Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …

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

Gene expression in human tissue has primarily been studied on the transcriptional level,
largely neglecting translational regulation. Here, we analyze the translatomes of 80 human …

Protein digestion using a dedicated protease represents a key element in a typical mass
spectrometry (MS)-based shotgun proteomics experiment. Up to now, digestion has been …

This study investigates the challenge of comprehensively cataloging the complete human
proteome from a single-cell type using mass spectrometry (MS)-based shotgun proteomics …

Proteomes are characterized by large protein-abundance differences, cell-type-and time-
dependent expression patterns and post-translational modifications, all of which carry …

Peptide‐centered shotgun analysis of proteins has been the core technology in mass
spectrometry based proteomics and has enabled numerous biological discoveries, such as …

Proteins are the key biological actors within cells, driving many biological processes integral
to both healthy and diseased states. Understanding the depth of complexity represented …

Alternative splicing is a critical determinant of genome complexity and, by implication, is
assumed to engender proteomic diversity. This notion has not been experimentally tested in …

Background Mass spectrometry-based proteomics enables the global identification and
quantification of proteins and their posttranslational modifications in complex biological …