The advent of proteomics techniques for protein identification (PrI) represented a major step
forward in protein chemistry, 1, 2 and indeed, a legion of laboratories are now using different …

Proteomics is the study of proteins, their time-and location-dependent expression profiles, as
well as their modifications and interactions. Mass spectrometry is useful to investigate many …

A key problem in computational proteomics is distinguishing between correct and false
peptide identifications. We argue that evaluating the error rates of peptide identifications is …

Novel protein discovery and immunopeptidomics depend on highly sensitive de novo
peptide sequencing with tandem mass spectrometry. Despite notable improvement using …

In proteomics, de novo sequencing is the process of deriving peptide sequences from
tandem mass spectra without the assistance of a sequence database. Such analyses have …

While peptide identifications in mass spectrometry (MS)-based shotgun proteomics are
mostly obtained using database search methods, high-resolution spectrum data from …

De novo peptide sequencing has improved remarkably in the past decade as a result of
better instruments and computational algorithms. However, de novo sequencing can …

The conventional approach in modern proteomics to identify proteins from limited
information provided by molecular and fragment masses of their enzymatic degradation …

Bioinformatics tools for proteomics, also called proteome informatics tools, span today a
large panel of very diverse applications ranging from simple tools to compare protein amino …

De novo peptide sequencing is the only tool for extracting peptide sequences directly from
tandem mass spectrometry (MS) data without any protein database. However, neither the …