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1
MS-DIAL / Re: MSDIAL Beginner
Last post by James -
Hi phgreer,

Does the facility that ran your samples have any training support available for data analysis? This might be helpful for getting you started. You can also try to follow the MS-DIAL tutorial if you haven't already: https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial.html

To try to answer your questions:

1. The most important thing is that you choose a library that matches the way your data were acquired. Were the data acquired with GC-MS or LC-MS/MS? If the latter, was it in positive or negative mode? If, for example, your samples were analysed using LCMS/MS, with positive mode electrospray ionisation (ESI), you could use the "ESI(+)-MS/MS from authentic standards (16,481 unique compounds)" library from MSDIAL's set of curated libraries. The facility might also have access to a more comprehensive commercial library. If you are unsure how your samples were analysed, you should check with the person who acquired your data.

2. The libraries we are talking about above are what is required in the identification tab - if you download from MSDIAL it will be in .msp format, which is basically just a text file. But if you have an excel file with retention times from your samples, it sounds like the facility has already done some data analysis of your samples for you? If so, depending on your needs you might not need to use MSDIAL at all. Hard to say with info in your post.

3. Yes that is OK, MSDIAL processing will run without standards, or QC samples for that matter. Standards are useful if you want to confirm the identification of particular metabolites or quantify the metabolites in your sample, but it is probably OK not to have them for a qualitative, untargeted metabolomics project.

Cheers,
James
2
MS-DIAL / MSDIAL Beginner
Last post by phgreer -
Hi everyone,

I'm just starting out with using MSDIAL and have a few initial questions. Would be great if anyone was able to help out with all or any of these please :) I am working with metabolomics data acquired from drosophila samples. My questions are:

1. In terms of selecting a library to use, I've had a look at the MSDIAL website and the downloads available on MONA at https://mona.fiehnlab.ucdavis.edu/downloads ,but I'm unclear on how to go about selecting one. For e.g. are they all suitable for all sample types or organism specific?

2. I understand that I also need to upload a library text file under the identification tab. I received an excel file with retention times from the facility that carried out the data acquisition. I'm wondering if this is what I would need to attach here (in text format) or if it's something else I would need to upload?

3. Finally, when I come to the section where I input samples to process:  from the files sent to me by the facility that acquired the data I don't think I have anything that can be input as a standard in the class ID column when adding all my samples. Is it okay only to be entering pooled, QC and sample info ( and not any standards) or am I missing something?

If anyone can offer me any advice re the above it would be a massive help to me. Thanks :)
3
R / QExactive MS1 metabolomics
Last post by np28 -
I have direct infusion positive mode MS1 data from the QExactive, multiple replicates gathered across several batches across many months. Most of the software / R packages I have seen like XCMS, MS-DIAL, etc. seem to deal primarily with LC-MS data. What would a data-processing pipeline for this data look like and is there already an established workflow in R for DIMS data? I would like to go from ThermoRAW files to a background corrected, deisotoped, adduct-collapsed matrix of samples vs features.
4
Other / File Conversion - LECO Data
Last post by Mark Bernards -
I am having trouble finding a way to convert Leco data (*.smp) from a Pebasus BT system into netCDF or mzML for import into XCMS. Can anyone suggest software or a mechanism to do this?

Mark
5
MS-DIAL / Re: MS-DIAL 5 stability
Last post by Hiroshi Tsugawa -
Hi Ville

thanks for letting us know this issue. We will quickly check the second issue.
On the other hand, could you please let me know more details about the first thing?

Which ms-dial version did you use?
What type of data is imported?

Thanks,
Hiroshi
6
MS-DIAL / MS-DIAL 5 stability
Last post by Ville Koistinen -
Hello,

In our research group, we have been trying to transfer to use MS-DIAL 5 but have run into some issues. So far we have recognized two separate problems:

  • The program is unstable in certain computers and will crash unexpectedly before even setting all the parameters for the peak picking. It seems to be unrelated to the known issues, such as the decimal comma used by many language settings.
  • The parameters can be set but the peak picking will instantly fail resulting in crashing once you press "run" apparently because the msp database given by the user contains something that crashes it. One thing that will result in this situation is if the database accidentally contains any negative ions if you are running a positive mode project or vice versa.

While we are fixing our databases, could the parser that reads the database ignore any wrong/faulty entries in the database file to allow peak picking to initiate or give a warning/error message if the database has issues that prevents using it?

Best regards,
Ville
7
Job opportunities / Experimental Officer in Metabolomics - University of Birmingham
Last post by e.voros -
Location:   University of Birmingham, Edgbaston, Birmingham UK
Salary:   Full time starting salary is normally in the range of £34,980 to £44,263, with potential progression to £46,974
Hours:   Full-Time
Contract Type:   Fixed Term 2-year post with the potential for extension
Closes:   28th of November 2023
Job Ref:   99212

Summary of Role
The post has been created by an exciting collaboration between Phenome Centre Birmingham and the Horizon 2020 PrecisionTox consortium and will contribute to fulfilling their shared research objectives with a focus on applying mass spectrometry metabolomics to study human health and toxicology.
The post holder will be involved in the application of LC-MS metabolomics to multiple toxicological and human health-related projects in PCB, working with a team whose expertise spans analytical chemistry, bioinformatics, biostatistics, metabolic biochemistry, and toxicology.
The post will focus on 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. The metabolomics will be conducted under QA/QC within a CRO-like environment. Sample types routinely analysed include human cell lines, tissues, biofluids, and multiple model organism extracts (C. elegans, Drosophila, Zebrafish, D. magna, Xenopus). The post will involve scientific collaborations within and external to the University of Birmingham, including members of the PrecisionTox consortium. It will initially be for 2 years with potential for extension.
This post is one of two currently being recruited (the other being Research Associate in Metabolomics, 102786); please note that only one of these posts will be filled.
Main Duties
•   Perform metabolomics and lipidomics analysis (metabolic phenotyping) by applying hybrid LC-MS(/MS) assays - combine untargeted and targeted analysis - to various biological sample types.
•   Perform manual sample preparation methods using state-of-the-art Beckmann Coulter robotics platforms to maximise metabolite extraction while enabling high-throughput sample handling of low biomass samples.
•   Maintain records of protocols and procedures applied during study planning, sample preparation, and LC-MS data acquisition – within a QA/QC environment.
•   Ensure optimal operation of PCB instrumentation, routine maintenance, and troubleshooting problems.
•   Potential to implement novel metabolic phenotyping methodologies to enhance the capabilities and capacity of the PCB.
•   Work with the PCB team to achieve objectives and manage expectations of collaborators.
•   Support project management, from sample arrival to assisting with reports to collaborators.
•   Contribute to the dissemination of high-quality studies in peer-reviewed journals, conferences, and to the general public.

Person Specification
•   First degree in chemistry/biochemistry (or equivalent field)
•   Higher degree (Masters or PhD) in (bio)analytical chemistry or equivalent work-related experience (essential)
•   Experience working in an industrial (e.g. CRO), government, or academic laboratory with a focus on liquid chromatography-mass spectrometry for the analysis of small molecules. (essential)
•   Hands-on skills in LC-MS, preferably with experience with Thermo Scientific instrumentation. (essential)
•   Hands-on experience in sample preparation for mass spectrometry.
•   Detailed knowledge of laboratory safety and QA/QC practices.

Informal enquires to Prof Mark Viant (m.viant@bham.ac.uk) and Dr Andrew Southam (a.d.southam@bham.ac.uk)
To download the full job description and details of this position and submit an electronic application online please click on the
Apply Online button:
https://edzz.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_6001/requisitions/preview/3458/?keyword=experimental&mode=location
Valuing excellence, sustaining investment
We value diversity and inclusion at the University of Birmingham and welcome applications from all sections of the community and are open to discussions around all forms of flexible working.

8
XCMS / Trying to run XCMS script in R and having trouble
Last post by Mason -
Hey everyone,

I am very new to R, but am somewhat familiar with metabolomics.
I am trying to better understand how to run XCMS through R, and have watched several videos and (tried) to run through several vignettes. I am still not completely understanding something though as I keep running into errors.

For example, in the CAMERA documentation, there is some example code for preprocessing with xcms that goes like this:
(code is from https://www.bioconductor.org/packages/release/bioc/html/CAMERA.html)

library(CAMERA)
file<-system.file('mzML/MM14.mzML',package="CAMERA")
xs<-xcmsSet(file,method="centWave",ppm=30,peakwidth=c(5,10))

When I try to run this, I get the following error:
Error in xcmsSet(file, method = "centWave", ppm = 30, peakwidth = c(5,  :
Chromatographic peak detection failed for all files! The first error was: Error in validObject(.Object): invalid class “xcmsPeaks” object: superclass "mMatrix" not defined in the environment of the object's class

Can anyone help me with this? Is the code the example I'm trying to recreate deprecated?

Is there a good source of information that you all learned how to run xcms in R?

Thanks, sorry if there is an obvious answer to this.

9
MS-DIAL / Re: Questions about MSDial in command line
Last post by matthchau -
Sorry to re-ask again my question, but i can't progress without reply :(

In my first issue, i don't know where i need to search.

For my second point, i used this line in the GC-parameter file
Code: [Select]
Number of threads: 8
But this line have really no impact.

Thanks for your reply
regards
10
MS-DIAL / "MS1 factor" and "RT factor"
Last post by FalcoB -
Hi,

my question refers to the MS-Dial parameters "MS1 factor" and "RT factor". As I understand right, the parameters determine the weighting of mass and retention time (deviations) used for calculating the total score of an feature annotated by the post-identification process.

However, are those parameter also relevant when using an MSP-file for feature annotation,
i.e. do the values for "MS1 factor" and "RT factor" also have impact on the total score calculation of an MSP-file annotated feature?

Can anyone comment on this?
Thanks!

Best regards
FalcoB