3 node installer?
Hi Filippo, I forwarded your request to the developers of the node, they will look into that! Best
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Virus in the PD3 node installer?
Hi Filippo, I forwarded your request to the developers of the node, they will look into that! Best
11/16/22
Haru Yoshikawa
,
Gerhard Dürnberger
4
4/14/22
limma node
Dear Gerhard, I was going to post another question about limma at 'IMP PD Nodes' google group
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limma node
Dear Gerhard, I was going to post another question about limma at 'IMP PD Nodes' google group
4/14/22
David Domjan
,
Viktoria Dorfer
5
12/26/21
No. of dynamic modifications
Hey Viktoria, That is great to hear. Sadly though, I am only using MS Amanda in conjunction with PD.
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No. of dynamic modifications
Hey Viktoria, That is great to hear. Sadly though, I am only using MS Amanda in conjunction with PD.
12/26/21
lin...@uw.edu
,
Viktoria Dorfer
2
12/7/21
Add line to mzid output?
Hi Andy, sorry for the late reply, that message somehow got lost...So you would expect the value to
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Add line to mzid output?
Hi Andy, sorry for the late reply, that message somehow got lost...So you would expect the value to
12/7/21
Conor Jenkins
,
Viktoria Dorfer
10
3/18/21
Extremely Long Search Time with FAIMS data
Thank you very much! I will test and give you feedback as soon as possible. Best, -C On Thu, Mar 18,
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Extremely Long Search Time with FAIMS data
Thank you very much! I will test and give you feedback as soon as possible. Best, -C On Thu, Mar 18,
3/18/21
Juraj Lenco
2/12/21
apQuant instalation issue
Please, check if the installer at Protein Chemistry Facility (imp.ac.at) is OK. It doesn't do
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apQuant instalation issue
Please, check if the installer at Protein Chemistry Facility (imp.ac.at) is OK. It doesn't do
2/12/21
Carlos Alberto Gueto Tettay
, …
Jay Mendez
4
2/1/21
Changing temporary file name
What if you know the person personal On Mon, Feb 1, 2021, 7:50 AM Viktoria Dorfer <viktoria.dorfer
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Changing temporary file name
What if you know the person personal On Mon, Feb 1, 2021, 7:50 AM Viktoria Dorfer <viktoria.dorfer
2/1/21
Carlos Alberto Gueto Tettay
,
Viktoria Dorfer
3
2/1/21
Number of cores
I guess it is tradeoff speed/resources. thanks! Carlos On Fri, Jan 29, 2021 at 5:47 PM Viktoria
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Number of cores
I guess it is tradeoff speed/resources. thanks! Carlos On Fri, Jan 29, 2021 at 5:47 PM Viktoria
2/1/21
Carlos Alberto Gueto Tettay
,
Viktoria Dorfer
3
2/1/21
nonspecific search
this is really helpful! Carlos On Fri, Jan 29, 2021 at 5:42 PM Viktoria Dorfer <viktoria.dorfer@fh
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nonspecific search
this is really helpful! Carlos On Fri, Jan 29, 2021 at 5:42 PM Viktoria Dorfer <viktoria.dorfer@fh
2/1/21
Honglan Li
,
Viktoria Dorfer
2
1/14/21
Is there any way that run percolator after MS Amanda (without PD)
Hi! Yes, if you run MS Amanda within Skyline a Percolator validation is performed after the search.
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Is there any way that run percolator after MS Amanda (without PD)
Hi! Yes, if you run MS Amanda within Skyline a Percolator validation is performed after the search.
1/14/21
Da Qi
,
Viktoria Dorfer
11
9/28/20
Search failed.
Hi Da! great that it finally works! Concerning the different durations of the files: this is expected
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Search failed.
Hi Da! great that it finally works! Concerning the different durations of the files: this is expected
9/28/20
Viktoria Dorfer
,
Nick Hartel
3
4/27/20
Announcement
New Standalone Version for MS Amanda (MS Amanda 2.0)
Hi Nick, in the standalone version you can specify neutral losses for user-defined modifications by
unread,
Announcement
New Standalone Version for MS Amanda (MS Amanda 2.0)
Hi Nick, in the standalone version you can specify neutral losses for user-defined modifications by
4/27/20
Marc Isaksson
,
Viktoria Dorfer
5
4/17/20
Cannot run MSAmanda from commandline in Ubuntu 18.4
Thanks Victoria, now it works! By the way, how to set up several threads for DB searching in the
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Cannot run MSAmanda from commandline in Ubuntu 18.4
Thanks Victoria, now it works! By the way, how to set up several threads for DB searching in the
4/17/20
Marc Isaksson
,
Viktoria Dorfer
11
12/12/19
MS Amanda (v.2.0.0.9695), as part of SearchGUI(v.3.3.16), fails to parse MGF-files
Hi Victoria, thank you!!! Now it finally works, and I managed to import MS Amanda results into
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MS Amanda (v.2.0.0.9695), as part of SearchGUI(v.3.3.16), fails to parse MGF-files
Hi Victoria, thank you!!! Now it finally works, and I managed to import MS Amanda results into
12/12/19
Viktoria Dorfer
,
Harald Barsnes
5
9/19/19
New Standalone Version for MS Amanda
Hi Viktoria, Thanks! I can confirm that it now works as expected. :) Best regards, Harald On
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New Standalone Version for MS Amanda
Hi Viktoria, Thanks! I can confirm that it now works as expected. :) Best regards, Harald On
9/19/19
Carrie Chou
,
Viktoria Dorfer
2
9/13/19
MS Amanda and TMT-10plex labeled data
Hi Carrie, MS Amanda can unfortunately not tell you, which of your 10 samples have been
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MS Amanda and TMT-10plex labeled data
Hi Carrie, MS Amanda can unfortunately not tell you, which of your 10 samples have been
9/13/19
Attila Kertesz-Farkas
,
Viktoria Dorfer
5
8/2/19
max rank limit
Hi Viktoria, Thanks, I already saw the release notes. Can't wait to get my hands on it! :) A. On
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max rank limit
Hi Viktoria, Thanks, I already saw the release notes. Can't wait to get my hands on it! :) A. On
8/2/19
Andrew Collins
,
Viktoria Dorfer
3
8/2/19
MzIdentML incorrect
Hi Andrew, we have fixed that issue in the new standalone version (v. 2.0.0.13723). There is now an
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MzIdentML incorrect
Hi Andrew, we have fixed that issue in the new standalone version (v. 2.0.0.13723). There is now an
8/2/19
Andy Jones
,
Viktoria Dorfer
5
8/2/19
Some improvements to the MS Amanda mzIdentML output
Hi Andy, we finally have a new version of MS Amanda available that includes your requested changes on
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Some improvements to the MS Amanda mzIdentML output
Hi Andy, we finally have a new version of MS Amanda available that includes your requested changes on
8/2/19
schulzes...@gmail.com
,
Viktoria Dorfer
3
8/2/19
MS Amanda stores databases internally?
Hi, the new MS Amanda standalone versions now enables to have the same database name if they are in
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MS Amanda stores databases internally?
Hi, the new MS Amanda standalone versions now enables to have the same database name if they are in
8/2/19
Erik de G
, …
André Lüttig
15
6/19/19
apQuant error in PD2.3
I also just saw, that there was an error in your Processing Step C, as ptmRS was not executed and
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apQuant error in PD2.3
I also just saw, that there was an error in your Processing Step C, as ptmRS was not executed and
6/19/19
Erik de Graaf
,
Viktoria Dorfer
2
5/23/19
Fragment ion type matches in PD2.2 and 2.3
Hi Erik, thanks for reporting that! I had a look at the code and it is definitely a bug but just a
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Fragment ion type matches in PD2.2 and 2.3
Hi Erik, thanks for reporting that! I had a look at the code and it is definitely a bug but just a
5/23/19
Simon Perkins
,
Viktoria Dorfer
4
4/18/19
Fragment Ion Matches
Hi Simon, the matched ions output is in the current release in the PD version and will be in the next
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Fragment Ion Matches
Hi Simon, the matched ions output is in the current release in the PD version and will be in the next
4/18/19
erik.d...@gmail.com
,
Viktoria Dorfer
2
4/12/19
MSamanda 2.0 protein C-terminal variable modifcation not possible
Hi Erik, thanks for reporting this, we will have a look at it. It needs some refactoring of our code,
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MSamanda 2.0 protein C-terminal variable modifcation not possible
Hi Erik, thanks for reporting this, we will have a look at it. It needs some refactoring of our code,
4/12/19
erik.d...@gmail.com
,
Viktoria Dorfer
3
4/11/19
Installing MS Amanda in PD2.2
Hi Viktoria, Thanks for your reply. The unblocking did the trick. I thought it was not needed as it
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Installing MS Amanda in PD2.2
Hi Viktoria, Thanks for your reply. The unblocking did the trick. I thought it was not needed as it
4/11/19
Viktoria Dorfer
,
Chia-wei Lin
3
2/1/19
Announcement
New MS Amanda version for PD 2.X available!
Hi Chia-wei, in principle yes. There is a version of MS Amanda for PD 2.3, but that will not work
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Announcement
New MS Amanda version for PD 2.X available!
Hi Chia-wei, in principle yes. There is a version of MS Amanda for PD 2.3, but that will not work
2/1/19