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51
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.

52
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.

53
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
54
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
55
MS-DIAL / Questions about MSDial in command line
Last post by matthchau -
Hello,

Thanks for your help and your great software :)

I have 2 projects with MSDial ; and for each project, i have 1 "issue" :(

1st project :
*************
This project is based on Windows app. I would like to performed my GCMS treatment with MSDial (4.8) in command line, for optimize my results. For that, i need to have the possibiliy to export the aligned file (Area and Height).
How i can do that ? Actually i just obtain 1 .msdial file per sample. In linux version, i obtain this files, but not in windows.


2nd project :
**************
This project is based on Linux app. For routine treatment, i have one linux server. All data treatment is perfect.
But, when i increase the number of thread, nothing change.
How i can increase that ?


Thanks again for your help,
regards
58
Job opportunities / Research Scientist/Project Manager, Macrophage
Last post by bellasmith -
We are looking for research scientists/project managers to lead research and development (R&D) groups focusing on macrophage therapeutic discovery and development, including macrophage isolation and culture, macrophage reprogramming, and macrophage characterization.

In order to provide high-quality macrophage-related research services to our customers, work experience with relevant CROs, CMOs, or pharmaceutical companies is required for candidates.
60
MS-DIAL / Proper Conversion for Waters .raw Files
Last post by jack.trimble -
Hi everyone,

I am trying to use MS-DIAL to analyze MS/MS files from a Waters Xevo QQQ instrument, and having difficulties converting the files. I am able to use the software perfectly fine with my Agilent .d files, but the converted .raw files always yield the same error message: No peaks detected. Check polarity settings. Despite the files being converted to .abf, they are not properly being read by MS-DIAL. From what I've seen online and in other posts, I believe the files might be converted incorrectly (they are below 9KB). I have tried converting them to mzML files as well, with the same result. Has anyone else had this issue before?