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Messages - eterlova

1
MS-DIAL / Re: MSDIAL in Mac
Quote from: jiungwenchen – on
I wrote an instruction for running MS-DIAL on Linux and Mac: https://github.com/Jiung-Wen/msdial
Unfortunately, they both have command line interface only.

Thank you, jiungwenchen, this is super helpful! I am an absolute novice to this, so excuse the stupid question!

I've got through the steps in your tutorial, but cannot figure out how to start MsfinderConsoleApp, what should I do instead?

Code: [Select]
> wget http://prime.psc.riken.jp/compms/msfinder/download/repository/macOS/MsfinderConsole_v352_mac.zip
> unzip MsfinderConsole_v352_mac.zip
> mv MS-FINDER\ ver.\ 3.52\ MacOS MS-FINDER_ver._3.52_MacOS/
> chmod +x  MS-FINDER_ver._3.52_MacOS/MsfinderConsoleApp 
> MsfinderConsoleApp
zsh: command not found: MsfinderConsoleApp

2
Compound identification / Cannot find spiked standards in the annotated compound list
Hello all, a noobie here.

I am trying to make sense of my LC-MS^n data. Before running my samples on the instrument, I spiked them with two internal standards (lidocaine and biochanin A). I preprocessed my files using the standard xcms pipeline, but I cannot find my standards in the rowData(results) file. I know what m/z and RT to expect, but the compounds that best correspond to these, differ in RT time by 20.33 and 0.248 seconds (respectively). This is a big difference, isn't it?

I then used m/z only search of compounds in MassBank using these data, and neither lidocaine not biochanin were identified as matches.

What should I do with all this? are the peak-picking parameters my problem? The parameters I used were chosen by IPO package using polled samples. How do I now that my tweaking them improved the situation rather than made it worse?

Best,
Lisa
3
XCMS / adding sample annotation after PeakPicking and RTcorrection?
Hello all,

I am trying to preprocess my LCMS data, and now at the point of correspondance, which (as I understand) relies on knowing the type of the sample to filter out the peaks present in too few of replicas. But apparently I never read in my sample annotation file, so my xdata file does not have a $sample_group column. Is there a way to add the annotation now or do I have to start over again?

Best,
Lisa
4
XCMS - Cookbook / Is there a way to attach sample info after PeakPicking and RTcorrection?
**sorry! I think it's a wrong place for my question


Hello all,

I am trying to preprocess my LCMS data, and now at the point of correspondance, which (as I understand) relies on knowing the type of the sample to filter out the peaks present in too few of replicas. But apparently I never read in my sample annotation file, so my xdata file does not have a $sample_group column. Is there a way to add the annotation now or do I have to start over again?

Best,
Lisa