Artificial intelligence in molecular medicine
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Prediction of peptide mass spectral libraries with machine learning
J Cox - Nature Biotechnology, 2023 - nature.com
The recent development of machine learning methods to identify peptides in complex mass
spectrometric data constitutes a major breakthrough in proteomics. Longstanding methods …
spectrometric data constitutes a major breakthrough in proteomics. Longstanding methods …
AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics
Abstract Machine learning and in particular deep learning (DL) are increasingly important in
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention …
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention …
MSBooster: improving peptide identification rates using deep learning-based features
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS)
experiments relies on computational algorithms for matching acquired MS/MS spectra …
experiments relies on computational algorithms for matching acquired MS/MS spectra …
Noncanonical splicing junctions between exons and transposable elements represent a source of immunogenic recurrent neo-antigens in patients with lung cancer
A Merlotti, B Sadacca, YA Arribas, M Ngoma… - Science …, 2023 - science.org
Although most characterized tumor antigens are encoded by canonical transcripts (such as
differentiation or tumor-testis antigens) or mutations (both driver and passenger mutations) …
differentiation or tumor-testis antigens) or mutations (both driver and passenger mutations) …
Accurate de novo peptide sequencing using fully convolutional neural networks
De novo peptide sequencing, which does not rely on a comprehensive target sequence
database, provides us with a way to identify novel peptides from tandem mass spectra …
database, provides us with a way to identify novel peptides from tandem mass spectra …
Most non-canonical proteins uniquely populate the proteome or immunopeptidome
Combining RNA sequencing, ribosome profiling, and mass spectrometry, we elucidate the
contribution of non-canonical translation to the proteome and major histocompatibility …
contribution of non-canonical translation to the proteome and major histocompatibility …
What can ribo-seq, immunopeptidomics, and proteomics tell us about the noncanonical proteome?
Abstract Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of
the human genome and proteome by illuminating thousands of noncanonical sites of …
the human genome and proteome by illuminating thousands of noncanonical sites of …
Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights
into changes in protein expression, cell signaling, cross-talk and epigenetic pathways …
into changes in protein expression, cell signaling, cross-talk and epigenetic pathways …