A Beginner’s Guide to Proteomics – Understanding Protein Importance and How to Study Them

You may have heard of proteins in different contexts- supplements for intense workouts, nutrients to keep your body healthy, catalysers of biochemical reactions at university. Proteins play fundamental roles in metabolic reactions, immune response, tissue growth and maintenance – your body is dependent on them for survival. 

Proteins are made up of one of more strands of amino acids defined by the genetic code and fold up post synthesis into 3D structures. A protein is born after DNA (genetic command center) is transcribed into RNA which is then translated into protein by recognition of 3 nucleotide bases (codons). 

Owing to their biological prominence, scientists aim to characterize the structures, spatial distribution and temporal dynamics of all the proteins within a given biological system (proteome). How proteins differ between healthy versus disease individuals or how the environment modulates the protein activity is also of interest. This scientific field is referred to as proteomics. 

Interestingly, proteomes vary spatially (cell type and localization), temporally and from the surrounding environmental conditions. Most proteins also undergo post-translational modifications which are not encoded in the genome which include: phosphorylation (addition of phosphate groups), methylation (addition of methyl groups) glycosylation (addition of sugars). Understanding the different protein forms is especially relevant in treating diseases as they act as potential biomarkers – cancer cells, for example are characterized with altered glycosylation patterns compared to healthy cells and can thus be targeted for therapeutics. 

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Scientists rely on the highly sensitive and analytical mass spectrometry, to quantify protein presence and abundance. This technique uses the mass to electrical charge ratio of the molecules to generate spectrums. Scientists often use the below workflow to quantify and analyze proteins:

  1. Proteins are studied from biological samples (body fluids, tissues, organs)
  2. The sample is isolated, enzymatically digested “trimmed down” into smaller fragments and purified before being inserted in the mass spectrometer 
  3. The mass spectrometer plots a spectrum with varying peaks (mass to charge ratios of fragmented proteins) which are identified by biochemical fragmentation pathways – signatures which allow the identification of specific amino acids
  4. Based on these pathways, the amino acids can be pieced together, like pieces to a 100 pieced puzzle, to yield the final studied protein sequence 
  5. The obtained protein sequences are then confirmed using bioinformatic tools (methods and software tools for understanding biological data) such as BLAST (Basic Local Alignment Search Tool) which compares the newly found protein sequence against known databases