Proteomics - Peptide and Protein ID using OpenMS tools
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?
Objectives of the tutorial:
- Protein identification from LC-MS/MS raw files.
Proteomics - Peptide and Protein ID using OpenMS tools
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-oms/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-id-using-openms-tools
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?
Objectives of the tutorial:
- Protein identification from LC-MS/MS raw files.
stortebecker
bgruening
Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How can protein N-termini be enriched for LC-MS/MS?
- How to analyze the LC-MS/MS data?
Objectives of the tutorial:
- Run an N-TAILS data analysis.
Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/ntails/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-ntails
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How can protein N-termini be enriched for LC-MS/MS?
- How to analyze the LC-MS/MS data?
Objectives of the tutorial:
- Run an N-TAILS data analysis.
stortebecker
bgruening
Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- What are MS1 features?
- How to quantify based on MS1 features?
- How to map MS1 features to MS2 identifications?
- How to evaluate and optimize the results?
Objectives of the tutorial:
- MS1 feature...
Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-quant-sil/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-quantification-via-stable-isotope-labelling-sil
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- What are MS1 features?
- How to quantify based on MS1 features?
- How to map MS1 features to MS2 identifications?
- How to evaluate and optimize the results?
Objectives of the tutorial:
- MS1 feature quantitation and mapping of quantitations to peptide and protein IDs.
stortebecker
bgruening
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?
Objectives of the tutorial:
- Protein identification from LC-MS/MS raw files.
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-id
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?
Objectives of the tutorial:
- Protein identification from LC-MS/MS raw files.
stortebecker
bgruening
Proteomics - Secretome Prediction
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to predict cellular protein localization based upon GO-terms?
- How to combine multiple localization predictions?
Objectives of the tutorial:
- Predict proteins in the cellular secretome by using...
Proteomics - Secretome Prediction
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/secretome-prediction/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-secretome-prediction
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to predict cellular protein localization based upon GO-terms?
- How to combine multiple localization predictions?
Objectives of the tutorial:
- Predict proteins in the cellular secretome by using GO-terms.
- Predict proteins in the cellular secretome by using WolfPSORT.
- Combine the results of both predictions.
stortebecker
bgruening
Proteomics - Label-free versus Labelled - How to Choose Your Quantitation Method
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- What are benefits and drawbacks of different quantitation methods?
- How to choose which quantitation method bests suits my need?
Objectives of the tutorial:
- Choose your quantitation method.
Proteomics - Label-free versus Labelled - How to Choose Your Quantitation Method
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-label-free-versus-labelled-how-to-choose-your-quantitation-method
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- What are benefits and drawbacks of different quantitation methods?
- How to choose which quantitation method bests suits my need?
Objectives of the tutorial:
- Choose your quantitation method.
stortebecker
bgruening
Proteomics - Protein FASTA Database Handling
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to download protein FASTA databases of a certain organism?
- How to download a contaminant database?
- How to create a decoy database?
- How to combine databases?
Objectives of the tutorial:
- Creation of a...
Proteomics - Protein FASTA Database Handling
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/database-handling/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-protein-fasta-database-handling
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to download protein FASTA databases of a certain organism?
- How to download a contaminant database?
- How to create a decoy database?
- How to combine databases?
Objectives of the tutorial:
- Creation of a protein FASTA database ready for use with database search algorithms.
stortebecker
bgruening
