AUTHOR=Whiteaker Jeffrey R. , Lundeen Rachel A. , Zhao Lei , Schoenherr Regine M. , Burian Aura , Huang Dongqing , Voytovich Ulianna , Wang Tao , Kennedy Jacob J. , Ivey Richard G. , Lin Chenwei , Murillo Oscar D. , Lorentzen Travis D. , Thiagarajan Mathangi , Colantonio Simona , Caceres Tessa W. , Roberts Rhonda R. , Knotts Joseph G. , Reading Joshua J. , Kaczmarczyk Jan A. , Richardson Christopher W. , Garcia-Buntley Sandra S. , Bocik William , Hewitt Stephen M. , Murray Karen E. , Do Nhan , Brophy Mary , Wilz Stephen W. , Yu Hongbo , Ajjarapu Samuel , Boja Emily , Hiltke Tara , Rodriguez Henry , Paulovich Amanda G. TITLE=Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens JOURNAL=Frontiers in Immunology VOLUME=12 YEAR=2021 URL=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.765898 DOI=10.3389/fimmu.2021.765898 ISSN=1664-3224 ABSTRACT=

Immunotherapies are revolutionizing cancer care, producing durable responses and potentially cures in a subset of patients. However, response rates are low for most tumors, grade 3/4 toxicities are not uncommon, and our current understanding of tumor immunobiology is incomplete. While hundreds of immunomodulatory proteins in the tumor microenvironment shape the anti-tumor response, few of them can be reliably quantified. To address this need, we developed a multiplex panel of targeted proteomic assays targeting 52 peptides representing 46 proteins using peptide immunoaffinity enrichment coupled to multiple reaction monitoring-mass spectrometry. We validated the assays in tissue and plasma matrices, where performance figures of merit showed over 3 orders of dynamic range and median inter-day CVs of 5.2% (tissue) and 21% (plasma). A feasibility study in clinical biospecimens showed detection of 48/52 peptides in frozen tissue and 38/52 peptides in plasma. The assays are publicly available as a resource for the research community.