Decoding approaches for protein identification

A system for characterizing proteins in a sample comprising:

• a substrate having a plurality of proteins from a sample, wherein individual proteins in the plurality of proteins are attached to unique spatial addresses on the substrate;
• a detector configured to detect a series of affinity binding measurements associated with sequentially applying a series of tagged affinity reagents to the individual proteins in the plurality of proteins attached to the unique spatial addresses on the substrate and configured to produce an outcome set comprising positive binding outcomes and negative binding outcomes for the individual proteins in the plurality of proteins with the tagged affinity reagents;
• and
• a computing system configured to:
• obtain a database comprising a set of candidate proteins, and for each candidate protein, a probability of observing a positive binding outcome or negative binding outcome with each of the tagged affinity reagents;
• characterize the plurality of proteins attached to the substrate by determining with a computer, using the database comprising the set of candidate proteins and the probabilities, and the outcome set, identity information for a probable group of candidate proteins in the database corresponding to each of the individual proteins attached to the substrate;
• and
• store the characterization of each individual protein in the plurality of proteins and their corresponding unique spatial addresses on the substrate to a computer memory to characterize the individual proteins present in the sample.

A non-transitory computer-readable media having computer program instructions stored therein, the computer program instructions being configured such that, when executed by one or more computing devices, the computer program instructions cause the one or more computing devices to:

• receive an outcome set indicating positive binding outcomes and negative binding outcomes taken from a process of sequentially applying a series of tagged affinity reagents to individual proteins in a plurality of proteins attached to unique spatial addresses on a substrate;
• receive a database comprising a set of candidate proteins, and for each candidate protein, a probability of observing a positive binding outcome or negative binding outcome of the individual proteins with each of the tagged affinity reagents;
• characterize the individual proteins of the plurality of proteins attached to the substrate by determining with a computer, using the database comprising the set of candidate proteins and the probabilities, and the outcome set, identity information for a probable group of candidate proteins in the database corresponding to each of the individual proteins attached to the substrate;
• and
• store the characterization of the individual proteins of the plurality of proteins and their corresponding unique spatial addresses on the substrate to a computer memory to characterize the individual proteins present in the sample.