MS Amanda

1–30 of 82

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David Domjan, Viktoria Dorfer5

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 Dorfer2

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 Dorfer10

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

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 Mendez4

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 Dorfer3

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 Dorfer3

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 Dorfer2

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 Dorfer11

9/28/20

Hi Da! great that it finally works! Concerning the different durations of the files: this is expected

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Hi Da! great that it finally works! Concerning the different durations of the files: this is expected

9/28/20

Viktoria Dorfer, Nick Hartel3

4/27/20

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

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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 Dorfer5

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 Dorfer11

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 Barsnes5

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 Dorfer2

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 Dorfer5

8/2/19

Hi Viktoria, Thanks, I already saw the release notes. Can't wait to get my hands on it! :) A. On

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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 Dorfer3

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 Dorfer5

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 Dorfer3

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 Lüttig15

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 Dorfer2

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 Dorfer4

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 Dorfer2

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 Dorfer3

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 Lin3

2/1/19

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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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

Kenneth Lum, Viktoria Dorfer2

2/1/19

Triplex-Isobaric Peptide Termini Labeling

Hi Kenneth, this is in principle possible in MS Amanda. The problem in your case is, that this is not

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Triplex-Isobaric Peptide Termini Labeling

Hi Kenneth, this is in principle possible in MS Amanda. The problem in your case is, that this is not

2/1/19

Juraj Lenco, Viktoria Dorfer2

12/11/18

Two dynamic modifications at peptide N-term

Hi Juraj, there have definitely been two dynamic modifications in the previous version but somehow it

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Two dynamic modifications at peptide N-term

Hi Juraj, there have definitely been two dynamic modifications in the previous version but somehow it

12/11/18

Todd, Viktoria Dorfer2

10/31/18

MSAmanda slow to store spectra

Hi Todd, sorry for my late response. We are currently working on that issue and have already

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MSAmanda slow to store spectra

Hi Todd, sorry for my late response. We are currently working on that issue and have already

10/31/18

Bo, Viktoria Dorfer2

8/13/18

How to connect the spectrumID in mzid to the spectra in mgf or mzML file

Hi Bo, for each PSM the mzid file contains the 'cvparam' with the accession number MS:1000796

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How to connect the spectrumID in mzid to the spectra in mgf or mzML file

Hi Bo, for each PSM the mzid file contains the 'cvparam' with the accession number MS:1000796

8/13/18

Michael Porter, Viktoria Dorfer3

7/18/18

Error with mgf title

Hi Viktoria, I was running 2.0.0.9695, but I noticed that there is a newer version available (2.0.

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Error with mgf title

Hi Viktoria, I was running 2.0.0.9695, but I noticed that there is a newer version available (2.0.

7/18/18

kathi.n...@gmail.com, … Dorfer Viktoria7

7/6/18

Error message: Could not process spectra due to the following exception: constraint failed

Hi Art, the version 2.2.6.11097 can be downloaded from here: http://ms.imp.ac.at/index.php?action=

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Error message: Could not process spectra due to the following exception: constraint failed

Hi Art, the version 2.2.6.11097 can be downloaded from here: http://ms.imp.ac.at/index.php?action=

7/6/18

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