MS Amanda

Dear Gerhard, I was going to post another question about limma at 'IMP PD Nodes' google group

Hey Viktoria, That is great to hear. Sadly though, I am only using MS Amanda in conjunction with PD.

Hi Andy, sorry for the late reply, that message somehow got lost...So you would expect the value to

Thank you very much! I will test and give you feedback as soon as possible. Best, -C On Thu, Mar 18,

Please, check if the installer at Protein Chemistry Facility (imp.ac.at) is OK. It doesn't do

What if you know the person personal On Mon, Feb 1, 2021, 7:50 AM Viktoria Dorfer <viktoria.dorfer

I guess it is tradeoff speed/resources. thanks! Carlos On Fri, Jan 29, 2021 at 5:47 PM Viktoria

this is really helpful! Carlos On Fri, Jan 29, 2021 at 5:42 PM Viktoria Dorfer <viktoria.dorfer@fh

Hi! Yes, if you run MS Amanda within Skyline a Percolator validation is performed after the search.

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

Hi Nick, in the standalone version you can specify neutral losses for user-defined modifications by

Thanks Victoria, now it works! By the way, how to set up several threads for DB searching in the

Hi Victoria, thank you!!! Now it finally works, and I managed to import MS Amanda results into

Hi Viktoria, Thanks! I can confirm that it now works as expected. :) Best regards, Harald On

Hi Carrie, MS Amanda can unfortunately not tell you, which of your 10 samples have been

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

Hi Andrew, we have fixed that issue in the new standalone version (v. 2.0.0.13723). There is now an

Hi Andy, we finally have a new version of MS Amanda available that includes your requested changes on

Hi, the new MS Amanda standalone versions now enables to have the same database name if they are in

I also just saw, that there was an error in your Processing Step C, as ptmRS was not executed and

Hi Erik, thanks for reporting that! I had a look at the code and it is definitely a bug but just a

Hi Simon, the matched ions output is in the current release in the PD version and will be in the next

Hi Erik, thanks for reporting this, we will have a look at it. It needs some refactoring of our code,

Hi Viktoria, Thanks for your reply. The unblocking did the trick. I thought it was not needed as it

Hi Chia-wei, in principle yes. There is a version of MS Amanda for PD 2.3, but that will not work

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

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

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

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

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