Proteomics — Community Home
This is a new, experimental "Community Home" for a given topic. It is intended to highlight community contributions over the years to a topic!2024 Year in Review
So many new additions to our community!
1
Events
2
Learning Pathways
5
Tutorials
5
Recordings
5
Workflows
Events
Learning Pathways
Tutorials
- Clinical Metaproteomics 5: Data Interpretation
- Clinical Metaproteomics 3: Verification
- Clinical Metaproteomics 4: Quantitation
- Clinical Metaproteiomics 1: Database-Generation
- Clinical Metaproteomics 2: Discovery
Recordings
- Recording of Clinical Metaproteomics 5: Data Interpretation
- Recording of Clinical Metaproteomics 3: Verification
- Recording of Clinical Metaproteomics 4: Quantitation
- Recording of Clinical Metaproteiomics 1: Database-Generation
- Recording of Clinical Metaproteomics 2: Discovery
Workflows
2023 Year in Review
So many new additions to our community!
2
Contributors
Contributors
2022 Year in Review
So many new additions to our community!
26
Faqs
Faqs
- Why do we have a variant mapping file when it is not being used in the workflow?
- How many search engines can you use in SearchGUI?
- What kind of variants are seen in the output?
- The workflows contain several Query tabular for text manipulation, is there a tutorial for that?
- Can I use these workflows on datasets generated from our laboratory?
- Example histories for the proteogenomics tutorials
- In the MVP platform, is it possible to view the genomic location of all the peptides?
- Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference?
- Is it possible to replace the existing alignment tools such as HISAT and Freebayes with other tools?
- Does MaxQuant in Galaxy support TMT, iTRAQ, etc.?
- MSStats: what does ‘compare groups = yes’ mean? And the comparison matrix to define the contrast between the 2 groups?
- How many proteins can be identified and quantified in shotgun proteomics?
- Additional resources to learn more about proteomic data analysis
- For the “quantitation method” what is the default if I just leave it as “None”? Label free?
- Does MaxQuant give as output possibility the PSMs and PEPs?
- What does it mean to normalize the LFQ intensities?
- If you use a mqpar file, can you include modifications that are not in the Galaxy version? For instance, propionamide (Cys alkylation by acrylamide).
- Do you need to merge the databases? Because you can select multiple fasta files in MaxQuant.
- When can you use (or cannot use) Match between runs in MaxQuant?
- What is Gene Ontology (GO)?
- What is the principle of an enrichment analysis?
- Do we need a contaminant FASTA for MQ in galaxy?
- The Build tissue-specific expression dataset tool (step one) exits with an error code.
- What is the advantage of breaking down protein to peptides before mass spec?
- Can EncyclopeDIA be run on a DIA-MS dataset without a spectral library?
- What advantages does a Chromatogram Library have over a DDA-generated library or predicted spectral library?
2021 Year in Review
So many new additions to our community!
5
Tutorials
8
Recordings
13
Faqs
5
Workflows
1
Contributors
Tutorials
- MaxQuant and MSstats for the analysis of TMT data
- EncyclopeDIA
- MaxQuant and MSstats for the analysis of label-free data
- Peptide Library Data Analysis
- Machine Learning Modeling of Anticancer Peptides
Recordings
- Recording of EncyclopeDIA
- Recording of Introduction to proteomics, protein identification, quantification and statistical modelling
- Recording of Annotating a protein list identified by LC-MS/MS experiments
- Recording of Proteogenomics 1: Database Creation
- Recording of Metaproteomics tutorial
- Recording of Proteogenomics 3: Novel peptide analysis
- Recording of MaxQuant and MSstats for the analysis of label-free data
- Recording of Proteogenomics 2: Database Search
Faqs
- What other methods are available to study the functional state of the microbiome within Galaxy?
- I have a really large search database, what search strategies do you recommend for searching my mass spectrometry dataset?
- Which search algorithms are recommended for searching the metaproteomics data?
- Can I use these workflows on datasets generated from our laboratory?
- Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?
- What software tools are available to determine taxonomic composition from mass spectrometry data?
- I have FASTQ files from metagenomics or metatranscriptomics datasets? How can I convert them into a protein FASTA file for metaproteomics searches?
- How does one convert RAW files to MGF peak lists within Galaxy?
- How does one compare metaproteomics measurements from two experimental conditions?
- Which version of SearchGUI and PeptideShaker shall I use for this tutorial?
- Which isobaric labeled quantification methods does MaxQuant in Galaxy support?
- Including custom modifications into MaxQuant in Galaxy?
- Do I need to create collections to run MaxQuant analysis or can I use single sample inputs?
Workflows
- MaxQuant MSstatsTMT Training
- EncyclopeDIA-GTN
- Proteomics: MaxQuant and MSstats LFQ workflow
- Copy of PeptideDataAnalysis (imported from uploaded file)
- PeptideML
Contributors
2020 Year in Review
So many new additions to our community!
7
Tutorials
8
Workflows
1
Contributors
Tutorials
- Library Generation for DIA Analysis
- DIA Analysis using OpenSwathWorkflow
- Statistical analysis of DIA data
- metaQuantome 3: Taxonomy
- metaQuantome 2: Function
- metaQuantome 1: Data creation
- Label-free data analysis using MaxQuant
Workflows
- DIA_lib_OSW
- DIA_Analysis_OSW
- DIA_analysis_MSstats
- DIA_analysis_MSstats
- metaquantome-taxonomy-workflow
- metaquantome-function-worklow
- metaQuantome_datacreation_workflow
- Proteomics: MaxQuant workflow
Contributors
2019 Year in Review
So many new additions to our community!
2
Tutorials
4
Workflows
8
Contributors
Tutorials
Workflows
- ProteoRE ProteomeAnnotation Tutorial (release 2.0)
- 'Proteome Annotation'
- 'Biomarkers4Paris' Workflow
- MS Imaging Loading Exploring Data
Contributors
2018 Year in Review
So many new additions to our community!
4
Tutorials
3
Workflows
4
Contributors
Tutorials
- Mass spectrometry imaging: Loading and exploring MSI data
- Proteogenomics 1: Database Creation
- Proteogenomics 3: Novel peptide analysis
- Proteogenomics 2: Database Search
Workflows
- GTN Proteogemics3 Novel Peptide Analysis
- GTN Proteogemics2 Database Search
- GTN Proteogenomics1 Database Creation
Contributors
2017 Year in Review
So many new additions to our community!
7
Tutorials
1
Slides
10
Workflows
9
Contributors
Tutorials
- Peptide and Protein ID using OpenMS tools
- Metaproteomics tutorial
- Peptide and Protein ID using SearchGUI and PeptideShaker
- Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
- Label-free versus Labelled - How to Choose Your Quantitation Method
- Protein FASTA Database Handling
- Detection and quantitation of N-termini (degradomics) via N-TAILS
Slides
Workflows
- Peptide And Protein ID Via OMS Using Two Search Engines
- Proteomics: Peptide and Protein ID using OpenMS
- Metaproteomics_GTN
- Proteomics: Peptide and Protein Quantification via stable istobe labeling
- ProteinID SG PS Tutorial WF datasetCollection
- Peptide And Protein ID Tutorial
- Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper
- Tails Triple Dimethyl OpenMS2.1
- Proteomics: database handling including mycoplasma
- Proteomics: database handling
Contributors
Cumulative Data as CSV
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