The comparative quantitative analysis of complex protein samples can be achieved either with 2DE gel-based proteomics or mass spectrometry-based approaches using isobaric tagging like iTRAQ and TMT. Proteome Factory applies both technologies depending on their individual strengths for a particular project and customer's requirements.
iTRAQ and TMT are chemical labels which are reacted with complex protein samples after proteolysis to peptides. Up to eight differentially labelled samples are pooled, separated in a first dimension by strong cation exchange chromatography (or reversed phase chromatography at high pH) and analysed by LCMSMS for protein identification and quantification on a large scale. Many hundred proteins are identified and quantified routinely. The actual number of proteins which is accessible depends on sample complexity and the proteins' dynamic concentration range.
iTRAQ (isobaric tagging for relative and absolute quantification) is available in 4-plex and 8-plex formats, while TMT (tandem mass tags) is available in 2-plex, 6-plex and (since recently) 10-plex formats.
In case more samples need to be analysed than doable with one kit, samples can be analysed successively in different experiments. One label is then applied to a common sample which is usually a pool of representative samples.
As an alternative, label-free quantification should be considered. It is mostly used with very long one-dimensional LCMSMS analyses of the samples, followed by bioinformatic analysis for protein identification and quantification.