LC-MS/MS is the reference method for global high-throughput analysis of complex proteomes. DC Biosciences offer a range of services to meet your everyday proteomics expertise requirements.
In a typical “bottom-up” LC-MS/MS workflow, biological samples are obtained (1) and proteins extracted (2) then optionally fractionated (3).
Purified proteins are digested into peptides (4) which can be subjected to fractionation – typically “offline” HPLC such as SAX, high-pH RP or HILIC – and/or enrichment for specific categories – e.g. phospho-peptides – (5).
After clean-up (6), peptides are analysed by LC-MS/MS (7), which creates Raw files containing spectra. There are then analysed (8) using specific software (MaxQuant, Proteome Discoverer) to match spectra to expected peptide sequences.
Data can then be further analysed and annotated using available knowledge bases – GO, KEGG, etc… – (9)
The usual acquisition mode is Data Dependent Acquisition (DDA), which aims to fragment for each duty cycle the “n” most abundant species. Data Independent Acquisition (DIA) – where all eluting peptides are simultaneously fragmented to generate complex spectra – is becoming more common and we are now offering it for the first time. More more about Acquisition methods.
DC Biosciences offers a number of relative quantitative proteomics services, such as Tandem Mass Tagging (TMT), Isobaric tags for relative and absolute quantitation (iTRAQ), Stable isotope labeling with amino acids in cell culture (SILAC), label free and DIA.