Proteomics

Proteomics is a quite diverse field that can be partitioned into general and quantitative workflows. Quantitative proteomics is focused on determining the amount of protein or protein PTM in a sample, while more general workflows cover a broad area of protein mass spectrometry. Many proteomics cores attempt to cover both general and quantitative workflows, but more often than not the lack of proper instrumentation and particular operator expertise can limit the ability of a given core to provide the best of both workflows. To provide focus and be a top-tier service provider, the IDeA National Resource for Quantitative Proteomics is focused only on quantitative proteomics. 

Quantitative proteomics applications in biomedical research can be categorized into discovery and targeted-validation phases. Discovery-phase proteomics refers to the large-scale identification and quantification of proteins or protein PTMs from a complex biological sample such as cells in culture, tissues, or plasma. High-resolution, rapid-sampling mass spectrometers operating in data-dependent or independent modes are the foundation of discovery-phase proteomics. Discovery-phase proteomics generally utilizes 10s of samples and generates 1000s of candidate proteins for follow-up studies. Targeted proteomics typically follows the discovery phase. For targeted proteomics, specialized mass spectrometers are used to specifically quantify levels of a small set of proteins in a large number of samples. Targeted proteomics generally utilizes 100s of samples to measure 10s of target proteins. Discovery and targeted proteomics use different types of mass spectrometer configurations, methods, and data analyses; accordingly, many proteomics core facilities are specialized in one or the other subspecialty, but both are often applied in successive phases of research endeavors. To be a comprehensive quantitative proteomics provider, we provide both discovery and targeted workflows.