Tandem mass spectrometry, which is an ideal match for the large-scale protein identification and quantification in complex biological systems.
In this approach, a protein sequence database is used to calculate all putative peptide candidates in the given setting (proteolytic enzymes, miscleavages, post-translational modifications).
Such derivative patterns are used as templates to find a sufficiently close match within experimental mass spectra, which serves as the basis for peptide/protein identification.
However, more and more high-quality mass spectra are being acquired by the collective contribution of the scientific community, which will continuously expand the coverage of peptide spectral libraries.
For a peptide spectral library, to reach a maximal coverage is a long-term goal, even with the support of scientific community and ever-growing proteomic technologies.
[citation needed] However, the optimization for a particular module of the peptide spectra library is a more manageable goal, e.g. the proteins in a particular organelle or relevant to a particular biological phenotype.