Pioneering work by, among others, the groups of Hunt and Mann at the start of this century
opened up the era of mass spectrometry (MS)-based phosphoproteomics. 1− 3 Through …

In shotgun proteomics, peptide and protein identification is most commonly conducted using
database search engines, the method of choice when reference protein sequences are …

Spectral matching sequence database search engines commonly used on mass
spectrometry-based proteomics experiments excel at identifying peptide sequence ions, and …

In the past decade, tandem mass spectrometry (MS/MS)-based bottom-up proteomics has
become the method of choice for analyzing post-translational modifications (PTMs) in …

Motivation De novo peptide sequencing based on tandem mass spectrometry data is the key
technology of shotgun proteomics for identifying peptides without any database and …

Protein phosphorylation is a post-translational modification crucial for many cellular
processes and protein functions. Accurate identification and quantification of protein …

Chemoproteomics has emerged as a key technology to expand the functional space in
complex proteomes for probing fundamental biology and for discovering new small …

Accurate full-length sequencing of a purified unknown protein is still challenging nowadays
due to the error-prone mass-spectrometry (MS)-based methods. De novo identified peptide …

Introduction Data-independent acquisition (DIA) is an emerging technology for large-scale
proteomic studies. DIA data analysis methods are evolving rapidly, and deep learning has …

Due to their oftentimes ambiguous nature, phosphopeptide positional isomers can present
challenges in bottom‐up mass spectrometry‐based workflows as search engine scores …