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1
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.
2
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!
3
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
4
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.
5
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
6
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.
8
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
9
HMDB / How to create a csv HMDB database without programming
Last post by !ndium -
This post contains instructions for how to create a HMDB Metabolites CSV database for searching mass spectrometry spectra without using scripts such as Python or R scripts. Two options will be described with Option 1 not requiring any specialized software and the simplest approach. Options 2 uses freeware and is useful to convert sdf files. Some biofluid specific HMDB databases only appear to be available as sdf files so Options 2 may come in useful.

Option 1.
  • Navigate to the HMDB.ca website and from the top menu select “Metabolites” from the Browse dropdown
  • Choose your filters, apply the filter then select the Export button which should be below the filters on the right side (the entire database is approx 248K entries)
  • The export may take a few minutes. Try again if it does not work the first time. Once it completes the file will either automatically be downloaded to your browsers default download location or a Save As box will pop up depending on how you have things configured. Notice that the file does not have an extension. Rename the file as desired and add the .CSV extension on the end.
  • Open the file in Excel.
  • Modify as needed. For example, delete any columns you don't want, and change column headers so they recognizable by your mass spec software. For example, the Agilent MassHunter Qualitative software recognizes the following column headers:

    Formula
    Retention Time, RT
    Mass
    Compound Name, Compound, Cpd, Name
    Description, Notes, Comments
    CasId, CAS
    KeggId, KEGG
    HmpId, HMP
    Structure

Option 2.
  • Download the freeware Datawarrior from: https://openmolecules.org/datawarrior/download.html
  • Load the sdf file. Delete any columns, then go to File > Save Special > Textfile…
    Alternatives to deleting the columns in Datawarrior is to import the file from within Excel by navigating to Data > From Text and selecting the desired columns using the Excel import wizard. Alternatively you can just edit the file directly in Excel. If an error is returned when searching the csv file, considered running the Excel CLEAN function on some of the columns.


Other biofluid specific databases available through the https://www.tmicwishartnode.ca/databases/ website are offered as sdf files and, since they are subsets of the main HMDB database, are much smaller. The same biofluid databases are offered through the HMDB.ca website but only as zipped XML files.
10
MS-DIAL / Re: MSDIAL 5.1 crashing with timsTOF data
Last post by triston.groff -
I don't have a solution to this problem, but commenting to say that this has been my experience too using timsTOF Flex. Weirdly, MSDIAL version 4 works but version 5 doesn't.

I think that with MSDIAL 5, they stopped recommending converting to .ibf format because supposedly raw .d files are readable, but this has not been my experience.

Maybe this should be an issue that is opened on the MSDIAL GitHub issues page. I believe this is where they now would like issues to be posted.

Take care,
Triston