Mass Spectrometry

Important considerations for each stage of quantitative proteomics

Sample Preparation. To maximize quality protein identifications and reproducibility, MSF clients should ensure:

Project Requirements of Clients:

MSF clients must provide replicate samples of digested protein (i.e., peptides). Minimum four replicates per sample group is recommended, and a starting concentration of 25 micrograms per sample for complex proteomes. All peptides must be de-salted prior to injection using C18 spin columns, ZipTip^TM, or similar. Recommended protocol.

Targeted Protein Q MS Methods

These are methods for quantitating a limited number of known proteins with high precision and accuracy in a total protein extract. This method can be particularly useful for low abundance targets.A certain amount of method development/previous data or sample preparation is required regardless of which of these methods are used.

Schematic of PRM Targeted Analysis

To label or not to label?

Discovery-based Quantitative MS methods,(“shotgun” proteomics), aim to identify as many proteins in a sample as possible and can be completed on a wide range of samples with minimal method development.

Metabolomics is the profiling of small molecules (<1500 Da) of a given sample at a specific time. Metabolites can be endogenous or exogenous, involved in primary or secondary metabolism. Untargeted metabolomics requires matrix and general target dependent sample extraction performed by user in advance. Data analysis is also specialized, MSF has a license for the Agilent Mass Profile Professional software there is also free software available.

What is quantitative proteomics?