PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization

A novel protein identification framework, PILOT_PROTEIN,
has been
developed to construct a comprehensive list of all unmodified proteins
that are present in a living sample. It uses the peptide identification
results from the PILOT_SEQUEL algorithm to initially determine all
unmodified proteins within the sample. Using a rigorous biclustering
approach that groups incorrect peptide sequences with other homologous
sequences, the number of false positives reported is minimized. A
sequence tag procedure is then incorporated along with the untargeted
PTM identification algorithm, PILOT_PTM, to determine a list of all
modification types and sites for each protein. The unmodified protein
identification algorithm, PILOT_PROTEIN, is compared to the methods
SEQUEST, InsPecT, X!Tandem, VEMS, and ProteinProspector using both
prepared protein samples and a more complex chromatin digest. The
algorithm demonstrates superior protein identification accuracy with
a lower false positive rate. All materials are freely available to
the scientific community at http://pumpd.princeton.edu.