Real-time spectral library matching for sample multiplexed quantitative proteomics

ABSTRACT: Sample multiplexed quantitative proteomics has proved to be a highly versatile means to assay molecular phenotypes. Yet, stochastic precursor selection and precursor coisolation can dramatically reduce the efficiency of data acquisition and quantitative accuracy. To address this, intelligent data acquisition (IDA) strategies have recently been developed to improve instrument efficiency and quantitative accuracy for both discovery and targeted methods. To this end we sought to develop and implement a new real-time library searching (RTLS) workflow that could enable intelligent scan triggering and peak selection within milliseconds of scan acquisition. To ensure ease of use and general applicability, we built an application to read in diverse spectral libraries and file types from both empirical and predicted spectral libraries. We demonstrate that RTLS methods enable improved quantitation of multiplexed samples, particularly with consideration for quantitation from chimeric fragment spectra. We used RTLS to profile proteome responses to small molecule perturbations and were able to quantify up to 15% more significantly regulated proteins in half the gradient time as traditional methods.

INSTRUMENT(S): Orbitrap Eclipse, Orbitrap Ascend

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932)

SUBMITTER: Devin Schweppe  

PROVIDER: MSV000091200 | MassIVE | Fri Feb 03 17:15:00 GMT 2023

SECONDARY ACCESSION(S): PXD039855

REPOSITORIES: MassIVE