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MS-DIAL / v5.1 to 5.2 - can't choose lipidomics solvent type?
Last post by nmoreno -Does anyone know the reason why you aren't able to pick solvent types when you choose lipidomics as an analysis? I see in version 5.1 you can, but 5.2, you cannot. Was this change for a reason or are one of the settings changing the ability to choose the solvent type?
Thank you!
-N
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MS-DIAL / "MS method type" is missing in measurement parameters
Last post by TOE -I´m trying to use MSDIAL v 5.2.240424.3 to analyze LC-MS/AIF. However, upon creating a new project the section "MS method type" is missing in the measurement parameter mask (see screenshot). What causes/how can I fix this problem.
Thanks for your help!
Tom
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MS-DIAL / RT range in aligned spot EIC
Last post by mattcake -I'm completely new to MSDial and trying to employ it in a non-omics application to assess similarities between samples in a study of breakdown products of small molecules exposed to a mix of inorganics. The issue I'm experiencing may simply be due do my inexperience or the quality of my chromatography, which has a distinctly ion-exchange flavour and, partly because of that, my peaks are somewhat wide.
Anyway, the issue is that in the "EIC of Aligned Spot" section of MSDial, I see a tiny retention time range for most (though not all) of my peaks, much narrower than the overall peak width. In all the guidance for MSDial that I've looked through, I haven't seen a similar effect. I've attached a grab of the Aligned Spot EIC and the full EIC for comparison. Probably it's a simple error in how I've set up the processing, but if anyone could give me a pointer I'd really appreciate it.
Thanks for help me out,
Matt
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MS-DIAL / Re: MsdialConsoleApp gcms problem: The given key '0' was not present in the diction
Last post by QizhiSu -6
MS-DIAL / Re: RT correction
Last post by drchrispook -Yeah, I don't like this. Instead I've worked out that converting your data to mzML means you can just add an RT shift to the time value of each scan. I've just done a fixed shift but if I spend a couple more hours sampling different shifts between my batches I could use a function to correct it instead.
Please tell me more about this, is this done in ProteoWizard? I follow your blog and have benefitted when converting .L to .msp and merging them, so thank you.
Hi, I found the script I wrote to do this and have put it up on GitHub and Zenodo.
https://zenodo.org/doi/10.5281/zenodo.11095185
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Job opportunities / Experimental Officer in Metabolomics - University of Birmingham
Last post by e.voros -Closing date for applications: 28th of April 2024
If you are interested in applying for the post please find further details on the University of Birmingham’s job site.
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MS-DIAL / MS-DIAL 5 Concatenate Data from Pos and Neg Ion Modes
Last post by perciaccante -I am a new user of MS-DIAL and I am trying to combine peak lists from positive and negative ion modes. The "Amalgamation of different polarity peak list' " button is greyed out, and I am not sure what I must do to make it available.
I have tried using the R-GUI for MS-CLEAR, but it provides an error "replacement has 1 row, data has 0". I followed the instructions in the tutorial for preparing the folders with the data.
I also tried using MSCombine but it also errored out after running for several hours.
I would appreciate any and all advice on how to concatenate the data from different ion modes. Thanks!
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MS-DIAL / MSDIAL 5 Template for Internal Standards
Last post by FernandoTobias -I am trying to upload the list of internal standard from the equiSPLASH mix in MSDIAL5 and I'm unsure where to load it in the new software.
1. Do I add it during the Identification Step as a "Text" Database?
2. If yes, what is the suggested template for it? The 4.9 template does not seem to work anymore and the software closes without any error messages after I click "Run."
Thank you
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R / Question regarding running XCMS and Camera in newest version of RStudio
Last post by Metabollbd -We used to run our analyses with the following script in RStudio.
“library(xcms)
xset<-xcmsSet(method="centWave", prefilter=c(0,0), ppm=15, peakwidth=c(5,20), snthr=2)
xset1<-retcor(xset, method="obiwarp", plottype=c("deviation"))
xset2<-group(xset1, bw=2, minfrac=0.5, mzwid=0.015)
xset3<-fillPeaks(xset2)
dr<-diffreport(xset3, filebase="file_name", eicmax=20)
library(CAMERA)
xset4<-xsAnnotate(xset3)
xset5<-groupFWHM(xset4, perfwhm=0.6)
xset6<-groupCorr(xset5)
xset7<-findIsotopes(xset6)
xset8<-findAdducts(xset7, polarity="negative")
write.csv(getPeaklist(xset8), file="file_name2.csv")”
This has stopped working when we installed the new version of RStudio.
I am not too familiar with coding and will appreciate some help here.
Thank you.