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.
Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA.
Richard C
RC
Baliban
Peter A
PA
Dimaggio
Mariana D
MD
Plazas-Mayorca
Benjamin A
BA
Garcia
Christodoulos A
CA
Floudas
D000465:Algorithms; D016000:Cluster Analysis; D030562:Databases, Protein; D010446:Peptide Fragments / Q000737:chemistry; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics; D012372:ROC Curve; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry
D010446:Peptide Fragments; D011506:Proteins