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Messages - triston.groff

1
MS-DIAL / Re: MSDIAL 5.1 crashing with timsTOF data
I don't have a solution to this problem, but commenting to say that this has been my experience too using timsTOF Flex. Weirdly, MSDIAL version 4 works but version 5 doesn't.

I think that with MSDIAL 5, they stopped recommending converting to .ibf format because supposedly raw .d files are readable, but this has not been my experience.

Maybe this should be an issue that is opened on the MSDIAL GitHub issues page. I believe this is where they now would like issues to be posted.

Take care,
Triston
2
MS-DIAL / Re: Peak detection: Amplitude calc
If you have some prior knowledge of features before hand, your best bet is to determine this in the vendor software. You just need to determine a suitable cutoff to call "noise" that you have some confidence is a lower intensity than a low-intensity biological peak. There is no right or wrong, one size fits all. You must examine your data before setting the MS-DIAL parameters because they may not be appropriate for every analysis.
3
MS-DIAL / Re: How to do multiple regression or PCA in MS Dial?
PLS-DA may be better for this since it is supervised. Anyway, this can be done by assigning Class ID ['option' tab in toolbar],
 normalizing (must assign class first; I prefer LOWESS + an internal standard)[data visualization tab], then doing stats in the tool that is also under the data visualization tab (can't remember name off the top of my head).

Take care,
Triston
5
MS-DIAL / Re: Assigning Class ID using Console App?
I know that this topic has not been posted for a long time now, but there is very little documentation on MsdialConsoleApp and this is the only search engine match online regarding class assignment in the console app, so I am bumping this... hope this doesn't break any forum rules.

Take care,
Triston
6
MS-DIAL / Re: Command line to multiple cores for msdial
I think that you would set this in the method file. I will be using a cluster running linux soon for MsdialConsoleApp and MsfinderConsoleApp (if I can get this one to work), so I will try and update when that happens. This github repo might be helpful to you.

Take care,
Triston

7
MS-DIAL / Re: MsfinderConsoleApp unusable from a shared Linux installation
Any information on utilizing MsfinderConsoleApp would be very helpful! Overall, there is a lack of information and documentation available on the console versions of CompMS apps, especially MsfinderConsoleApp. From what I can tell, most every post on this forum involving MsfinderConsoleApp goes unanswered.
8
MS-DIAL / Re: Options for Noise Cleaning of MS2 spectra for Build an Inhouse Spectral Library?
Using CorrDec will help. I recommend reading the tutorial for creating an AMRT library. This was very helpful to me. CorrDec requires multiple injections at different intensities to deconvolute spectra. The tutorial says to do a 7 point serial dilution with 1 compound/vial, but this was too costly for us, so instead we did 10 non-isobaric compounds per vial and did injection series with increasing injection volume.

Good luck!

-Triston
9
MS-DIAL / Re: Possible to export MSDIAL alignment results from console app?
I have been trying to figure this out for so long!!! This would be VERY helpful. As far as I can tell, all uses of the console application require GUI application as well. For many situations, it would be nice to be able to get results without opening the GUI. Exporting results tables would allow for a full analysis with the console application, but it would also be nice to be able to perform ion amalgamation, RT correction, and other MS-DIAL functions from the command line.
10
MS-DIAL / Re: Extracting MS2 peaks from PASEF DIA data
I have a related question.. Hypothetically, say an LC feature (with CCS = -1) of mz = 250.0100 and RT of 3.5 gives rise to two separate ion-mobility features with CCS of 150 and 170, and the feature with CCS of 150 has a different fragmentation pattern than the feature with CCS of 170.

  • Feature 1 (LC): mz = 250.0100, RT = 3.5 min, CCS = -1
  • Feature 2 (IM #1): mz = 250.0100, RT = 3.5 min, CCS = 150
  • Feature 3 (IM #2): mz = 250.0100, RT = 3.5 min, CCS = 170

Is the MS2 spectrum that is displayed of the fragmentation for the LC peak (as in, is the spectrum the same for all three features), or does MSDIAL read the PASEF frames in the file and can distinguish the spectra between the two IM features with different mobilities? I hope I explained that well... @Hiroshi Tsugawa

PS - I do not have experience with dia-PASEF data, but dda-PASEF data is not a problem for me to do what you are describing @simionkreimer , but I do sometimes have problems with MSDIAL crashing when working with PASEF data.

Take care,
Triston
11
MS-DIAL / Re: ABF converter in CMD
In addition to drop in signal intensity (to be expected apparently), I have also noticed some missing peaks when using centroided *.mzML files as input for the ABF converter. For me, my processing steps were:
profile Sciex *.wiff files --[msConvert peak picking 1- ]--> centroid *.mzML --[ABF converter]--> *.abf

I find the best results I get, however, are obtained by simply loading *.wiff files directly into MS-DIAL, or going straight from *.wiff to *.abf without centroiding if using the MsdialConsoleApp.

PS - These were SWATH DIA files

Cheers,
Triston
12
MS-DIAL / Re: Merging pos and neg feature lists
Dear Anna and Hiroshi,

I know this topic is very old, but I was having the same issues as Anna but I solved the issue (at least mine).

In Section 5-12-2 of the MSDIAL tutorial, Step #1 says to export "Peak list result", and later on in the image below Step #4, the peak list (from a sample, instead of the alignment result export) is being applied to the Alignment Spots. I did not have a crash when the alignment export from positive polarity is applied to the alignment spots in negative polarity, and vice versa.

Another source of this crash can be the advanced settings under the MS2Dec tab of the MSDIAL project processing parameters. When isotopic peaks are not filtered, this also causes a crash.

I hope this post helps others with a similar issue in the future.

Cheers,
Triston
13
MS-DIAL / Re: Error in sample processing in MS DIAL
Do not have an answer for you, but this also happens to me. Sometimes if I re-convert the files (even if I know there is nothing wrong with the file based on viewing in SeeMS), or use less threads, I do not have the issue.
14
MS-DIAL / Re: MSMS only export (msp or mat)
Hi gabbyblack,
If I understand correctly, you want to export peaks with MS2 acquisition right? If so, you can filter both Peak Spot Tables and Alignment Spot Tables using the filters just to the right of the file list. You can also filter by ref matched, unknown, unique, etc. Once filtered, open up the peak table and there is a button on the upper left that allows you to export to MS-FINDER. By default, it checks every feature in the table, but you can actually click "uncheck all" or uncheck the ones you don't want to send. Then, you can export all the checked features in the table to MS-FINDER. Hope this helps.

-T
15
MS-DIAL / Re: Exporting CorrDec deconvolution results from the console app
Hi joewandy,

I am currently doing something similar to generate an in-house AMRT spectral library, using the protocol in the SI of https://doi.org/10.3390/metabo9110251 (Tada et al, 2019). Essentially, I have created batch scripts to sort data files into compound-specific folders, then create MS-DIAL projects within the folders using the MsdialConsoleApp.exe similar to what you have shown below. MsdialConsoleApp.exe processes files on a per-folder basis, and during this process it creates *.msp2 files within the folder that may be able to be collected using a batch script and then imported to MS-FINDER using MsfinderConsoleApp.exe, but this I am unsure about. I think, though, it is best to view in the GUI even though this is tedious.

From my understanding (though I could be wrong), there are a couple of reasons it is necessary to manually inspect the results in the MS-DIAL GUI application. One is the RT correction from CorrDec; I have had times where my internal standards weren't detected for every sample and I needed to re-process. Another is that, at least for a library, you want to take a spectrum from an injection where the signal is not saturated/too low. Once you determine the optimal spectrum in the dilution series, this can be manually exported into MS-FINDER. If you don't care about choosing the optimal, it is pretty easy to export an entire peak/alignment spot table to MS-FINDER in MSP format. This does awhile, as I have 1600 project files to go through. Once the spectra are imported into MS-FINDER, they can all be exported as MSP or mgf. Maybe you know already know this though.

I had problems viewing the alignment result in the MSDIAL GUI ( v4.80 ) when opening project files created by the MsdialConsoleApp. I read somewhere on this forum that the problem began after v4.48 (starting with v4.6 ), so I started opening the project files with v4.48 GUI and had no more issues.

I have been processing my library files by first converting *.wiff files to *.mzML (performing centroiding with peakPicking ms levels 1- ), then converting the centroided *.mzML files to binary *.abf files. I have noticed that for my reverse-phase files (both *.abf and *.mzML), the data files in MS-DIAL do not have all the features that I can see in SeeMS.. even for the *.mzML files, the intensity is decreased by 10^3 or 10^4 compared to when viewing the same *.mzML files in SeeMS and all of the features are not detected in MSDIAL (I have used minimum peak intensity from 0-1000). I do not have this problem for my HILIC files, which were processed the same way. I would not have noticed this quickly without opening up the project files. Sorry to distract from your issues.. I will probably make a separate thread for this.