PepSeq
algorithm · Heuristic
Interactive de novo peptide sequencing application in BioLynx, the biopolymer analysis component of the MassLynx suite. The manual is explicit that it is user-driven rather than automatic: PepSeq “has been designed as an interactive program that allows the user to make decisions at each step in deducing the sequence of a peptide”. It scores and annotates spectra on the a, b, y and z ions, and takes input either from a MassLynx data file or as a plain mass and intensity list. Three modes: typing a candidate sequence to see its theoretical fragments annotated against the spectrum; FindTag, which builds a set of sub-sequences whose series ions best match the spectrum and extends them step or leap-wise until the molecular weight matches the user-supplied precursor; and MassSeq, a separately purchased option that performs the sequencing automatically from the precursor mass, modifications and a mass-accuracy estimate. There is no methods paper: the method is documented only in the vendor manual, which is catalogued here as the accompanying resource. Provenance runs Micromass UK Ltd to Waters Corporation, and the Version 4.0 guide catches the handover in progress, carrying a Waters part number and a Micromass part number side by side over a 1993-2002 Micromass UK Ltd copyright.
| Kind | algorithm |
| Family | Heuristic |
| Deep learning | no |
| Acquisition | DDA |
Papers
- MassLynx NT BioLynx & ProteinLynx Guide (2001, resource)
- A Proteomics Approach to the Identification of Mammalian Mitochondrial Small Subunit Ribosomal Proteins (2000, Journal of Biological Chemistry, peer-reviewed)