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1
MS-DIAL / Re: Very, very weird quant issue in MS-DIAL v4.92
Last post by drchrispook -
Agh1 is the MS-DIAL quant. Look at the difference between the large (2e7) and small peaks (2e6). When I look at them in TOPPView (agh2)  or my own Python integration script that uses PyOpenMS (agh3) they're all at 2e7. There's no difference in mass accuracy between any of the runs. It's <1.5ppm. This is very weird and I don't like it. I've never seen anything like this in >5 years of MS-DIAL analysis.
2
MS-DIAL / Very, very weird quant issue in MS-DIAL v4.92
Last post by drchrispook -
Documented here: https://x.com/drchrispook/status/1795768077893923092

A random subset of peaks in my data are being underidentified in MS-DIAL processing (v4.9.221218). This only shows up when I run a PCA and get a massive division in the data. It's about 10% of features and the difference varies feature-by-feature. The one I'm presenting here is cholesterol as it's a good example, but there are many others. Most of the features show no such issue, however. My internal standards are fine.

I'll attach images of the quant to another post.
3
MS-DIAL / AIF not working in MS-DIAL v5
Last post by drchrispook -
Hello, it seems that MS-DIAL v5 cannot process AIF data. I have AIF data with one MS1 scan and one MS2 scan. I have been processing it in MS-DIAL v4 but have found an issue with quantification so I've been trying v5. The video tutorial is based on v5.1.0 but that version of the software isn't available to download.
https://www.youtube.com/watch?v=ns_x3K0lpeU

I have tried:
v5.2.240424.3
ver5.2.240218
ver.5.1.231120

None of these work. They all crash, even with all defaults set. The only variable I change is the threads option to speed things up, so I set it to 16. Notably, none of these versions have an option to enter an AIF experiment text file as you do in v4 and as is described in the video above for v5.1.0. This must have been removed somewhere in the evolution, presumably because that information is relatively easy to extract from data by analysing the scan types and periodicity. The same goes for SWATH.

I've tried data in .raw format and .mzML. Note that these files all work in v4 but are misquantified in either format. That's a different bug (see my twitter thread here: https://x.com/drchrispook/status/1795768077893923092) and this post is alerting people to the AIF issue.
4
MS-DIAL / Re: RT range in aligned spot EIC
Last post by JMS -
Hi Matt-are you still having trouble with this? What are your identification and alignment settings with regards to retention time? Is this LCMS data?
5
MS-DIAL / v5.1 to 5.2 - can't choose lipidomics solvent type?
Last post by nmoreno -
Hey all,

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
6
MS-DIAL / "MS method type" is missing in measurement parameters
Last post by TOE -
Hi,

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
7
MS-DIAL / RT range in aligned spot EIC
Last post by mattcake -
Hello all,

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
9
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
10
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.