Relative Protein Quantification - Measurement of dynamic protein concentration changes


For most biological questions purely qualitative information regarding the presence or absence of protein(s) in a given sample is not sufficient. Instead, quantitative knowledge is required to study protein and/or PTM concentration changes between conditions, time points, disease states, strains, mutants, etc. Acquiring quantitative information using mass spectrometry is challenging and requires an optimal experimental design, reproducible sample preparation protocols as well as a consistent, stable and reproducible LC-MS performance. In the field of proteomics, two conceptually different quantification strategies exist:  Label-free and label-based quantification, latter including several different approaches, depending on how isotope-labels are introduced into the sample, for example SILAC, 15N-labeling,  dimethyl, TMT, iTRAQ, or synthetic peptide or protein spike-ins. All these listed approaches are supported by BayBioMS, for more detailed information please use the navigation menu on the left side of this page.

Each strategy and approach has its specific advantages and disadvantages in terms of throughput, costs, precision and accuracy. Hence the optimal workflow has to be chosen for every new project accordingly.


The final outcome of a relative quantitative proteomic analysis is a list of identified proteins or peptides. Further, for each protein and peptide in this list a protein and peptide ratio is reported, which describes the concentration difference between two samples of the dataset, typically a control sample (as defined by the project leader) and a sample of interest. If biological and/or technical replicate samples were prepared, also a statistical significance value gets provided, which estimates how likely the observed protein or peptide ratio is statistically significant.