Complement Reporter Ion Quantification with a Quadrupole-Ion Trap Instrument

ABSTRACT: Proteomics workflows have traditionally been divided into discovery-based and targeted approaches, with instrumentation optimized for each. Discovery experiments typically utilize high-resolution analyzers such as the Orbitrap™, while targeted workflows rely on the sensitivity and specificity of triple quadrupole systems. Recently, a quadrupole-ion trap instrument (Stellar™ MS), demonstrated superior performance for targeted applications compared to traditional triple quadrupoles. In this study, we expand the capabilities of this platform to multiplexed shotgun proteomics using complement reporter ion quantification in an ion trap (iTMTproC). Benchmarking with standards shows that iTMTproC achieves quantification accuracy and interference reduction comparable to MultiNotch MS3 on the Orbitrap Fusion Lumos™, a dedicated quadrupole-ion trap-Orbitrap™ tribrid instrument for this method. We further validate the approach through a developmental time-series analysis of vertebrate embryos, revealing data quality equivalent to MultiNotch MS3 with greater sensitivity. These findings significantly extend the functionality of targeted instrumentation, underscoring the versatility of quadrupole-ion trap systems and providing cost-effective access to highly accurate quantitative multiplexed shotgun proteomics.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Xenopus Laevis (african Clawed Frog) Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Embryo, Cell Suspension Culture, Cell Culture

SUBMITTER: Edward Cruz  

LAB HEAD: Martin Wuhr

PROVIDER: PXD062540 | Pride | 2025-09-08

REPOSITORIES: Pride