Related papers: Foundation model for mass spectrometry proteomics
Motivation: Mass spectrometry-based proteomics is among the most commonly used methods for scrutinizing proteomic profiles in different organs for biological or medical researches. All the proteomic analyses including peptide/protein…
Mass spectrometry is a widely used method to study molecules and processes in medicine, life sciences, chemistry, catalysis, and industrial product quality control, among many other applications. One of the main features of some mass…
Mass spectrometry, especially so-called tandem mass spectrometry, is commonly used to assess the chemical diversity of samples. The resulting mass fragmentation spectra are representations of molecules of which the structure may have not…
As in many other scientific domains, we face a fundamental problem when using machine learning to identify proteins from mass spectrometry data: large ground truth datasets mapping inputs to correct outputs are extremely difficult to…
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…
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,…
Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…
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 methods have been developed for \emph{de novo} peptide…
Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and…
Shotgun proteomics is a high-throughput technology used to identify unknown proteins in a complex mixture. At the heart of this process is a prediction task, the spectrum identification problem, in which each fragmentation spectrum produced…
A vast majority of mass spectrometry data remains uncharacterized, leaving much of its biological and chemical information untapped. Recent advances in machine learning have begun to address this gap, particularly for tasks such as spectral…
The ultimate target of proteomics identification is to identify and quantify the protein in the organism. Mass spectrometry (MS) based on label-free protein quantitation has mainly focused on analysis of peptide spectral counts and ion peak…
Mass spectrometry is a widespread approach to work out what are the constituents of a material. Atoms and molecules are removed from the material and collected, and subsequently, a critical step is to infer their correct identities based…
The identification and property prediction of chemical molecules is of central importance in the advancement of drug discovery and material science, where the tandem mass spectrometry technology gives valuable fragmentation cues in the form…
Tandem mass spectra capture fragmentation patterns that provide key structural information about a molecule. Although mass spectrometry is applied in many areas, the vast majority of small molecules lack experimental reference spectra. For…
Intelligent spectrum management is crucial for improving spectrum efficiency and achieving secure utilization of spectrum resources. However, existing intelligent spectrum management methods, typically based on small-scale models, suffer…
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…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
Mass spectrometry based clinical proteomics has emerged as a powerful tool for highthroughput protein profiling and biomarker discovery. Recent improvements in mass spectrometry technology have boosted the potential of proteomic studies in…
De novo peptide sequencing from mass spectrometry (MS) data is a critical task in proteomics research. Traditional de novo algorithms have encountered a bottleneck in accuracy due to the inherent complexity of proteomics data. While deep…