Proteomics projects may involve
1) Identification of proteins from some source
2) Measuring relative differences in protein expression
3) Finding post-translational modifications of a protein
Services we offer that will aid in protein identification include in-gel digestion from isolated gel bands/spots or in-solution digestion followed by LC/MS/MS or LC/LC/MS/MS or MALDI-TOF/TOF
We have several tools for database searching in house, such as MASCOT and Spectrum Mill, and users may use these to review their data online.
Differential protein expression projects may use the gel electrophoresis services and use PDQuest to find spots that change in intensity. We also have expertise in using isotope labels for differential proteomics including ICAT, ITRAQ, 18O and metabolic labeling. We have peak extractor scripts to determine ratios of peptides from the different conditions and our database tools can be modified to get protein ID using different labeling strategies.
Finding modifications to protein sequence often requires a larger amount of purified protein than a simple ID. Intact protein measurements can indicate the extent of a modification. Running unmodified proteins can serve as a control. Using multiple enzymatic digestions can increase coverage which increases the chance of seeing a modified peptide. Computers are available in the facility which give users access to raw data which they may use to search for modifications.