biostudies-literatureMcGann CDBundesministerium f?r Bildung und ForschungHorizon 2020 Framework ProgrammeNHGRI NIH HHSNIGMS NIH HHSAndy Hill CARE Fund2836-2846https://www.ebi.ac.uk/biostudies/studies/S-EPMC11554524biostudies-literatureUnknown22(9)Sample multiplexed quantitative proteomics assays have 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. Toward this end, we sought to develop and implement a new real-time spectral 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 fileJournal of proteome researchReal-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics.PMC11554524031L0168T32 HG000035R35 GM150919823839Zabrouskov VGabriel WBarshop WDBergen DLin CMcAlister GCHuang JSchweppe DKMcGann CDMelani RDCanterbury JDWilhelm MfalseReal-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics.Sample multiplexed quantitative proteomics assays have 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. Toward this end, we sought to develop and implement a new real-time spectral 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 file2023-01-01T00:00:00Z2023 Sep2025-04-18T20:47:34.01Z2025-04-07T08:53:19.155ZS-EPMC115545243755790010.1021/acs.jproteome.3c00085