The questions this addresses are:
- How to mine public databases to retrieve info?
- How to build a selection strategy by applying successive biochemical/cellular criteria to a list of gene/protein?
- How to select biomarkers candidates using experimental information (transcriptomics &...

The questions this addresses are:
- How do I look at differentially expressed taxa?
- Can we get top 5 or 10 taxa present in the sample?
- How can I visualize my results?

\nThe objectives are:
- A taxonomy and quantitational analysis of metaproteomic mass spectrometry data.

The questions this addresses are:
- How to filter out technical contaminants?
- How to check for tissue-specificity?
- How to perform enrichment analysis?
- How to map your protein list to pathways (Reactome)?
- How to compare your proteome with other studies?

\nThe objectives are:
-...

The questions this addresses are:
- How to analyze tandem-mass-tag (TMT) labelled shotgun (DDA) data analysis in MaxQuant and MSstats?
- Which proteins are differentially abundant between KMT9α knock-down and control cells?

\nThe objectives are:
- Learn how to use MaxQuant and MSstats for...

The questions this addresses are:
- What are benefits and drawbacks of different quantitation methods?
- How to choose which quantitation method bests suits my need?

\nThe objectives are:
- Choose your quantitation method.

The questions this addresses are:
- How to predict cellular protein localization based upon GO-terms?
- How to combine multiple localization predictions?

\nThe objectives are:
- Predict proteins in the cellular secretome by using GO-terms.
- Predict proteins in the cellular secretome by...

The questions this addresses are:
- How to create a customized Protein Database from RNAseq data?

\nThe objectives are:
- Generating a customized Protein sequence database with variants, indels, splice junctions and known sequences.

The questions this addresses are:
- How to identify variant proteoforms in MS data by searching with the customized Protein database?

\nThe objectives are:
- A proteogenomic data analysis of mass spectrometry data to identify and visualize variant peptides.

The questions this addresses are:
- How to utilize quantitative properties of amino acids and peptide sequence to analyse peptide data?

\nThe objectives are:
- Calculate descriptors
- Quantitative analysis of peptide sequence properties

The questions this addresses are:
- How do I look at differentially expressed proteins?
- How do I get top 5 or 10 function present in the sample?
- How can I visualize my results?

\nThe objectives are:
- A functional and quantitational analysis of metaproteomic mass spectrometry data.

The questions this addresses are:
- 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?

\nThe objectives are:
- MS1 feature quantitation and mapping of quantitations to peptide and...

The questions this addresses are:
- How do I perform functional and taxonomy analysis on metaproteomics data?
- How can I perform quantitation on metaproteomics data?
- How do I create inputs that can be used in metaquantome to examine differentially expressed proteins?

\nThe objectives...

The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?

\nThe objectives are:
- Protein identification from LC-MS/MS raw files.

The questions this addresses are:
- How does the peptide identification work in data independent acquisition (DIA) mass spectrometry (MS) data?
- What is a spectral library and how to generate a spectral library using Maxquant, diapysef and OpenSwath tools?

\nThe objectives are:
- Generating...

The questions this addresses are:
- How to analyze data independent acquisition (DIA) mass spectrometry (MS) data using OpenSwathWorkflow?
- How to detect different Spike-in amounts of Ecoli in a HEK-Ecoli Benchmark DIA dataset?

\nThe objectives are:
- Analysis of HEK-Ecoli Spike-in DIA data...

The questions this addresses are:
- How to perform statistical analysis on DIA mass spectrometry data?
- How to detect and quantify differentially abundant proteins in a HEK-Ecoli Benchmark DIA datatset?

\nThe objectives are:
- Statistical analysis of a HEK-Ecoli Benchmark DIA dataset
-...

The questions this addresses are:
- How to verify the spectra of novel proteoforms?
- How to assign genomic allocation to these novel proteoforms?

\nThe objectives are:
- How to assign and visualize the genomic localization of these identified novel proteoforms?

The questions this addresses are:
- Which machine learning (ML) algorithm is superior in classifying anticancer peptides (ACPs) and non-anticancer peptides (non-ACPs)?

\nThe objectives are:
- Learn, how to calculate peptide descriptor
- Learn, how to create training data set from features?
...

The questions this addresses are:
- How can protein N-termini be enriched for LC-MS/MS?
- How to analyze the LC-MS/MS data?

\nThe objectives are:
- Run an N-TAILS data analysis.

The questions this addresses are:
- How to perform label-free shotgun (DDA) data analysis in MaxQuant and MSstats?
- Which proteins are differentially abundant in the two types of cutaneous squamous cell carcinomas?

\nThe objectives are:
- Learn how to use MaxQuant and MSstats for the...

The questions this addresses are:
- How to perform label-free analysis in Maxquant?
- Which are the most abundant proteins in serum?
- How successful was the depletion of those in our experiment?

\nThe objectives are:
- Analysis of human serum proteome samples with label-free quantification...

The questions this addresses are:
- How to perform quantitative analysis using DIA data with the help of EncyclopeDIA?
- How to perform quantitation with or without Chromatogram Libraries?

\nThe objectives are:
- Understand the difference between DDA and DIA methods
- Performing...

The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?

\nThe objectives are:
- Protein identification from LC-MS/MS raw files.

The questions this addresses are:
- 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?

\nThe objectives are:
- Creation of a protein FASTA database ready for use with...

The questions this addresses are:
- How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?
- How can I perform taxonomy analysis and visualize metaproteomics data?
- How can I perform functional analysis on this metaproteomics...

The questions this addresses are:
- Did the tryptic digestions work?
- Is there an intensity gradient in the data?
- How good is the m/z accuracy?

\nThe objectives are:
- How to upload an imzML file into Galaxy
- Getting an overview of the MSI data with the MSI quality control tool
- How...

Slides for Proteomics

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021.

Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for...

The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises.

This one-week intensive summer school in bioinformatics will focus on data analysis and high throughput biology, with a special focus on R/Bioconductor and its application to a wide range of topics across bioinformatics and computational biology. The course is intended for researchers who are...