Increasing the Throughput and Reproducibility of Activity-Based Proteome Profiling Studies with Hyperplexing and Intelligent Data Acquisition

ABSTRACT: Intelligent data acquisition (IDA) strategies, such as real-time database search (RTS), have improved the depth of proteome coverage for experiments that utilize isobaric labels and gas phase purification techniques (i.e., SPS-MS3). While most applications of IDA have been focused on the analysis of protein abundance, these approaches have recently been applied to activity-based proteome profiling (ABPP) studies aimed at characterization of protein site engagement by small molecules. In this work, we extend IDA capabilities offered by vendor software through a new program called InSeqAPI. First, we demonstrate robust performance of InSeqAPI in the analysis of biotinylated cysteine peptides from ABPP experiments. Then, we describe PairQuant, a method within InSeqAPI designed for the hyperplexing approach that utilizes protein-level isotopic labeling and peptide-level TMT labeling.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: Hanna Budayeva  

PROVIDER: MSV000092113 | MassIVE | Tue Jun 06 14:41:00 BST 2023

REPOSITORIES: MassIVE