biostudies-literatureUnknownDes Soye BJNorthwestern Memorial FoundationWalder FoundationNorthwestern University Clinical and Translational Sciences InstituteNIH Office of the DirectorNational Cancer InstituteNCI NIH HHSNational Institute of General Medical SciencesNIH HHSNIGMS NIH HHSCharge detection mass spectrometry (CDMS) is a well-established technique that provides direct mass spectral outputs regardless of analyte heterogeneity or molecular weight. Over the past few years, it has been demonstrated that CDMS can be multiplexed on Orbitrap analyzers utilizing an integrated approach termed individual ion mass spectrometry (I²MS). To further increase adaptability, robustness, and throughput of this technique, here, we present a method that utilizes numerous integrated equipment components including a Kingfisher system, SampleStream platform, and Q Exactive mass spectrometer to provide a fully automated workflow for immunoprecipitation, sample preparation, injection, and subsequent I²MS acquisition. This automated workflow has been applied to a cAnalytical chemistryhttps://www.ebi.ac.uk/biostudies/studies/S-EPMC11825902biostudies-literatureAutomated Immunoprecipitation, Sample Preparation, and Individual Ion Mass Spectrometry Platform for Proteoforms.PMC11825902S10 OD025194P30 CA060553NCI CCSG P30 CA060553P41 GM108569SCI16Des Soye BJFellers RTForte EHollas MARMelani RDKafader JOMcGee JPKelleher NLWilkins JTCompton PDfalseAutomated Immunoprecipitation, Sample Preparation, and Individual Ion Mass Spectrometry Platform for Proteoforms.Charge detection mass spectrometry (CDMS) is a well-established technique that provides direct mass spectral outputs regardless of analyte heterogeneity or molecular weight. Over the past few years, it has been demonstrated that CDMS can be multiplexed on Orbitrap analyzers utilizing an integrated approach termed individual ion mass spectrometry (I²MS). To further increase adaptability, robustness, and throughput of this technique, here, we present a method that utilizes numerous integrated equipment components including a Kingfisher system, SampleStream platform, and Q Exactive mass spectrometer to provide a fully automated workflow for immunoprecipitation, sample preparation, injection, and subsequent I²MS acquisition. This automated workflow has been applied to a c2024-01-01T00:00:00Z2024 Aug2026-07-15T18:06:49.912Z2026-07-08T03:08:43.272ZS-EPMC118259023914375710.1021/acs.analchem.4c01962