Automated Multienzyme Digestion Workflows for Confident Characterization of Challenging Posttranslational Modifications in Therapeutic Antibodies by LC–MS/MS

Identification of Protein Cysteine Modifications Using Unbiased Mass Spectrometry-Based Proteomics.

A protocol for untargeted metabolomics using anion-exchange chromatography and high-resolution mass spectrometry

Summary Polar metabolites are challenging to analyze using common reverse-phase chromatography. However, these molecules are most essential for deciphering biological phenotypes. Here, we present a protocol for polar metabolite analysis based on anion-exchange chromatography coupled with high-resolution mass spectromet...

Protocol for identifying glycosylated RNAs using solid-phase chemical conjugation and glycosidase release

Summary RNA glycosylation plays a critical role in cellular signaling. Here, we present a protocol for enriching glycoRNAs from cultured cells and clinical tissues using a solid-phase chemoenzymatic technique. We describe steps for employing galactose oxidase (GAO) to selectively oxidize terminal sugar residues, enabli...

AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics

Mass spectrometry (MS)-based proteomics now routinely profiles proteomes at scale, but extracting biological insight and integrating complementary modalities remains challenging. Here, we present AlphaPeptTools, a Python package for the analysis of MS-proteomics data built on the AnnData data structure of the scverse....

Protein digest extraction strategies improve the identification of lipidated peptides in bottom-up proteomics.

Alteration of proteins by attaching lipid moieties is a type of post-translational modification that affects the properties of proteins. It plays a role in various physiological processes, mostly due to direct interaction with cell membranes. Proteomic identification of lipoproteins typically depends on detecting their...

Quantification of Site-Specific Disulfide Bond Redox States in Proteins by Parallel Reaction Monitoring-Mass Spectrometry (PRM-MS).