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11 materials found

Authors: Jan Slifka  or Matthias Fahrner 


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?

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

Scientific topics: Proteomics

Keywords: proteomics, DDA, TMT

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?

The 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 '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?

The 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?

The 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?

The 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 '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?

The 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 '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?

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

Scientific topics: Proteomics

Keywords: proteomics, label-free

Resource type: hands-on tutorial

DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind Data Stewardship Wizard, and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

A Gentle Introduction to DSW for Convergers

Data Stewardship Wizard brings together data stewards and researchers to efficiently compose data management plans (DMPs) for their research projects. Data stewards capture their knowledge and expertise in so-called knowledge models that are turned into smart...

Scientific topics: Data management, Data governance

Keywords: Data managment plan, data stewardship, data management, software tools

Resource type: Video, Slides, Webinar

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data governance, Data management

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides

Galaxy Proteomics workshop Prague 2018

Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic

Scientific topics: Proteomics

Keywords: Galaxy, training, proteomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides