the centroid ms1 parameter is also used to construct EIC chromatogram which is used for ion quantification. If you set 0.01 Da for this, the EIC of e.g. m/z 200.000 is constructed by summing ions from 199.99 until 200.01. Thanks,
if you can give me an example to reproduce the behavior, please send the demo data set. I know, this kind of behaviors can be occurred for some reasons in software programing, but it cannot be fixed unless I can reproduce it by myself...Your community feedback is highly appreciated. Thanks,
thanks for asking. The calculation method of metabolite concentration e.g. by using calibration curves is currently not supported in MRMPROBS. As Ondrej wrote, the program was originally designed for mrm. However, now it can be used for all data types. For example, in using DIA data, as Ondrej wrote, I am using MRMPROBS with the pseudoMRM (Precursor->Product) method to quantify metabolites by MS/MS chromatograms instead of MS1 chromatogram which MS-DIAL supports. I explained this idea in this article. https://www.mdpi.com/2218-1989/9/6/119/htm
ms-finder and the other related tools like sirius and gnps are the program to facilitate annotation for unknown spectra. And therefore, the annotation result of such structure elucidation programs should contain many false annotations, and users have to deal with the data by their own ways (biology and chemistry background knowledge etc). The best practice to annotate metabolite is to use the experimental spectral libraries from massbank, gnps, and mona. And you can use such a library kit to be used in MS-DIAL program. http://prime.psc.riken.jp/compms/msdial/main.html#MSP
sorry, I cannot understand your purpose actually. >>The tasks that have to be done are matching precursors to according MS2 spectra (which is called deconvolution i guess?), identification and quantification. Maybe, many programs can do these procedures. What is your issue?
sorry, I cannot reproduce your issue of RUN1. After I choose "use retention time" in identification and alignment tabs, the program executes samples without the error messeage.
...anyway... >>MS Dial seems to expect the presence of alkanes from the dictionary in each sample, right? Yes, but for example, in my practical use, I analyze one alkane sample before the sequence for biological samples is started. Then, I make the alkane dictionary file. Then, the file is used to calculate RI values for all of biological samples data.
>> do I really need alkanes in each sample? No, but in my practical use, the alkane sample is analyzed "each batch sequence". Maybe, for a large-scale project, in my experience, 50-60 samples were analyzed each week (in which one alkane mixture is also analyzed), then, a total of 1000 biological samples was analyzed by MS-DIAL. Then, I prepared the alkane dictionary file to calculate RI values for "the week's biological samples peaks". Then, the RI values were used for annotation and for peak alignment.
The conversion code to serialize/deserialize the lbm/lbm2 files is not publicly available yet. The lbm2 file contains many non-publicly available lipids information which is only used in our institute. In future, I will distribute the program of course. Please wait for a while. Thanks,
Sorry, please let me know more detail... 1. did you double-click the one shown in the alignment navigator (left-bottom of msdial window). 2. then, did you click "show ion table" in the center panel of ms-dial window.
you should be changed to [M+Na]+ for the sodium adduct information. According to the SMILES code, the exact mass is 874.4714. Because the precursor m/z is 897.46, it can be expected as [M+Na]+ because the exact mass of Na+ is 22.9892. Thanks,
