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Messages - Hiroshi Tsugawa

MS-DIAL / Re: missing values: MSDIAL doesn't display all comounds from the uploaded mzML-file
Dear Jana and Bruce

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.

MS-DIAL / Re: Areas of EquiSplash Lipidomix

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.

MS-DIAL / Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)
Hi Shuai

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.

MS-DIAL / Re: Injection volume and Y variable

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.


MS-DIAL / Re: Identical lipids with same retention time in Bruker PASEF data (MS Dial 4 paper)
Dear users,

Sorry for my late action. Yes, Shuai is right.

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)

MS-DIAL / Re: Not all my internal standards are detected

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,

MS-DIAL ver. 4.60-dev

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

#Centroid parameters
MS1 tolerance   0.01
MS2 tolerance   0.025

#Isotope recognition
Maximum charged number   2

#Data processing
Number of threads   1

#Peak detection parameters
Smoothing method   LinearWeightedMovingAverage
Smoothing level   3
Minimum peak width   5
Minimum peak height   10000

#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

#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

#Ion mobility
Ion mobility data   FALSE