Artificial neural network models for prediction of de novo sequencing of chains of amino acids
US12340874B1 · Verily Life Sciences · priority 2017
| Patent | US12340874B1 ↗ |
| Status | Active |
| Priority date | 2017-11-03 |
| Filed | 2018-10-25 |
| Published (granted) | 2025-06-24 |
| Assignee | Verily Life Sciences (printed Verily Life Sciences LLC) |
| Current assignee | Verily Health Inc |
Abstract
The present invention relates to proteomics, and techniques for predicting de novo sequencing of chains of amino acids, such as peptides, proteins, or combinations thereof. Particularly, aspects of the present invention are directed to a computer implemented method that includes obtaining a digital representation of a mass spectrum, the digital representation including a plurality of container elements, encoding, using an encoder portion of a bidirectional recurrent neural network of long short term memory cells and gated recurrent unit cells, each container element as an encoded vector, decoding, using a decoder portion of the bidirectional recurrent neural network, each of the encoded vectors into a sequence of amino acids; and recording the sequence of amino acids as a multi-dimensional data set of amino acids types and a probability of each of the amino acid types in each position of the complete amino acid sequence.
Why it is here
Verily: neural-network de novo sequencing of peptides and proteins from MS/MS spectra.
Inventors (3)
Krishnan Palaniappan, Peter Cimermancic, Roie Levy
An inventor links to an author page only where the same person is evident, never on a name alone.
Catalogued papers it cites (9)
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003)
- De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004)
- NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005)
- Performance Evaluation of Existing De Novo Sequencing Algorithms (2006)
- De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007)
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009)
- Novor: Real-Time Peptide de Novo Sequencing Software (2015)
- UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry (2016)
- De novo peptide sequencing by deep learning (2017)
Matched from the patent’s 20 literature citations by the rules the paper citation graph uses.
Catalogued patents it cites (1)
- US11573239B2 Methods and systems for de novo peptide sequencing using deep learning
Cited by (2 patent families, 2 organisations)
- Anhui University academic: CN121354744A
- Suzhou Yuannao Intelligent Technology company: CN120853678A
Every family, of any applicant, that cites this one, as Google Patents lists them; an assignee is given its English name.