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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

Updated: Jun 18, 2026

A High Throughput, Multiplexed and Targeted Proteomic CSF Assay to Quantify Neurodegenerative Biomarkers and Apolipoprotein E Isoforms Status

A High Throughput, Multiplexed and Targeted Proteomic CSF Assay to Quantify Neurodegenerative Biomarkers and Apolipoprotein E Isoforms Status

Published on: October 20, 2016

Quality Control-A Stepchild in Quantitative Proteomics: A Case Study for the Human CSF Proteome.

Svitlana Rozanova^1,2, Julian Uszkoreit^1,2, Karin Schork^1,2

¹Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, 44801 Bochum, Germany.

|March 29, 2023

Summary

Quality assessment of mass spectrometry (MS) data is crucial for accurate biomarker discovery in proteomics. This study provides practical guidance and a free tool (MaCProQC) to evaluate MS data quality for reliable quantitative proteomics.

Keywords:

FASP cerebrospinal fluid in-solution digestion label-free quantification mass spectrometry proteomics quality control

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Last Updated: Jun 18, 2026

A High Throughput, Multiplexed and Targeted Proteomic CSF Assay to Quantify Neurodegenerative Biomarkers and Apolipoprotein E Isoforms Status

A High Throughput, Multiplexed and Targeted Proteomic CSF Assay to Quantify Neurodegenerative Biomarkers and Apolipoprotein E Isoforms Status

Published on: October 20, 2016

Absolute Quantification of Aβ1-42 in CSF Using a Mass Spectrometric Reference Measurement Procedure

Absolute Quantification of Aβ_1-42 in CSF Using a Mass Spectrometric Reference Measurement Procedure

Published on: March 21, 2017

Sample Preparation for Endopeptidomic Analysis in Human Cerebrospinal Fluid

Sample Preparation for Endopeptidomic Analysis in Human Cerebrospinal Fluid

Published on: December 4, 2017

Area of Science:

Proteomics and Mass Spectrometry (MS)
Biomarker Discovery
Neurodegenerative Disease Research

Background:

Mass spectrometry (MS)-based quantitative proteomics is vital for biomarker discovery.
Analytical conditions during MS data acquisition can compromise accuracy.
Comprehensive quality assessment of MS data is often overlooked due to complexity.

Purpose of the Study:

To practically address the quality assessment of quantitative MS data.
To provide guidance for critically interpreting MS data quality in proteomics.
To introduce a free, open-source tool for systematic MS data quality control.

Main Methods:

Evaluation of MS data quality at raw data, identification, and quantification levels.
Assessment of four independent cerebrospinal fluid (CSF) datasets.
Development and application of the MaCProQC tool with defined quality metrics.

Main Results:

Sample processing differences impact MS data quality across all evaluated levels.
Varying impacts of sample processing on the quality of quantitative proteomics data were observed.
MaCProQC facilitates systematic, rapid, and uncomplicated data comparison.

Conclusions:

Effective quality assessment is essential for reliable quantitative proteomics.
The MaCProQC tool aids in interpreting MS data quality for biomarker studies.
This work enhances the accuracy and reproducibility of neurodegenerative disease biomarker research.