The development of new ion-activation/dissociation methods continues to be one of the most
active areas of mass spectrometry owing to the broad applications of tandem mass …

Proteogenomics is an area of research at the interface of proteomics and genomics. In this
approach, customized protein sequence databases generated using genomic and …

Learning effective protein representations is critical in a variety of tasks in biology such as
predicting protein function or structure. Existing approaches usually pretrain protein …

De novo peptide sequencing from tandem MS data is the key technology in proteomics for
the characterization of proteins, especially for new sequences, such as mAbs. In this study …

Next-generation sequencing allows the analysis of genomes, including those representing
disease states. However, the causes of most disorders are multifactorial, and systems-level …

The diversity of peptides displayed by class I human leukocyte antigen (HLA) plays an
essential role in T cell immunity. The peptide repertoire is extended by various …

De novo sequencing software has been widely used in proteomics to sequence new
peptides from tandem mass spectrometry data. This study presents a new software tool …

All tumors accumulate genetic alterations, some of which can give rise to mutated, non-self
peptides presented by human leukocyte antigen (HLA) molecules and elicit T-cell …

Computational proteomics is the data science concerned with the identification and
quantification of proteins from high-throughput data and the biological interpretation of their …

Mass spectrometry has become the method of choice for the qualitative and quantitative
characterization of protein mixtures isolated from all kinds of living organisms. The raw data …