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Quantitative Proteomics

What is protemomics?

Proteomics is the large-scale study of proteomes. A proteome is a set of proteins produced in an organism, system, or biological context under a specific set of conditions or disease state. We may refer to, for instance, the proteome of a species (for example, Homo sapiens) or an organ (for example, the liver). The proteome is not constant; it differs from cell to cell and changes over time. To some degree, the proteome reflects the underlying transcriptome. However, protein activity (often assessed by the reaction rate of the processes in which the protein is involved) is also modulated by many factors in addition to the expression level of the relevant gene.

In its present state, it is dependent on decades of technological and instrumental developments. These developments have included advances in mass spectrometry (MS) technology, protein fractionation techniques, bioinformatics, etc. Proteomics relies on three basic technological cornerstones that include a method to fractionate complex protein or peptide mixtures, MS to acquire the data necessary to identify individual proteins, and bioinformatics to analyze and assemble the MS data. While MS and bioinformatic components are somewhat similar in most applications, there are two distinct methods to separate complex protein samples in proteomics. Proteomics is critically dependent on bioinformatics to process the raw mass spectral data into protein data. While routinely used by every laboratory, the most critical software programs are those that take peptide mapping and/or tandem MS results and determine the protein or peptide sequence that most closely matches the experimental data. GenePrint LifeSciences provides the most robust proteomics data analysis tailored to your needs.


Proteomics is used to investigate:

  • When and where proteins are expressed;
  • Rates of protein production, degradation, and steady-state abundance;
  • How proteins are modified (for example, post-translational modifications (PTMs) such as phosphorylation);
  • The movement of proteins between subcellular compartments;
  • The involvement of proteins in metabolic pathways;
  • How proteins interact with one another.

Proteomics can provide significant biological information for many biological problems, such as:

  • Which proteins interact with a particular protein of interest (for example, the tumour suppressor protein p53)?
  • Which proteins are localised to a subcellular compartment (for example, the mitochondrion)?
  • Which proteins are involved in a biological process (for example, circadian rhythm)


Several high-throughput technologies have been developed to investigate proteomes in depth. The most commonly applied are mass spectrometry (MS) -based techniques such as Tandem-MS and gel-based techniques such as differential in-gel electrophoresis (DIGE). These high-throughput technologies generate huge amounts of data. Databases are critical for recording and carefully storing this data, allowing the researcher to make connections between their results and existing knowledge. GenePrint LifeSciences is proud to offer both gel based (DIGE) and gel free (mass spectrometry-MS) proteomics services.


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