Sequence-to-sequence translation from mass spectra to peptides with a transformer model
A fundamental challenge in mass spectrometry-based proteomics is the identification of the
peptide that generated each acquired tandem mass spectrum. Approaches that leverage …
peptide that generated each acquired tandem mass spectrum. Approaches that leverage …
A learned score function improves the power of mass spectrometry database search
Motivation One of the core problems in the analysis of protein tandem mass spectrometry
data is the peptide assignment problem: determining, for each observed spectrum, the …
data is the peptide assignment problem: determining, for each observed spectrum, the …
De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments
K Eloff, K Kalogeropoulos, O Morell, A Mabona… - bioRxiv, 2023 - biorxiv.org
Bottom-up mass spectrometry-based proteomics is challenged by the task of identifying the
peptide that generates a tandem mass spectrum. Traditional methods that rely on known …
peptide that generates a tandem mass spectrum. Traditional methods that rely on known …
A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data
A core computational challenge in the analysis of mass spectrometry data is the de novo
sequencing problem, in which the generating amino acid sequence is inferred directly from …
sequencing problem, in which the generating amino acid sequence is inferred directly from …
NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics
Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the
high-throughput analysis of protein composition in biological tissues. Many deep learning …
high-throughput analysis of protein composition in biological tissues. Many deep learning …
π-PrimeNovo: An Accurate and Efficient Non-Autoregressive Deep Learning Model for De Novo Peptide Sequencing
Peptide sequencing via tandem mass spectrometry (MS/MS) is fundamental in proteomics
data analysis, playing a pivotal role in unraveling the complex world of proteins within …
data analysis, playing a pivotal role in unraveling the complex world of proteins within …
Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins
Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly
developing novel strategies for the analyses and interpretations of complex, degraded …
developing novel strategies for the analyses and interpretations of complex, degraded …
Deep learning methods for de novo peptide sequencing
W Bittremieux, V Ananth, WE Fondrie, C Melendez… - 2024 - chemrxiv.org
Protein tandem mass spectrometry data is most often interpreted by matching observed
mass spectra to a protein database derived from the reference genome of the sample being …
mass spectra to a protein database derived from the reference genome of the sample being …
A multi-species benchmark for training and validating mass spectrometry proteomics machine learning models
Training machine learning models for tasks such as de novo sequencing or spectral
clustering requires large collections of confidently identified spectra. Here we describe a …
clustering requires large collections of confidently identified spectra. Here we describe a …
Shining a Light on the Dark-Field of the Metaproteome
H Duan - 2024 - ruor.uottawa.ca
Metaproteomics has emerged as a powerful tool for studying human gut microbiomes.
However, the intricate nature of these microbial communities often surpasses the analytical …
However, the intricate nature of these microbial communities often surpasses the analytical …