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Last post by MichaelNug -
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R / Re: XCMS in R
Last post by Jan Stanstrup -
Quadrupole instruments sometimes save data as chromatograms and not spectra.
You can try converting your original files with msconvert from Proteowizard and add: --simAsSpectra --srmAsSpectra
R / XCMS in R
Last post by lindahernandez -

I'm new using LCMS to identify venom profiles. I'm trying to visualize and analyze data in R using XCMS. I have tried  with this code to read rawdata
cdffiles <-list.files("~/LCMS/cdf/Dave", recursive=T, full=T)
xrms<-readMSData(cdffiles, mode = "onDisk", centroid= TRUE)

but I have got this error
No MS 1 data present.

Then when I tried this code to create xcmsSet object, I received a similar error
Error in readRawData(fileName(object), includeMSn = includeMSn) :
  No MS1 data found in file C:/Users/jc554411/Documents/LCMS/cdf/Dave/A13.mzXML!

I export the data from the LCMS 2020 SHIDMAZU.

Can someone help me?


Linda  :)
XCMS Online / Retention time correction
Last post by gabrieljoyce -

I'm supposed to analyze my LC-Orbitrap data on XCMS, however I'm observing a retention time shift on my chromatogram.

The standard error is about 1% for a specific range in my chromatogram, and I observe about half a minute of retention time shift in a 40 minute run.

I was wondering, can XCMS successfully correct such big retention time shifts? Is there a specific standard deviation for XCMS's retention time correction?

Birmingham Metabolomics Training Centre / Multiple Biofluid and Tissue Types for Metabolomics
Last post by BMTC -
Multiple Biofluid and Tissue Types, From Sample Preparation to Analysis Strategies for Metabolomics

Start Date: Wednesday 25th September 2019
End Date: Friday 27th September 2019

Location: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham

Course Overview

This 3-day course provides a theoretical overview and hands-on training to apply multiple sample preparation and UPLC-MS methods to characterise the metabolomes of complex biological samples using the mass spectrometer (Xevo QToF G2-XS - a maximum of 4 people working on the instrument in a session). The course is led by experts in the field who have experience of the analysis of microbial, plant and mammalian samples, and illustrates the different approaches that are available to analyse a range of biological samples and applying complementary liquid chromatography approaches to maximise the coverage of the metabolome.

Topics Covered

  • Introduction to dealing with the complexity of biological samples using UPLC-MS
  • Overview of different sample collection, sample quenching and sample extraction methods
  • The challenges of working with cellular and tissue samples
  • Overview of different UPLC methods including HILIC and reversed phase methods
  • Hands-on sample preparation of plasma, urine, cell and tissue samples
  • Monophasic and biphasic solvent extraction methods to target polar and non-polar metabolites
  • SPE and liquid-liquid sample clean-up methods
  • Hands-on HILIC and reversed-phase liquid chromatography
  • Hands-on UPLC-MS analysis for untargeted studies (maximum of 4 people)
  • Overview of data analysis and metabolite identification
  • Problem solving and tips and tricks session with the experts


The course is aimed at PhD students and post-doctoral researchers who have been actively applying metabolomics.

Early-bird Registration: £1,040 (Rate expires: 6 September 2019)
Standard Registration: £1,155 (Rate expires: 24 September 2019)

Course link & Registration:
Birmingham Metabolomics Training Centre / Introduction to Metabolomics for the Microbiologist
Last post by BMTC -
Introduction to Metabolomics for the Microbiologist

Start Date: Wednesday 9th October 2019
End Date: Friday 11th October 2019

Location: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham

Course Overview

This three-day course introduces how untargeted metabolomics can be applied to study microbial systems in academic and industrial research. The course provides an overview of the metabolomics pipeline, experimental design, sample preparation and data acquisition. The course is led by experts in the field of metabolomics and will include lectures, hands-on laboratory sessions in sample preparation and data acquisition and computer workshops focused on data processing and data analysis.

Topics Covered

  • Introduction to metabolomics, both targeted and untargeted approaches
  • Experimental design and the importance of quality control samples in untargeted metabolomics
  • Analytical strategies applied in metabolomics with a focus on mass spectrometry
  • Hands-on laboratory sessions focused on sample preparation and to include metabolic quenching and extraction procedures, intracellular and exometabolome samples, and polar and non-polar extraction methods
  • Hands-on laboratory sessions focused on sample analysis for untargeted metabolomics studies using an Acquity UPLC coupled to a Xevo QToF mass spectrometer
  • Hands-on workshop focused on data processing and data analysis
  • An introduction to metabolite identification
  • Question and answer session with the experts


This course is aimed at individuals with minimal experience of applying metabolomics in their research and no or limited experience of using a liquid chromatography – mass spectrometer. The attendees will leave the course understanding and being able to apply the metabolomics pipeline in their research.

Early-bird Registration: £980 (Rate expires: 20 September 2019)
Standard Registration: £1,090 (Rate expires: 8 October 2019)

Course link & Registration:
Birmingham Metabolomics Training Centre / Online: Metabolomics: Understanding Metabolism in the 21st Century
Last post by BMTC -
Metabolomics: Understanding Metabolism in the 21st Century

Start Date: Monday 23rd September 2019
End Date: Friday 18th October 2019

Location: Online (FutureLearn)

Course Overview

Metabolomics is an emerging field that aims to measure the complement of metabolites (the metabolome) in living organisms. The metabolome represents the downstream effect of an organism’s genome and its interaction with the environment. Metabolomics has a wide application area across the medical and biological sciences. The course provides an introduction to metabolomics, describes the tools and techniques we use to study the metabolome and explains why we want to study it. By the end of the course you will understand how metabolomics can revolutionise our understanding of metabolism.

Topics Covered

  • Metabolism and the interaction of the metabolome with the genome, proteome and the environment
  • The advantages of studying the metabolome
  • The application of hypothesis generating studies versus the use of traditional hypothesis directed research
  • The use of targeted and non-targeted studies in metabolomics
  • An interdisciplinary approach with case-studies from clinical and environmental scientific areas
  • Important considerations in studying the metabolome
  • Experimental design and sample preparation
  • The application of mass spectrometry in metabolomics
  • An introduction to data processing and analysis
  • Metabolite identification


The course is primarily aimed at final year undergraduate science students and research scientists who are interested in learning about the application of metabolomics to understand metabolism. However, metabolomics is a new tool to the scientific community and this course will provide a valuable introduction to scientists at any stage in their careers. It is not essential to have any previous knowledge of the subject area but a reasonable knowledge and understanding of science would be beneficial.


Course link & Registration: