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2
MS-DIAL / Re: RT correction
Last post by drchrispook -
Quote from: agentfourty7 – on
Quote from: drchrispook – on
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
3
Job opportunities / Experimental Officer in Metabolomics - University of Birmingham
Last post by e.voros -
We are recruiting an Experimental Officer in Metabolomics to join our team at the University of Birmingham. Phenome Centre Birmingham (PCB) has an international reputation specialising in toxicological and biomedical metabolomics.  We have an exciting opportunity for an enthusiastic and committed chemist or biochemist who has experience in LC-MS metabolomics. This fixed-term position is ideally suited for someone who gained experience in applying high-throughput analytical methods, including advanced robotic sample preparation and state-of-the art hybrid LC-MS metabolomics assays that combine untargeted analyses with targeted measurements of metabolic biomarkers.

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.
4
MS-DIAL / MS-DIAL 5 Concatenate Data from Pos and Neg Ion Modes
Last post by perciaccante -
Hello,

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!
5
MS-DIAL / MSDIAL 5 Template for Internal Standards
Last post by FernandoTobias -
Hello,

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
6
R / Question regarding running XCMS and Camera in newest version of RStudio
Last post by Metabollbd -
Hello:

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.
7
MS-DIAL / There is no peak information
Last post by AlexandreGB -

Hello everyone,

I'm experiencing the following error "There is no peak information in ..." when loading the preprocessing parameters for the samples. I've checked the polarity, sample size, and selected parameters. I've tried loading different files, and I've also attempted to convert the file to centroid and load it, but I'm still encountering the same problem. Could someone help me with this issue? I've attached a file with some details. Thank you very much for your help.

Files: .RAW (Waters)
Acquisition mode: HDMSe
Instrument: Cyclic IMS
8
MS-DIAL / How to analyze Shimadzu .qgd files using MS-DIAL
Last post by Oryza -
I have received scan+MRM data .qgd files from Shimadzu TQ 8050 GCMS. Is it possible to use MS-DIAL to analyze these data?

These are for plant metabolites and it looks like MSDIAL has some libraries.

However, It's sad there is a very little community support from MS-DAIL developers, looks like authors do not want us to try their software.

If someone could help me with a protocol, I'd be really grateful.
10
MS-DIAL / Re: MSDIAL 5.1 crashing with timsTOF data
Last post by mecolley -
Thank you Triston!

I even tried converting to IBF format first and loading that into 5.x, but the software crashes. I'll post a reply to the GitHub repository - thank you for the tip.

Best,
Maddie