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Messages - romanas chaleckis

1
MS-DIAL / Re: InChIKey Generation
I also have a same problem - my workaround is to use just the first layer of the InChIKey plus the UHFFFAOYSA-N. Separation of enantiomers (second layer of the InChIKey) is anyway rare on classic LC-MS.

@Hiroshi Tsugawa
I am not sure MS-DIAL/MS-FINDER is generating InChIKeys by itself. It seems there is some library in MS-DIAL which contains UHFFFAOYNA-N ending. Perhaps changing UHFFFAOYNA-N to UHFFFAOYSA-N would resolve the confusion?
5
MS-DIAL / Re: MS/MS Spectra in mzML File
do you have the right precursor mass in the MS2 spectra data? in your screenshot it looks like all the MS2 spectra are for m/z ~764 ion
8
MS-DIAL / Re: MSDial-Multithreading
In data processing "Analysis parameter setting" tab click the "Advanced" and in the Multithreading input how many threads you want to use.
10
MS-DIAL / Re: Delete features
as far I as know no option to delete - just add comment for filtering/sorting. Manual addition of peaks is also not (yet?) implemented...
11
MS-DIAL / Re: Manual curation of Alignment
yes, I think that is expected. The third panel shows you how the integrations look on the actual data after correction.
12
Other metabolomics resources / metabolites.in/foods database
just wanted to give a shout for the non-targeted LC-MS metabolomics food database (metabolites.in/foods ; twitter @shokurepo4) created and maintained by Dr. Nozomu Sakurai at National Institute of Genetics in Japan). Over 200 foods methanol extracted and measured using a C18 column 90min gradient on a Finnigan-LTQ-FT with MS2 and MS3 spectra. If you have an unknown m/z and suspect it comes from food - check it there!
13
MS-DIAL / Re: MS2 spectrum missing peak information
Hi,

I agree that from Larissa's screenshots it can not be ruled out that MZmine and MS-DIAL are showing different spectra. However, in case of MZmine the spectrum can be traced back to file "141.mzXML" spectrum #1873. Is there a way to show such precise origin of the MS2 spectra in MS-DIAL? I hope this could help to settle the issue.

Best,
romas




14
MS-DIAL / Feature suggestion: correlation column in the alignment table
Hiroshi and MS-DIAL developers,
would it be possible to include the correlation column in the alignment table?
It was already included in 2.94 developmental version (screenshot attached). It is helpful to find in-source fragments as well as actually correlating metabolites.
15
Mass spectrometers / Re: Internal Standards for LCMS
Hi Niall,
I think for quantification with expensive isotopes you are much better off with targeted methods. For untargeted work we use internal standards for technical check (as Stacey suggests). In that case, depending on chromatography and matrix, cheap exogenous compounds not expected in samples can be used- e.g. Good's buffers for HILIC, drugs and pesticides for RP.
Cheers,
romas