Background Current practice in mass spectrometry (MS)-based proteomics is to identify
peptides by comparison of experimental mass spectra with theoretical mass spectra derived …

Proteoforms are the workhorses of the cell, and subtle differences between their amino acid
sequences or post-translational modifications (PTMs) can change their biological function …

Proteomic diversity in biological samples can be characterized by mass spectrometry (MS)-
based proteomics using customized protein databases generated from sets of transcripts …

Mass-spectrometry-based proteomics has become the standard approach for identifying and
quantifying proteins. A vital step consists of analyzing experimentally generated mass …

Massively parallel or second-generation sequencing-based genomic studies continuously
identify new genomic alterations that may lead to novel protein sequences, which are …

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

Database search is the most widely used approach for peptide and protein identification in
mass spectrometry-based proteomics studies. Our previous study showed that sample …

Mass-spectrometry-based proteomic analysis underestimates proteomic variation due to the
absence of variant peptides and posttranslational modifications (PTMs) from standard …

Multiomics approaches focused on mass spectrometry (MS)-based data, such as
metaproteomics, utilize genomic and/or transcriptomic sequencing data to generate a …

Proteogenomic approaches have gained increasing popularity, however it is still difficult to
integrate mass spectrometry identifications with genomic data due to differing data formats …