Related papers: Pep2Prob Benchmark: Predicting Fragment Ion Probab…
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…
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In…
Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same…
Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
There are numerous peptides discovered through past decades, which exhibit antimicrobial and anti-cancerous tendencies. Due to these reasons, peptides are supposed to be sound therapeutic candidates. Some peptides can pose low metabolic…
Nanobodies are small antibody fragments derived from camelids that selectively bind to antigens. These proteins have marked physicochemical properties that support advanced therapeutics, including treatments for SARS-CoV-2. To realize their…
Mass spectrometry provides a high-throughput approach to identify proteins in biological samples. A key step in the analysis of mass spectrometry data is to identify the peptide sequence that, most probably, gave rise to each observed…
Mass spectrometry (MS) is used widely in biomolecular structural analysis and is particularly dominant in the study of proteins. Despite its considerable power, state-of-the-art protein MS frequently suffers from limited reliability of…
Functional peptides have the potential to treat a variety of diseases. Their good therapeutic efficacy and low toxicity make them ideal therapeutic agents. Artificial intelligence-based computational strategies can help quickly identify new…
Mixture - modeling of mass spectra is an approach with many potential applications including peak detection and quantification, smoothing, de-noising, feature extraction and spectral signal compression. However, existing algorithms do not…
Tandem mass spectrometry (MS/MS) stands as the predominant high-throughput technique for comprehensively analyzing protein content within biological samples. This methodology is a cornerstone driving the advancement of proteomics. In recent…
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…
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…
Statistical models for proteomics data often estimate protein fold changes between two samples, A and B, as the average peptide intensity from sample A divided by the average peptide intensity from sample B. Such average intensity ratios…
In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has…
Motivation: Assigning statistical significance accurately has become increasingly important as meta data of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of…
De novo peptide sequencing algorithms have been widely used in proteomics to analyse tandem mass spectra (MS/MS) and assign them to peptides, but quality-control methods to evaluate the confidence of de novo peptide sequencing are lagging…
In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from…
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…