Melanie Föll

Affiliations

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

Editorial Roles

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

• Topic: Metabolomics
• Topic: Proteomics

Tutorials

• Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses ✍️ 🧐
• Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS 🧐
• Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes ✍️ 🧐
• Metabolomics / Predicting EI+ mass spectra with QCxMS 🧐
• Metabolomics / Mass spectrometry imaging: Finding differential analytes ✍️ 🧐
• Metabolomics / Mass spectrometry: LC-MS data processing 🧐
• Proteomics / Machine Learning Modeling of Anticancer Peptides 🧐
• Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) 🧐
• Proteomics / MaxQuant and MSstats for the analysis of TMT data ✍️ 🧐
• Proteomics / metaQuantome 1: Data creation 🧐
• Proteomics / metaQuantome 3: Taxonomy 🧐
• Proteomics / Proteogenomics 1: Database Creation 🧐
• Proteomics / DIA Analysis using OpenSwathWorkflow ✍️ 🧐
• Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker 🧐
• Proteomics / Proteogenomics 2: Database Search 🧐
• Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS 🧐
• Proteomics / Mass spectrometry imaging: Loading and exploring MSI data ✍️ 🧐
• Proteomics / Peptide and Protein ID using OpenMS tools 🧐
• Proteomics / Proteogenomics 3: Novel peptide analysis 🧐
• Proteomics / Metaproteomics tutorial 🧐
• Proteomics / MaxQuant and MSstats for the analysis of label-free data ✍️ 🧐
• Proteomics / Annotating a protein list identified by LC-MS/MS experiments 🧐
• Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method 🧐
• Proteomics / Protein FASTA Database Handling 🧐
• Proteomics / Statistical analysis of DIA data ✍️ 🧐
• Proteomics / Library Generation for DIA Analysis ✍️ 🧐
• Proteomics / Label-free data analysis using MaxQuant ✍️ 🧐
• Proteomics / Secretome Prediction 🧐
• Proteomics / metaQuantome 2: Function 🧐
• Proteomics / Biomarker candidate identification 🧐
• Proteomics / Peptide Library Data Analysis 🧐

Slides

• Metabolomics / Introduction to Metabolomics 🧐
• Metabolomics / Mass spectrometry: LC-MS preprocessing - advanced 🧐
• Metabolomics / Predicting EI+ mass spectra with QCxMS 🧐
• Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling ✍️ 🧐

FAQs

• Do I need to create collections to run MaxQuant analysis or can I use single sample inputs?
• Including custom modifications into MaxQuant in Galaxy?
• Which isobaric labeled quantification methods does MaxQuant in Galaxy support?
• What is the advantage of breaking down protein to peptides before mass spec?
• Do we need a contaminant FASTA for MQ in galaxy?
• When can you use (or cannot use) Match between runs in MaxQuant?
• Do you need to merge the databases? Because you can select multiple fasta files in MaxQuant.
• If you use a mqpar file, can you include modifications that are not in the Galaxy version? For instance, propionamide (Cys alkylation by acrylamide).
• What does it mean to normalize the LFQ intensities?
• Does MaxQuant give as output possibility the PSMs and PEPs?
• For the “quantitation method” what is the default if I just leave it as “None”? Label free?
• Additional resources to learn more about proteomic data analysis
• How many proteins can be identified and quantified in shotgun proteomics?
• MSStats: what does ‘compare groups = yes’ mean? And the comparison matrix to define the contrast between the 2 groups?
• Does MaxQuant in Galaxy support TMT, iTRAQ, etc.?

Video Recordings

• Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling 💬
• Proteomics / MaxQuant and MSstats for the analysis of label-free data 💬 🗣

Events

• Galaxy Training Academy 2025 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

43 Merged Pull Requests

See all of the github Pull Requests and github Commits by Melanie Föll.

• Maxquant and MSstats TMT: Adding missing MaxQuant parameters
  proteomics
• Update CONTRIBUTORS with my updated affiliations
  template-and-tools
• Update maxquant and msstats tutorial
  proteomics
• Update tutorial Maxquant LFQ
  proteomics
• Updating MaxQuant & MSstats tutorials

Reviewed 13 PRs

We love our community reviewing each other's work!

• fix typo in MaxQuant and MSstats for the analysis of label-free data
  template-and-tools
  proteomics
• QCxMS prediction tutorial
  template-and-tools
  metabolomics
• Fixes #4406
  proteomics
• New tutotial: Metabolomics LC-MS data processing
  review-needed
• Metabolomics - LCMS preprocessing update
  review-needed

External Links

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