The present application relates to the field of protein sequencing, more particularly to protein profiling using massively parallel sequencing with single-molecule sensitivity. Methods, assays and reagents are provided for sequencing individual protein or polypeptide molecules. Also provided are methods and assays for the parallel sequencing of proteins or polypeptides. To this end, particular labeled probes are used that are reactive with the N-terminal amino acid of the polypeptide molecules and can be detected while still associated with the polypeptide(s).