MS Amanda (v.2.0.0.9695), as part of SearchGUI(v.3.3.16), fails to parse MGF-files

[Marc Isaksson]

Hi, 

I tried to use MS Amanda (v.2.0.0.9695) as one of the search engines in SearchGUI(v.3.3.16) but did not manage to complete the 

search of any input MGF spectra file. As an example, I got the following error message in the SearchGUI console (same for all MGF files): 

_Thu Oct 10 23:28:13 CEST 2019 Processing Marc_P1908_284.mgf with MS Amanda.

Reading settings file...
Settings file successfully read.
Input files contain 81760 spectra

Searching file 'Marc_P1908_284.mgf'...
Error parsing mgf file at or after spectrum 'Marc_P1908_284.10.10.3 File:"Marc_P1908_284.raw", NativeID:"controllerType=0 controllerNumber=1 scan=10"'.
Error in parsing: RTINSECONDS=3.5201364
Search failed._

Apparently, this MS Amanda version has issues reading the MGF file and the retention time information associated with it. It does not matter if I generate the MGF files

with MSConvert as a standalone software nor within SearchGUI. 

Any idea what could be wrong here? 

Best,

Marc

[Viktoria Dorfer]

Hi Marc,

thanks for reporting this issue! Can you provide me with a sample mgf file where the MS Amanda search fails?

Thanks!

Viktoria

[Marc Isaksson]

Hi Victoria, 

I would just like to have an update on the issue that i reported. Did you find anything strange in the MGF files 

that I sent you? 

Best,

Marc

[Viktoria Dorfer]

Hi Marc,

sorry for my late reply. I had a look at the mgf file and the error has already been fixed in the latest MS Amanda version, which is however not shipped with the current SearchGUI version. I checked if the current version of MS Amanda would run in SearchGUI, which was successful. You can update MS Amanda in SearchGUI yourself performing the following steps:

* Download the latest version (2.0.0.14078) of MS Amanda Standalone here

* Right click on the downloaded .zip file and select the menu item "Properties" in the context menu.

* If visible, click "Unblock" at the bottom right of the Properties window.

* Click "OK" to close the Properties window.

* Extract the downloaded .zip file.

* Open a new file explorer and navigate to your SearchGUI installation folder

* There should be a folder "resources" and in there a folder "MS Amanda", navigate there

* Replace the three files "FHOOE_IMP.MSAmanda.Core.dll", "FHOOE_IMP.MSAmanda.Utils.dll", and "MSAmanda.exe" in this folder by corresponding files from the downloaded latest MS Amanda version

* Run SearchGUI

Please let me know if that worked!

Best regards,

Viktoria

[Marc Isaksson]

Hi Victoria, 

thank yhou very much for your help! Very much appreciated!

Best,

Marc

[Marc Isaksson]

Hi Victoria, I followed your advice and I got a little bit longer than last time, but the search still failed unfortunately. I downloaded the Standalone version and copied 

the three files you mentioned to the SearchGUI. I removed the downloaded MS Amanda folder thereafter since I thought it would be sufficient adding these three files (was that a bad decision?).

Anyhow, I got the following console output from SearchGUI: 

Wed Nov 20 16:18:43 CET 2019        Processing Marc_P1908_280.mgf with MS Amanda.
No fileformat choosen, using default fileformat .csv.
Using output fileformat .csv
Using output filename 'D:\Data_SearchGUI\Output\.SearchGUI_temp\Marc_P1908_280.ms-amanda.csv'

Reading settings file...
Settings file successfully read.

Perform Search
Input files contain 84663 ms2 spectra
Searching file 'Marc_P1908_280.mgf'...
Error parsing mgf file at or after spectrum 'Marc_P1908_280.336.336.5 File:"Marc_P1908_280.raw", NativeID:"controllerType=0 controllerNumber=1 scan=336"'.
Search failed. Best, Marc

On Tuesday, November 5, 2019 at 9:35:36 AM UTC+1, Viktoria Dorfer wrote:

[Viktoria Dorfer]

Hi Marc,

sorry for that, we will have another look into that!

I'll come back to you as soon as possible!

Best,

Viktoria

[Marc Isaksson]

Victoria, thanks for the quick response!

You can try to run the sample MGF file that I sent to you, perhaps that can help in the trouble shooting. 

Best,

Marc

[Viktoria Dorfer]

Hi Marc,

we found and fixed the issue - it had something to do with '.' and ',' as comma separator. You can download the latest version (v. 2.0.0.14665) here.

Please let me know if it worked!

Best regards,

Viktoria

[Marc Isaksson]

Thanks for the help! I will get back to you when I have tried it out. 

Best,

Marc

--
You received this message because you are subscribed to the Google Groups "MS Amanda" group.
To unsubscribe from this group and stop receiving emails from it, send an email to msamanda+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/msamanda/df7bdfff-692e-49b1-a397-e5c6634c4afd%40googlegroups.com.

[Marc Isaksson]

Hi Victoria, 

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

Best,

Marc