The purpose of discovery proteomics is to gather information about all proteins and protein forms in a biological sample. With only little previous knowlegde of the sample, mass spectrometry-assisted proteomics can identify thousands of proteins and protein forms in a single experiment. Sample fractionation allows for even deeper screening of your samples. Thus, discovery proteomics is typically the first step in any larger proteomics project.
On top of protein identification, mass spectrometry also allows for relative protein quantification, i.e. comparing protein abundances in different samples.
Employing mass spectrometry for discovery proteomics has many advantages:
- High sensitivity
- Unbiased approach
- no complex sample preparation needed
Application areas include expression profiling, host cell protein analysis, identification of chemical modifications, biomarker research, drug target discovery, mode of action studies, pathway modeling, and many more.
Schulze et al. re-analyzed various previously generated MS datasets, including a dataset provided by PolyQuant for this study. Their analysis comprised of more than 23 million spectra, facilitating a deep coverage of the proteome and revealing effects of culture conditions and sample processing on protein identification.