Protein Identification - Which protein(s) are present in my sample?
Almost every proteomic analysis starts with the question: Which proteins and peptides are detectable by mass spectrometry in a given sample at a given time point?
Most frequently, this question gets addressed by using a gel-based or gel-free shotgun proteomic analysis workflow.
One important prerequisite that needs to be fulfilled in order to perform a shotgun-based proteomic data analysis is the availability of genomic and/or transcriptomic information from the organism(s) or species of interest. From such data a theoretical open-reading-frame coded proteome database can be computed and used to analyze the proteomic LC-MS data.
The final outcome of a shotgun-based proteomic analysis is typically a list of identified proteins, in which for each protein a probability score gets computed, which serves as a measure for the likelihood that a given protein is correctly identified or a false-positive hit.