Global proteomic profiling studies enable identification and quantitation of thousands of proteins in biological samples. In these studies, high molecular weight proteins that are relatively abundant have better chance of being sampled by mass spectrometry than low molecular weight proteins that are less abundant. This is evident in most proteomics datasets where several biologically important protein classes including growth factors and cytokines are poorly represented. Extensive pre-fractionation of protein digests can improve proteome coverage and increase the likelihood of sampling low molecular weight/low abundant proteins. However, such strategies are often not feasible in large-scale proteomics projects as it would require more sample processing and instrument time.
In this study, we evaluated size exclusion chromatography and organic solvent-based protein precipitation methods for isolation/enrichment of low molecular weight/low abundant proteins. We present data from cancer cell lines and biofluids like plasma to demonstrate the utility of this approach to isolate/enrich low molecular weight proteins that are underrepresented in proteomics datasets. This strategy can be employed to investigate changes in expression levels of important classes of proteins including growth factors, cytokines and chemokines that are poorly represented in global proteomic profiling studies.