Use the top down analysis workflow in the BioPharma Finder application to precisely identify and characterize the molecular composition of an unknown intact protein.

For this type of experiment, intact precursor proteins are ionized and analyzed by mass spectrometry; isolated component peaks are then subjected to fragmentation. Each peak usually represents a single charge state of the unknown protein, but in some cases, each peak might represent a small number of isobaric proteins.

The BioPharma Finder application processes top down analysis experiments by searching for fragmentation matches within a database of known proteoforms for a specific organism, based on its sequenced genome. The application then compares the MS mass measurements and MS2 fragment ion data of the unknown proteins to those of the identified proteoforms (with known or predicted PTMs) to identify and characterize the unknown proteins. Identifications are not always exact, but may be matched within a fragmentation tolerance. To determine the best match, the application scores the matches by using various fragment-based scoring functions.