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Messages - mecolley

1
MS-DIAL / Re: MSDIAL 5.1 crashing with timsTOF data
Thank you Triston!

I even tried converting to IBF format first and loading that into 5.x, but the software crashes. I'll post a reply to the GitHub repository - thank you for the tip.

Best,
Maddie
2
MS-DIAL / MSDIAL 5.1 crashing with timsTOF data
Hello,

I have downloaded the latest 3 versions of MSDIAL and all of them crash when I try to analyze data from my timsTOF Pro2 and our timsTOF FleX instruments. The data was collected with PASEF and I have converted the files with the IBFConverter. The data opens and is analyzed well in MSDIAL version 4.90, but I cannot get the same IBF files to process in the newer versions.

Any updates on timsTOF data compatibility with MSDIAL 5.x? Does anyone have any advice?

Thank you,
Maddie
3
MS-DIAL / Gangliosides in the Lipidomic Library
Hello all,

I noticed that the website was updated to list the nomenclature of the larger gangliosides ( http://prime.psc.riken.jp/compms/msdial/lipidnomenclature.html ). I am particularly interested in the GD1a/b series and am currently annotating them by hand.

I downloaded the newest available versions and noticed that in the lipidomics library (positive and negative), gangliosides above GM3 are not available.

Any updates on when they will be included?

Best,
Maddie
4
MS-DIAL / Search lbm2 file
Hello,

I want to be able to search the lbm2 file, specifically to be able to view the Na+ in silico ms/ms for SM species. I am doing total laser fragmentation and lose the precursor entirely in a complex mixture and am matching without a precursor m/z. The easiest way to search is to import an msp library into NIST and do an "any peak" search for fragment ions and tap through the results. Since I do not have a "precursor" ion, I am doing a search sort of from the middle out.

However, most of the msp in silico library do not seem to contain Na+ adduct types for all lipid species.

Is there a way to either:
1. perform an "any ion" search like in NIST against the lbm2 library?
2. convert the lbm2 library to an msp?

Best,
Maddie
5
MS-DIAL / Convert msp2 to text format
Hello,

The .msp2 file that is generated when you do a search - how can we visualize this file? Or convert it to be visualized? I am trying to view what the in-silico MS2 spectrum would be for a random [M+Na]+ but cannot access the generated msp2 and the msp does not have Na+ info.

Thank you,
Maddie
6
MS-DIAL / Re: Version 5.1.22 Takes considerably longer than 4.90
Hello,

Adding to this now that all data sets have crashed multiple times. All files seem to load and during the "processing" bar, the software closes out and there is no project file made. My sample table is setup to have a QC and a blank. I made sure all of the files are the same polarity. I'm trying version 5.1.221224 now, but it's barely made it halfway through one file in the last hour.

I am excited to use the new version, so I am hoping for some potential solutions or ideas.
7
MS-DIAL / Re: Version 5.1.22 Takes considerably longer than 4.90
Follow up to this - one of my sample sets crashed without any notice or warning during the stage where it's loading each data file. Is there an error log somewhere so I can try to get to the bottom of why it's so slow and failing?
9
MS-DIAL / Version 5.1.22 Takes considerably longer than 4.90
Hello all,

I recently downloaded MS-DIAL 5.1.22 to re-analyze data which I have already processed in version 4.90 without issues. My data in version 4.90 took approximately 4 hours to analyze and we are on 24 hours in version 5.1.22 (and only halfway through). I didn't see in the new version anywhere to increase the number of threads.




(its stuck here)

My computer is not at any resource utilization cap and I still have 500 GB free on my C drive and 500 GB on my D drive where the data is being processed and saved. The IBF files for my timsTOF data were generated in the IBFcoverter located in the 4.90 version folder since my 5.1.22 file is missing an IBFconverter.

Any ideas? I'd love to use the new version, but I can't have my computer running this process for the next 72 hours... I am not sure it'll even pass!

Thank you,
Maddie
10
MS-DIAL / Where is the IBF converter in the new versions?
I am trying to load my timsTOF DDA data into version 5.1 and I noticed there isn't an IBF converter. Do I have to use an older version?

Also, when trying to load my older .ibf files that generated a good alignment file in version 4.90, the entire data set with my parameters fails the joint aligner and gap filling and can't generate a .eic file. Any suggestions?
11
MS-DIAL / Re: MS-DIAL 4.60 was released.
Hello Hiroshi,

I receive the same error as Sebas when attempting to open the IM-MS/MS tutorial data in the 4.60 version. I attached the picture for clarity.

In attempts to resolve, I did the following:
 - downloaded the lmb2 file from the MSDial website and moved the file into both the data folder and the program folder
- downloaded the lmb file from the MSDial website and moved the file into both the data folder and the program folder

Neither resolved the issue. However, the data opens perfectly fine in 4.48.

Thank you,
Maddie