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36 materials found

Scientific topics: Proteomics 


Hands-on for 'Biomarker candidate identification' tutorial

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 &...

Scientific topics: Proteomics

Keywords: proteomics, DDA, human

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 3: Taxonomy' tutorial

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.

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Annotating a protein list identified by LC-MS/MS experiments' tutorial

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:
-...

Scientific topics: Proteomics

Keywords: proteomics, DDA, human

Resource type: hands-on tutorial

Hands-on for 'MaxQuant and MSstats for the analysis of TMT data' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, DDA, TMT

Resource type: hands-on tutorial

Hands-on for 'Secretome Prediction' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, human

Resource type: hands-on tutorial

Hands-on for 'Label-free versus Labelled - How to Choose Your Quantitation Method' tutorial

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.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Proteogenomics 1: Database Creation' tutorial

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.

Scientific topics: Proteomics

Keywords: proteomics, proteogenomics

Resource type: hands-on tutorial

Hands-on for 'Proteogenomics 2: Database Search' tutorial

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.

Scientific topics: Proteomics

Keywords: proteomics, proteogenomics

Resource type: hands-on tutorial

Hands-on for 'Peptide Library Data Analysis' tutorial

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

Scientific topics: Proteomics

Keywords: proteomics

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 2: Function' tutorial

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.

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein Quantification via Stable Isotope Labelling (SIL)' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, DDA, SILAC

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 1: Data creation' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein ID using SearchGUI and PeptideShaker' tutorial

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.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Library Generation for DIA Analysis' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, DIA

Resource type: hands-on tutorial

Hands-on for 'DIA Analysis using OpenSwathWorkflow' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, DIA

Resource type: hands-on tutorial

Hands-on for 'Statistical analysis of DIA data' tutorial

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
-...

Scientific topics: Proteomics

Keywords: proteomics, DIA

Resource type: hands-on tutorial

Hands-on for 'Machine Learning Modeling of Anticancer Peptides' tutorial

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?
...

Scientific topics: Proteomics

Keywords: proteomics, ML, cancer

Resource type: hands-on tutorial

Hands-on for 'Proteogenomics 3: Novel peptide analysis' tutorial

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?

Scientific topics: Proteomics

Keywords: proteomics, proteogenomics

Resource type: hands-on tutorial

Hands-on for 'Detection and quantitation of N-termini (degradomics) via N-TAILS' tutorial

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.

Scientific topics: Proteomics

Keywords: proteomics

Resource type: hands-on tutorial

Hands-on for 'MaxQuant and MSstats for the analysis of label-free data' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, label-free

Resource type: hands-on tutorial

Hands-on for 'Label-free data analysis using MaxQuant' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, DDA, label-free

Resource type: hands-on tutorial

Hands-on for 'EncyclopeDIA' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, DIA

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein ID using OpenMS tools' tutorial

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.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Protein FASTA Database Handling' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Metaproteomics tutorial' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Mass spectrometry imaging: Loading and exploring MSI data' tutorial

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...

Scientific topics: Proteomics

Keywords: proteomics, mouse, imaging

Resource type: hands-on tutorial

Introduction to 'Proteomics'

Slides for Proteomics

Scientific topics: Proteomics

Resource type: slides

WEBINAR: Making sense of phosphoproteomics data with Phosphomatics

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...

Scientific topics: Protein modifications, Proteomics

Keywords: Phosphoproteomics

Mascot training course

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.

Scientific topics: Proteomics

Keywords: Protein identification, Protein Mass Spectrometry

Resource type: Slides, Video, Training materials

Bioinformatics Summer School 2019

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...

Scientific topics: Statistics and probability, Omics, RNA-Seq, Proteomics

Operations: Data handling