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Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used,…
Tandem Mass Spectrometry is a cornerstone technique for identifying unknown small molecules in fields such as metabolomics, natural product discovery and environmental analysis. However, certain aspects, such as the probabilistic…
Peptide identification in mass spectrometry-based proteomics is crucial for understanding protein function and dynamics. Traditional database search methods, though widely used, rely on heuristic scoring functions and statistical…
The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of…
Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrumentation and resulting data, sophisticated…
Recent advancements in protein structure prediction, particularly AlphaFold2, have revolutionized structural biology by achieving near-experimental accuracy ($\text{average RMSD} < 1.5\text{\AA}$). However, the computational demands of…
Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biomarkers for disease. However,…
Rationale: In a shotgun proteomics experiment with data-dependent acquisition, real-time analysis of a precursor scan results in selection of a handful of peaks for subsequent isolation, fragmentation and secondary scanning. This peak…
Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the…
De novo peptide sequencing is a fundamental computational technique for ascertaining amino acid sequences of peptides directly from tandem mass spectrometry data, eliminating the need for reference databases. Cutting-edge models usually…
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins…
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to…
Deep learning has advanced mass spectrometry data interpretation, yet most models remain feature extractors rather than unified scoring frameworks. We present pUniFind, the first large-scale multimodal pre-trained model in proteomics that…
Peptides are biomolecules comprised of amino acids that play an important role in our body. In recent years, peptides have received extensive attention in drug design and synthesis, and peptide prediction tasks help us better search for…
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…
Compound identification from tandem mass spectrometry (MS/MS) data is a critical step in the analysis of complex mixtures. Typical solutions for the MS/MS spectrum to compound (MS2C) problem involve comparing the unknown spectrum against a…
Small molecules in biological samples are studied to provide information about disease states, environmental toxins, natural product drug discovery, and many other applications. The primary window into the composition of small molecule…
Peptides offer great biomedical potential and serve as promising drug candidates. Currently, the majority of approved peptide drugs are directly derived from well-explored natural human peptides. It is quite necessary to utilize advanced…
Quantum-chemical fragmentation methods offer an efficient approach for the treatment of large proteins, in particular if local target quantities such as protein--ligand interaction energies, enzymatic reaction energies, or spectroscopic…
The tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged prefix and suffix subsequences, and then measures mass/charge ratios of these ions. The de novo peptide sequencing problem is to…