I am trying to have MS-DIAL detect partially-separated peaks and have so far been unsuccessful.
The attached result was generated using MS1 detection threshold 1000, smoothing level 0, minimum peak width 2, and retention time tolerance 0.01 min. I've also tried detection threshold 1000-3000, smoothing level 0-3, minimum peak width 2-5, and retention time tolerance 0.01-0.05 min without any better luck.
From what I can tell, MS-DIAL is splitting these closely-eluting peaks at the correct place, but it is only integrating the second peak. I am not seeing a anything in the peak spot viewer corresponding to the first peak, which I would expect to be about 2.00 min and 609.145 m/z.
How can I get the first peak integrated as well? Which parameters can I adjust? This is my test peak, but there are several other peaks like this in my samples.
Many thanks in advance for your help! Hope everyone is doing well out there :-)
Today I came across an odd behavior in MS-DIAL. When I export alignment results as GNPS export, all of the files are empty of any data; this only seems to happen when "Filtering by the ion abundances of blank samples" is selected. When it is not selected, all of the files look fine.
However, when I am exporting as "Raw data matrix (Area)" or "Representative spectra", it works whether or not I have selected the "Filtering by..." option. In fact, the file sizes are the same in both cases.
I tried this with several of my project (.mtd) files that I have successfully exported GNPS files from. I tried with three different versions of MS-DIAL (4.12, 4.18, 4.20). The same thing seems to happen.
I'm surprised I didn't notice this before, but I think I never actually selected "Filtering by..." when exporting. I generally set up my analysis parameters with the option "Remove features based on blank information" using "Sample max / blank average = 5 fold change".
Is this a known issue? Am I doing something wrong?
How can I export CorrDec results as an MSP file? I searched the MS-DIAL tutorial, this forum, and Google, but I did not find any information about this.
If I should export using the "Export -> Alignment results" option, how do I know whether I am exporting the CorrDec spectra or the MS2Dec spectra?
Can I download all of the CorrDec spectra from the alignment results at once, or do I need to download them one by one?
First of all, here is what I'm working with: --Water's .RAW files, converted to mzML or ABF --Acquired using Waters Xevo G2 QTOF in MSe mode --ESI (negative ionization) --Function 1: low collision energy (6V); centroided --Function 2: high collision energy ramp (20-50V); centroided --Function 3: lockmass --mass range: 100-1500 Da (both low and high collision energy functions) --MS-DIAL v4.12
I'm the most unclear about which "MS method type" to use and how to set up the Experiment file. According to the tutorial (https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#section-8-1), I should be using ‘All-ions with multiple CEs’ and set up the experiment file something like: ID MS Type Start m/z End m/z Name CollisionEnergy DecTarget(1:Yes, 0:No) 0 SCAN 100 1500 MS1 6 1 1 ALL 100 1500 MS2 20 1 2 ALL 100 1500 MS2 50 1
However, this does not quite make sense, because the 20V and 50V modes are just the two bounds of the ramp. The entire ramp is collected as a single data stream (function 2), not as two separate streams.
An earlier section of the tutorial (https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#section-1-4) also shows "MSE" as an option for MS Type, which makes more sense to me. However, this example only has the first 4 columns of the experiment file: (i.e. ID, MS Type, Start m/z, End m/z). This would suggest that the MS method type should be set to "SWATH-MS or conventional All-ions method".
I am also unclear on how to set up the "DecTarget" part of the experiment file. My chromatograms have many closely-eluting peaks, so I think I need to do deconvolution. Would I need to set DecTarget = 1 for all of the lines in the experiment file? Or just the line corresponding to the low energy channel (i.e. function 1).
In summary, my questions are: 1) How should I set up the experiment file correctly? Does each line in this file correspond to a data channel (e.g. function 1)? 2) Which "MS method type" should I select? 3) Given what I've described about my data and goals, are there any other data processing parameters that I should pay particular attention to? How about data file conversion parameters?
Thank you for all of your help. I'm very excited by the prospect of being able to do FBMN with our old MSe data!
What I'm trying to do now is to export the MS2 spectra from the DDA files only using the featureSpectra function. I want to integrate this with GNPS for FBMN.
If I run it on the unmodified XCMSnExp object, I get an error that it contains MS1 spectra.
The XCMS manual says "All subsetting methods try to ensure that the returned data is consistent. Correspondence results for example are removed if the data set is sub-setted by file, since the correspondence results are dependent on the files on which correspondence was performed. "
Even after reading the above, I still don't fully understand why it is necessary to remove the correspondence results. In my mind, after correspondence and peak filling, the XCMSnExp is a peak table with a bunch of metadata associated with it (I realize that this is an oversimplification and probably not true). And if so, why does correspondence have to be dropped when filtering by file?
At any rate, is there a way to do what I am trying to do? That is, pre-process MSe and DDA together (which I've successfully done) and then export MS2 data from only the DDA files. Basically, I'm trying to arrive at a set of MS1 features that is common to both MSe and DDA datasets. The ultimate goal is to utilize old MSe files to generate metadata about the features and then integrate that metadata into a feature-based molecular network.
I am trying to process over 2500 files from a UPLC-QTOF-MS dataset. The goal is to eventually increase this number to 10,000 and beyond. Currently I am using MZmine 2. I am fortunate to have access to a big server (80 core, 350+ GB RAM). However, it seems that the peak alignment step is not optimized for this number of samples. See my other post for more details about this issue: https://github.com/mzmine/mzmine2/issues/518
Any ideas on a more efficient peak alignment method? As far as I can tell, the raw data are already pretty well aligned; the UPLC seems to be fairly consistent. My main objective right now is to get all the samples/peaks into a single matrix.
I am actively trying different approaches, but it all takes time. I am hoping that someone else who has trod this ground before can offer advice to help save time and effort.
