Heuristic
21 methods · 1981–2021
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 21 methods is PAAS (1981); 20 more have followed.
| Methods | 21 |
| Papers describing them | 31 |
| Authors | 92 |
| Active | 1981-04-01 to 2021-11-23 |
| Kinds | algorithm (21) |
| Acquisition | DDA (20) |
Methods (21)
Oldest first, by the paper that describes each one.
- PAAS (1981): The 1981 original, and the earliest de novo peptide sequencing program in this catalog: a computer program that estimates the possible amino acid sequences of a peptide from its mass spectrum, with no database to search. It could also read a sequence from the PTH amino acids released by Edman degradation, which is what sequencing looked like before tandem MS.
- Improved PAAS (1983): The 1983 revision of PAAS, by the same Osaka group with Wollnik added. Sits between the 1981 original and PAAS 3, so the lineage spans three papers in four years.
- 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. The third of the Osaka group’s lineage, after PAAS (1981) and Improved PAAS (1983), and the most cited of the three.
- SEQPEP (1989): Computer program for interpreting high-energy collision tandem mass spectra of peptides.
- Lutefisk (1997): First widely-used heuristic de novo tool
- SeqMS (1998): 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 (2000): 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.
- Sequence pattern correlation (2002): Deduces peptide sequences without a database by cross-correlating an experimental CID spectrum with predicted sequence patterns from y and non-y fragmentation, claimed insensitive to mass tolerance.
- 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.
- Multi-pass CID spectrum interpretation (2005): Interprets low-energy CID product ion spectra from an ion trap in several passes, extracting the data rigorously and then building the sequence, rather than scoring candidate paths in one sweep.
- Proteomics-grade de novo sequencing (2005): Proteomics-grade de novo sequencing approach for large MS/MS data sets.
- Adaptive GA for tandem-MS peptide sequencing (2006): 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.
- ENPC (2006): Exhaustive composition enumeration
- 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.
- LysNDeNovo (2010): Heuristic de novo sequencing for Lys-N peptides fragmented by ETD, exploiting their long c-ion series.
- Positive charge derivatization de novo sequencing (2013): Positive charge derivatization + spectra merging
- CycloAnt (2017): Hybrid ant colony optimisation with local search that reconstructs cyclic peptide sequences from distorted mass spectra.
- Robust FL-Sequencing (2021): Full-length protein sequencing
Papers describing them (31)
- Computer program PAAS for the estimation of possible amino acid sequence of peptides (1981, Biological Mass Spectrometry, peer-reviewed)
- Improved PAAS, a computer program to determine possible amino acid sequences of peptides (1983, Biological Mass Spectrometry, peer-reviewed)
- 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 high-energy collision-induced dissociation spectra of singly protonated peptides by ‘seqms’, a software aid forde novo sequencing by tandem mass spectrometry (1998, 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)
- Q-Tof ESI-MS/MS and automated software interpretation for de novo sequencing of tryptic peptides from gel separated proteins (2000, Biochemical Society Transactions, abstract)
- 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)
- Sequence Pattern Correlation of Amino Acid in Collision‐induced Dissociation Electrospray Ionization Mass Spectrometry (2002, Chinese Journal of Chemistry, peer-reviewed)
- 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)
- An algorithm for interpretation of low‐energy collision‐induced dissociation product ion spectra for de novo sequencing of peptides (2005, Rapid Communications in Mass Spectrometry, peer-reviewed)
- Proteomics-Grade de Novo Sequencing Approach (2005, Journal of Proteome Research, peer-reviewed)
- A preliminary work on evolutionary identification of protein variants and new proteins on grids (2006, 20th International Conference on Advanced Information Networking and Applications - Volume 1 (AINA’06), peer-reviewed)
- De novo peptide sequencing using exhaustive enumeration of peptide composition (2006, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- Characterization of Polypeptides by Tandem Mass Spectrometry Using Complementary Fragmentation Techniques (2006, thesis)
- Protein Sequencing with an Adaptive Genetic Algorithm from Tandem Mass Spectrometry (2008, arXiv, preprint)
- A Preliminary Work on Evolutionary Identification of Protein Variants and New Proteins on Grids (2008, arXiv, postprint)
- Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer (2010, Analytical Chemistry, peer-reviewed)
- LysNDeNovo: An algorithm enabling de novo sequencing of Lys‐N generated peptides fragmented by electron transfer dissociation (2010, PROTEOMICS, peer-reviewed)
- De NovoSequencing of Tryptic Peptides Derived fromDeinococcus radioduransRibosomal Proteins Using 157 nm Photodissociation MALDI TOF/TOF Mass Spectrometry (2010, Journal of Proteome Research, peer-reviewed)
- Metaheuristics based de novo protein sequencing: A new approach (2011, Applied Soft Computing, peer-reviewed)
- Investigation of VUV photodissociation propensities using peptide libraries (2011, International Journal of Mass Spectrometry, peer-reviewed)
- High-Confidence de Novo Peptide Sequencing Using Positive Charge Derivatization and Tandem MS Spectra Merging (2013, Analytical Chemistry, peer-reviewed)
- CycloAnt (2017, Proceedings of the Genetic and Evolutionary Computation Conference, peer-reviewed)
- Highly Robust de Novo Full-Length Protein Sequencing (2021, Analytical Chemistry, peer-reviewed)