Proteomic Glossary of Terms

Activity-based Proteomics:

Identification and analysis of changes in active proteins in different cell types and under different conditions addressing the biochemical mechanisms of disease more directly than standard genomic and proteomic techniques.

Affinity Proteomics:

Affinity pull-downs are one of the most common types of proteomic experiments performed in any research laboratory. Combining such experiments with mass spectrometry can be challenging; but it is a very powerful approach when studying protein-protein interactions.

Antibody Protein Sequencing:

Antibody protein sequencing offers a mass spectrometry solution that accurately obtains the full amino acid sequence without requiring the cell line or DNA.


Area under the curve


The science of collecting and analysing complex biological data. Proteomics in combination with bioinformatics are used to analyse the expression levels and post-translational changes in the proteins of the tissues and biological fluids.

Clinical Proteomics:

The use of proteomics in the detection of disease biomarkers and the development of safer drugs.


A chromatogram is a graphical representation of separated eluents which can be used to identify compounds and to determine their relative concentrations within the mixture.


Compensation Voltage


Charge Variant Analysis. The analysis of charged variants is a regulatory requirement for bio-therapeutic proteins. These large heterogeneous molecules can be subject to a variety of enzymatic post-translational modifications during manufacture, such as glycosylation and lysine truncation.

Data-dependent Acquisition (DDA):

There are currently two broad approaches for generating bottom-up or “shotgun” MS proteomic data Data-dependent Acquisition and Data-independent Acquisition.

In DDA mode, the mass spectrometer selects the most intense peptide ions in a first stage of tandem mass spectrometry, and then they are fragmented and analysed in a second stage of tandem mass spectrometry.

Data-independent Acquisition (DIA):

In DIA mode, all peptides generated during the first MS cycle are fragmented in the second round.

The new standard in LC-MSMS-based proteomics for protein identification and label-free quantitation. This method can obtain deep and exhaustive coverage of multiple individual samples in contrast to the more-commonly practiced approach of data-dependent acquisition (DDA).

De novo Protein Sequencing:

De novo protein sequencing by mass spectrometry enables researchers to resurrect lost hybridomas, re-engineer protein backbones, and recombinantly reproduce key reagents with high consistency.


Electrospray ionisation mass spectrometry is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionised.

High-throughput Proteomics:

High-throughput proteomics is the core technique for large-scale protein characterisation. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity.


The high-resolution multi-attribute method (HR MAM) is a powerful high resolution accurate mass (HRAM) mass spectrometry (MS)-based workflow, delivering comprehensive characterisation and monitoring of biotherapeutic products.

Intact Protein Mass:

A method of determining the purity and molecular mass of a protein.

Isobaric Labelling:

Stable, isobaric labelling of peptides is an elegant method to enable the simultaneous analysis and relative quantitation of multiple samples by mass spectrometry-based proteomics.

Label-Free Quantitation:

Label-free quantitation (LFQ) between multiple, individually analysed samples via chromatogram realignment and peptide intensity normalisation provides an alternative to labelled quantitative approaches.


Liquid chromatography is a technique used to separate a sample into its individual parts. This separation occurs based on the interactions of the sample with the mobile and stationary phases.


liquid chromatography mass spectrometry combines the physical separation capabilities of liquid chromatography with the mass analysis capabilities of mass spectrometry.

LC-MSMS Data Acquisition:

LC-MSMS is the gold standard approach for global high-throughput analysis of complex proteomes.



Microbial Proteomics:

Microbial proteomics aids in the identification of the proteins associated with microbial activity, microbial host-pathogen interactions, and antimicrobial resistant mechanism.


Matrix-assisted laser desorption ionisation time-of-flight

MALDI-TOF Imaging:

MALDI-TOF imaging is a technique in cancer diagnostics and combines the advantages of mass spectrometry, the detection of numerous molecules, and spatial resolution in histological tissue sections and cytological preparations. This method enables the detection of proteins, peptides, lipids, carbohydrates or glycoconjugates and small molecules.


Mass spectrometry is an analytical tool useful for measuring the mass-to-charge ratio (m/z) of one or more molecules present in a sample.  These measurements can often be used to calculate the exact molecular weight of the sample components as well.

MS Spectrum:

An intensity vs. m/z (mass-to-charge ratio) plot.


The Orbitrap is an ion trap mass analyser that consists of two outer electrodes and a central electrode and can function as both an analyser and detector.


The evolving field of pharmacoproteomics enables drug developers and clinicians to identify proteins linked to early disease, effects of treatment, likelihood of relapse or resistance. A pharmacoproteomic profile of an individual can be established enabling prediction of a response to treatment.


Phosphorylation is a highly important modification. Phosphopeptides are low in abundance in the cell and are challenging to observe by mass spectrometry. A good phosphoproteome coverage requires specific enrichment of the phosphopeptides.

Post-translational modifications:

Protein post-translational modifications (PTMs) increase the functional diversity of the proteome by the covalent addition of functional groups or proteins, proteolytic cleavage of regulatory subunits, or degradation of entire proteins. These modifications include phosphorylation, glycosylation, ubiquitination, nitrosylation, methylation, acetylation, lipidation and proteolysis and influence almost all aspects of normal cell biology and pathogenesis.

Protein Identification:

Protein identification is the fundamental core of proteomic research. The proteomic scientist uses various methods to identify proteins and research their qualities.

Protein knockouts:

These allow researchers to rapidly develop reagents to block one or more functions of a newly discovered protein to facilitate studies of its role in cellular metabolism.

Protein microarray:

Method used to track the interactions and activities of proteins, and to determine their function.

Protein Profiling:

Protein profiling is defined in general as identifying the proteins expressed in a particular tissue, under a specified set of conditions and at a particular time. This information is useful in drug discovery and diagnosis as well as in understanding response mechanisms at the protein level.

Protein Turnover:

Cellular proteins are far from static entities; and are constantly undergoing synthesis and degradation. Changes in the rates that proteins are ‘turned over’ are central to understanding protein regulation in response to perturbations or stimuli.


A combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of peptides.


The collection of proteins found in a particular cell type under a particular set of environmental conditions.

Quantitative Proteomics:

Quantitative proteomics is a powerful approach used for both discovery and targeted proteomic analyses to understand global proteomic dynamics in a cell, tissue, or organism. Most quantitative proteomic analyses entail the isotopic labelling of proteins or peptides, which can then be differentiated by mass spectrometry.

Retention time (Tr):

Retention time is the time elapsed between sample introduction (beginning of the chromatogram) and the maximum signal of the given compound at the detector.


Stable isotope labelling with amino acids in cell culture (SILAC) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labelling.


Synchronous precursor selection (SPS MS3 on tribrid MS)

Structural Proteomics:

Structural proteomics is the determination of three-dimensional protein structures on a genome-wide scale to increase understanding of the relationship between protein sequence, structure, and function.

Tandem Mass Tag:

A tandem mass tag (TMT) is a chemical label that facilitates sample multiplexing in mass spectrometry-based quantitation and identification of peptides and proteins.

Tandem MS (MSMS, MS/MS, MS2)

Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analysers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples.


Transcriptomics is the study of the transcriptome—the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell—using high-throughput methods, such as microarray analysis.


Ubiquitin and ubiquitin-like modifiers have emerged as central components in cell biology. Like other post-translational modifications, the study of protein modification by ubiquitin relies on enrichment of either PTM-modified proteins or peptides.

The fascinating research field of proteomics is creating exciting advances in disease detection and therapy.

DC Biosciences is proud to offer our expertise in innovative proteomics and is dedicated to finding solutions for research in all fields of drug discovery and protein analysis. Our highly-specialised team sets the standard for reliable, cost-effective, and high-quality solutions for researchers.

“The whole process is very flexible and I particularly liked the possibility to work out the entire experimental setup and protocols with you beforehand.”

Nikita Gamper, University of Leeds (November 2020)

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Sarah Seiler Hogan, Unither Pharmaceuticals (November 2020)

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