1. A label-free method for quantifying post-translational protein modifications in a plurality of samples, each sample containing a mixture of proteins obtained from a biological sample, the method comprising: (a) obtaining peptides from the mixture of proteins in each sample of the plurality of samples by a process comprising cleaving the mixture of proteins in each sample into peptides using a protease to obtain a plurality of peptide samples; (b) enriching post-translationally modified peptides from each sample to obtain a plurality of enriched peptide samples, each sample being enriched for post-translationally modified peptides; (c) carrying out liquid chromatography-mass spectrometry (LC-MS) on the plurality of enriched peptide samples and obtaining MS data for the peptides in each sample of the plurality of samples, said MS data including mass to charge (m/z) ratio, charge (z), and relative retention time; (d) comparing the MS data obtained in step (c) to a known reference database in order to identify the post-translationally modified peptides; (e) compiling a database consisting of the MS data for all peptides across the plurality of enriched post-translationally modified peptide samples; (f) constructing extracted ion chromatograms (XICs) for each post-translationally modified peptide present in the database compiled in step (e) across the plurality of enriched peptide samples; and (g) quantifying each post-translationally modified peptide in the database across the plurality of enriched peptide samples by determining the peak height or area of each XIC, thereby quantifying post-translational protein modifications in the plurality of samples containing mixtures of proteins.