Heuristic
15 methods · 1984–2021
Heuristic: Hand-engineered interpretation rules rather than one global optimisation: extend a sequence peak by peak, enumerate the compositions that fit the mass, score what survives. The oldest approach here, and the closest to reading by hand.
Hand-engineered interpretation rules rather than one global optimisation: extend a sequence peak by peak, enumerate the compositions that fit the mass, score what survives. The oldest approach here, and the closest to reading by hand.
The earliest of its 15 methods is PAAS 3 (1984); 14 more have followed.
| Methods | 15 |
| Papers describing them | 17 |
| Authors | 59 |
| Active | 1984-08-01 to 2021-11-23 |
| Kinds | algorithm (15) |
| Acquisition | DDA (15) |
Methods (15)
Oldest first, by the paper that describes each one.
- PAAS 3 (1984): 1984 FORTRAN program that determines the probable amino acid sequence of a peptide from the sequence ion peaks of its mass spectrum, without a database. One of the earliest de novo peptide sequencing programs.
- SEQPEP (1989): Computer program for interpreting high-energy collision tandem mass spectra of peptides.
- Lutefisk (1997): First widely-used heuristic de novo tool
- SeqMS (2000): Software aid for automated interpretation of low-energy CID spectra for de novo sequencing by tandem MS.
- 2D Fragment Correlation (2000): 2D fragment correlation MS
- PepSeq (2001): 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.
- MALDI/TOF-TOF de novo sequencing (2002): Sequence-extension approach for de novo sequencing from MALDI TOF-TOF spectra.
- MALDI-QIT de novo sequencing (2003): Preliminary MALDI-QIT de novo
- Sequit (2004): Software for de novo peptide sequencing by MALDI post-source decay mass spectrometry.
- Proteomics-grade de novo sequencing (2005): Proteomics-grade de novo sequencing approach for large MS/MS data sets.
- ENPC (2006): Exhaustive composition enumeration
- Adaptive GA for tandem-MS peptide sequencing (2008): Adaptive genetic algorithm for protein sequencing from tandem MS. Represents peptides as GA individuals, evolves them against the observed spectrum; the adaptive component tunes mutation / crossover rates on the fly.
- 157 nm photodissociation de novo sequencing (2010): De novo sequencing algorithm written for 157 nm photodissociation spectra, which yield clean x-ion series rather than the mixed b/y ions of CID. Reports per-residue accuracy and distinguishes leucine from isoleucine, which equal-mass residues normally make impossible.
- Positive charge derivatization de novo sequencing (2013): Positive charge derivatization + spectra merging
- Robust FL-Sequencing (2021): Full-length protein sequencing
Papers describing them (17)
- PAAS 3: A computer program to determine probable sequence of peptides from mass spectrometric data (1984, Biological Mass Spectrometry, peer-reviewed)
- Computer program (SEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides (1989, Biological Mass Spectrometry, peer-reviewed)
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997, Rapid Communications in Mass Spectrometry, peer-reviewed)
- Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry (2000, Electrophoresis, peer-reviewed)
- De Novo Peptide Sequencing by Two-Dimensional Fragment Correlation Mass Spectrometry (2000, Analytical Chemistry, peer-reviewed)
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001, Analytical Chemistry, peer-reviewed)
- MassLynx NT BioLynx & ProteinLynx Guide (2001, resource)
- De novo sequencing of peptides using MALDI/TOF-TOF (2002, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- Searching Sequence Databases via De Novo Peptide Sequencing by Tandem Mass Spectrometry (2002, Molecular Biotechnology, peer-reviewed)
- “De novo” peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: A preliminary study (2003, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- Sequit: software for de novo peptide sequencing by matrix-assisted laser desorption/ionization post-source decay mass spectrometry (2004, Rapid Communications in Mass Spectrometry, peer-reviewed)
- Proteomics-Grade de Novo Sequencing Approach (2005, Journal of Proteome Research, peer-reviewed)
- De novo peptide sequencing using exhaustive enumeration of peptide composition (2006, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- Protein Sequencing with an Adaptive Genetic Algorithm from Tandem Mass Spectrometry (2008, arXiv, preprint)
- Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer (2010, Analytical Chemistry, peer-reviewed)
- High-Confidence de Novo Peptide Sequencing Using Positive Charge Derivatization and Tandem MS Spectra Merging (2013, Analytical Chemistry, peer-reviewed)
- Highly Robust de Novo Full-Length Protein Sequencing (2021, Analytical Chemistry, peer-reviewed)