Shotgun LC MS/MS is the basis of many Protein ID experiments. An unlabelled sample is fractionated and digested into peptides, then analysed by MS to identify parent proteins.
DC Biosciences offer a qualitative proteomics service for analysis of complex samples such as cell lysates, tissues and biofluids (e.g. plasma).
Fractionation is required in order to obtain high sample coverage. This can be performed at the organelle level (e.g. nuclear vs cytoplasm), protein level (e.g. multiple gel band analysis) or at peptide level by HPLC (e.g. high pH reverse phase chromatography) or using PTM enrichment methods. The more fractions, the more proteins identified.
A 2.5 hour run without fractionation generates 10 MS2 spectra equating to approximately ~13,500 peptides. Usually the ratio between identified peptides and protein IDs is 10/1. This would mean ~1,350 proteins are identified. This is much less than the usually expected proteome and highlights the importance for fractionation.
At DC Biosciences we tailor our protocols to your requirements to answer your biological questions.