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Messages - romanas chaleckis

1
MS-DIAL / Re: AIF data analysis
Hi, indeed the order of different scan types is vendor-specific. For example you can check the order in MZmine and if your scan type order is like in the attached screenshot then use your example 2 (ID0: SCAN, ID1: AIF). If you also set "DecTarget" 1 for the SCAN, then you will get deconvoluted in-source fragmentation.
4
MS-DIAL / Re: How to predict MS/MS spectrum of a given chemical that is not present in Pubchem
hi Sukis,

in such case you need to create custom database (tab separated .txt file) with compounds of your interest containing
Title   InChIKey   Short InChIKey   PubChem CID   Exact mass   Formula   SMILES   Comment

example file attached.
As far as I remember formula and smiles are the crucial fields.

Best, romas


6
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
probably the having multiple time segments in the method causes the issue. For the future try acquiring all data in one segment, or stop acquiring data in the 0-0.2min segment. Anyway, are you sure your flow-through peak with salts comes around 0-0.2min?

for the current files, if you want to use the MS2Dec and CorrDec in MS-DIAL, I am afraid you will have to check and crop (subset function in ProteoWizard MSconvert) the files one by one to make sure they match MS-DIALs experiment settings file. However, if you just want MS1 then proceed with simply filtering MS1 - no deconvoluted MS2 spectra in such case.
7
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
Hi Marites,

I think I found the problem - it is in the number of spectra in each experiment. Sometime around 0.25 min there are some scans "missing" and the number of missing scans seems to be different for each file (see attachment). However, MS-DIAL assumes that the number and order of scans is consistent and hence all the problems with intensities/CVs...

@Hiroshi Tsugawa - Probably the readin/assignment of collision energy has to be modified or at least a warning given if the number of spectra is varying between to MS1 spectra.

@7clouds7 - what is happening around 0.25min in your method?

Best,
romas
8
MS-DIAL / Re: MSP
1) these are not "errors" - these are warnings about the MSP file contents. different chemical formulas for same compound, different endings of inchikeys, RT differences - it is for your information. decide for your self how you deal with it - you can simply ignore or spends days for curation. and what else do you expect when tens of thousands of records are pooled from different sources?
2) and 3) copy-paste the msp library of your needs/dreams and save as text file with .msp ending ;) (I recommend notepad++ for such task)
10
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?
14
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