sorry, I cannot check the issue without more details, but did you start your project by centroid modes for both ms1 and ms2? You should select centroid at least for shimadzu qtof. For Thermo QE, profile mode should be selected. And in the case of lipidomics project, which type of solvent do you use? If you use ammonium formate in the solvent, you should change the setting of adduct type in the lipid annotation browser.
You can annotate the splash lipidomics standards by e.g. attached format files. (please fix the retention time information.) The attached file is for equisplash mixture. Then, using the SPLASH normalization in ms-dial becomes straightforward.
>> I unticked the gap-filling option so I wondered if this was the reason? Yes, this is the reason. Did you try the processing with the gap-filling option?
Please directly drag & drop your .d files into the data grid in analysis file setting window. You do not have to click the browse/select button.
Because .d file is recognized as a folder in the normal file browser dialog, I cannot provide the environment to recognize the .d file as a file format at this moment soon. Therefore, instead, I allowed the drag/drop option right now.
>>Is there a output file like .mtd2 to allow us to import back to MS-DIAL to manually check peak shapes? Use "-p" option. It will generate the mtd file to be loaded in the GUI app.
currently, there is no meaning of injection volume (in the previous version, it was used for calculation of lipid-semi quantitative values). For Y variable, if you do PLS or OPLS for the discriminant/regression analysis in MS-DIAL, the information is required.
sorry, maybe, there is no way to do it. If you can write the source code, maybe, you can write the code to do it. Otherwise, the simple way is to buy a workstation overcoming the memory issue.
As the procedure of MS-DIAL, the program detects the peak in the RT axis. Then, the ions are expanded in the drift axis. Then, the peaks are detected in the drift axis. The row containing -1 value means that this is the result of RT axis peak detection. Therefore, you will see the same RT results twice.
Now, for bruker tims-tof data, you do not have to convert .d file into ibf. (I hope) From next version (it will be uploaded in the mid of July), the MS-DIAL also supports the direct import of .d file containing pasef data. You can evaluate it by the following link. (the link is expired on 4 July, 2021) https://we.tl/t-Cv77aUpHIj
I just checked your positive ion mode data. It works fine. Of course, several IS compounds were not detected owing to the structure property. However, at least, I could detect the peaks that you wrote as "Not detected by MS DIAL in ESI pos" in the excel.
I also pasted the parameters that I used. Thanks,
Hiroshi MS-DIAL ver. 4.60-dev
#Project MS1 Data type Profile MS2 Data type Profile Ion mode Positive Target Metablomics Mode ddMSMS
#Data collection parameters Retention time begin 0 Retention time end 100 Mass range begin 0 Mass range end 2000 MS2 mass range begin 0 MS2 mass range end 2000
#Peak spotting parameters Mass slice width 0.1 Exclusion mass list (mass & tolerance)
#Deconvolution parameters Sigma window value 0.5 MS2Dec amplitude cut off 0 Exclude after precursor True Keep isotope until 0.5 Keep original precursor isotopes False
#MSP file and MS/MS identification setting MSP file Retention time tolerance 100 Accurate mass tolerance (MS1) 0.01 Accurate mass tolerance (MS2) 0.05 Identification score cut off 80 Using retention time for scoring False Using retention time for filtering False
#Text file and post identification (retention time and accurate mass based) setting Text file E:\0_SourceCode\BugReports\20210414_GrosFich\pos_mzrt_lib.txt Retention time tolerance 0.5 Accurate mass tolerance 0.01 Identification score cut off 85
#Advanced setting for identification Relative abundance cut off 0 Top candidate report False
#Adduct ion setting [M+H]+
#Alignment parameters setting Reference file E:\0_SourceCode\BugReports\20210414_GrosFich\210322_SWS_QC4_ESIpos_14.raw Retention time tolerance 0.05 MS1 tolerance 0.015 Retention time factor 0.5 MS1 factor 0.5 Peak count filter 0 N% detected in at least one group 0 Remove feature based on peak height fold-change False Sample max / blank average 5 Sample average / blank average 5 Keep identified and annotated metabolites True Keep removable features and assign the tag for checking True Gap filling by compulsion True
#Tracking of isotope labels Tracking of isotopic labels FALSE
