Proteome Profiling is a type of quantitative proteomics (relative and/or semi absolute) that reveals differences in protein expression across samples. For example if you have a set of samples (Treated vs Control or a time course 2h, 4h, 12h) and want to know what proteins are differently expressed, this is the right service for you. We employ differential mass spectrometry in the quantification process, if a large number of unidentified peptides are significantly different between the samples a follow up experiment for selected peptide identification can be performed. Initially the identification experiment will be performed in silico where the unidentified peptides will be matched against the proteins already identified in the sample set. Preferably the number of samples in each group should be at least 7.
Proteogenomics This relatively new field in biological mass spectrometry combines proteome profiling with sample specific genomic and transcriptomics information. It is called proteogenomics and is used to discover novel protein coding regions/genes and provide protein level-evidence confirming a protein coding potential of a gene, thereby improving genome annotation. With the fast development in methods to generate DNA and RNA sequence data, proteogenomic methods open up the possibility to connect the proteomics and genomics fields. Proteogenomics can be used for detection of novel protein species (mutated proteins, fusion proteins, pseudogenic proteins etc.).
Targeted Proteomics This is a very powerful technique for simultaneous determination of protein abundance for a selected set of proteins. This method actually "targets" peptides enzymatically digested from your target protein, so it is important to pick your peptides and method conditions carefully. Please come and talk to us if you are considering this type of experiment. This analysis also requires a good bit of preliminary analysis to ensure the method is robust and quantitative. By spiking in heavy-labeled peptides to a complex matrix as concentration standards, MRM/SRM can be used to construct a calibration curve that can provide the absolute quantification (i.e., copy number per cell) of the native, light peptide, and by extension, its parent protein. If the experiment is to determine differential expression between groups of samples, the minimum number of samples in each group should be 7.
Protein Identification Can be downstream of a Proteome Profiling or Proteogenomics experiment where the goal will be to identify a set of unknown peptides that are of importance to the profiling experiment. It can also be an experiment in it self, for example identify an unknown band on a SDS gel to verify the sequence of a mutation experiment or make sure that your pull-down worked properly.
Post Translational Modification Discovery Some Modifications are easier to find than others. We can look for specific modifications (Phosphorylations, etc..) or scan your data for unknown modifications, e.g. modifications that you did not know about (pretty cool no?). Your chances of detecting the modification you are interested in are completely dependent on the stability of that modification, how that modification affects peptide fragmentation in a mass spectrometer, the stoichiometry of the modification and numerous other variables. Basically, we don't have a clue most of the time whether we will be successful. You have to try it and see.
