Genomics-based neoantigen discovery can be enhanced by proteomic evidence, but there
remains a lack of consensus on the performance of different quality control methods for …

The analysis of shotgun proteomics data often involves generating lists of inferred peptide-
spectrum matches (PSMs) and/or of peptides. The canonical approach for generating these …

Sequencing of circulating tumor DNA (ctDNA) is a minimally invasive approach to reveal the
genomic alterations of cancer; however, its comparison with sequencing of tumor tissue has …

Background: The number of thyroidectomies in South Korea has been increasing rapidly
due to extensive checkups for thyroid cancer. However, few studies have examined the …

Accurate identification of novel peptides remains challenging because of the lack of
evaluation criteria in large-scale proteogenomic studies. Mirror proteases of trypsin and …

Background In shotgun proteomics, database searching of tandem mass spectra results in a
great number of peptide-spectrum matches (PSMs), many of which are false positives …

Abstract Characterization of endogenous neuropeptides produced from post-translational
proteolytic processing of precursor proteins is a demanding task. A variety of complex …

Proteogenomics refers to the integration of high-throughput genomics/transcriptomics with
proteomics data for genome annotation, novel gene discovery, and variant peptide detection …

Background One of the most important steps in peptide identification is to estimate the false
discovery rate (FDR). The most commonly used method for estimating FDR is the target …

Background Shotgun proteomics utilizes a database search strategy to compare detected
mass spectra to a library of theoretical spectra derived from reference genome information …