1
Show Posts
This section allows you to view all Show Posts made by this member. Note that you can only see Show Posts made in areas you currently have access to.
Messages - romanas chaleckis
2
MS-DIAL / Re: Not consistent Peak Intensity (Both Peak Height and Peak Area)
3
Sample preparation / Re: Strategies for resuspending in small volume after dry-down
4
MS-DIAL / Re: How to predict MS/MS spectrum of a given chemical that is not present in Pubchem
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
5
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
6
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
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!)
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
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)
9
Chromatography / Thermo GlycanPac AXH-1 columns for metabolomics
has anybody experience using Thermo GlycanPac AXH-1 columns for metabolomics?
Best,
romas
10
MS-DIAL / Re: InChIKey Generation
@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?
11
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
12
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
13
MS-DIAL / converting from ABF format to mzML
14
MS-DIAL / Re: MS/MS Spectra in mzML File
15