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 …
Deep learning methods for de novo peptide sequencing
Protein tandem mass spectrometry data are 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 …
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 essential in proteomics.
Unlike traditional database searches, deep learning excels at de novo peptide sequencing …
Unlike traditional database searches, deep learning excels at de novo peptide sequencing …
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 …
Metaproteomics beyond databases: addressing the challenges and potentials of de novo sequencing
Metaproteomics enables the large‐scale characterization of microbial community proteins,
offering crucial insights into their taxonomic composition, functional activities, and …
offering crucial insights into their taxonomic composition, functional activities, and …
De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments
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 …
[HTML][HTML] Pre-trained Maldi Transformers improve MALDI-TOF MS-based prediction
For the last decade, matrix-assisted laser desorption/ionization time-of-flight mass
spectrometry (MALDI-TOF MS) has been the reference method for species identification in …
spectrometry (MALDI-TOF MS) has been the reference method for species identification in …
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 …