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Proteomics - Proteome Identification and Quantification

There are five proteomics applications from FGCZ.

1. Proteome Identification and Quantification
2. Amino Acid Analysis
3. Glycan / Glycoprotein analysis
4. Interaction Proteomics
5. Characterization of purified biomolecules

Introduction

FGCZ supports a wide range of protein analysis and proteomics applications, such as:

• Identification of the protein content in purified or complex samples (i.e., gel bands)
• Quantification of thousands of proteins upon different treatments or conditions (i.e., discovery of biomarkers in clinical samples)
• Analysis of post-translational modifications (i.e., phosphorylation)
• Identification of drug targets
• Analysis of low-input samples (i.e., a few 100s or 1000s of cells)

The Method

The FGCZ supports various sample preparation workflows for different sample types, such as tissues, FFPE samples, cells, protein extracts, and biofluids (i.e., plasma and urine). The methods include:

• Automation in workflows
• Processing samples on the latest generation instruments using data dependent (DDA) and data independent (DIA) acquisition methods
• Analysis using the most appropriate software tool

The Workflow

Most workflows follow these steps:

1. Protein extraction with specific protocols
2. Enzymatic digestion of proteins to generate peptides (i.e., SP3, PreOmics iST, PCT, FASP, etc.)
3. Desalting of the peptide mixture
4. Injection of the peptides to an online LC-MS/MS system
5. Bioinformatics analysis
6. Statistical analysis and data visualization

The Output

Possible output formats vary depending on the requested analysis. All analyses include:

• A report with details of the applied methods
• The results of the analysis
• Delivery of the raw data

List of applications and services

FGCZ routinely supports the following Proteome Identification and Quantification services, but it offers many additional services not listed below.

Applications (examples)	Which service to order
Protein identification in simple or complex mixtures (i.e., gels, extracts)	Protein/Peptide Identification
Biomarker discovery in body fluids, tissues, cells, FFPEs	Proteome Quantification - Label-Free
High-throughput proteomics quantification	Proteome Quantification - Label-Free
Deep coverage proteome quantification	Proteome Quantification - TMT
Identification/quantification of proteins from low-input material (ideally 500-5000 cells)	Proteome Quantification - Label-Free (Low input analysis info - please contact us before ordering)
Large-scale phosphoproteomics analysis (with label-free approach)	Phosphopeptide Quantification - Label-Free
High coverage phosphoproteomics analysis (with label-based approach)	Phosphopeptide Quantification - TMT
Analysis of post-translational modifications (i.e., phospho, ubiquitin, acetyl, methyl)	Analysis of selected PTMs
Proteome-wide identification of protein N-Termini (TAILS)	N-Terminal characterization - TAILS
Setup of a quantification assay for a set of target proteins (panels, validation studies)	Targeted Quantification - Assay Setup
Quantification of target proteins (panels, validation studies)	Targeted Quantification
Any analysis not covered in the list above	Other (please contact us before ordering)

In some cases, FGCZ also offers:

Applications (examples)	Which service to order
Custom data analysis on FGCZ datasets	Bioinformatics analysis (only in special cases - please contact us before ordering)
Acquisition of LC-MS data	Data acquisition (LC-MS/MS) (only in special cases - please contact us before ordering)
Peptide/proteins HPLC fractionation	Other (please contact us before ordering)

References

This content is largely based on information from ETH Zurich functional genomics center https://fgcz.ch/omics_areas.html.