| Autor: |
Kline JT; Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States., Belford MW; Thermo Scientific, San Jose, California 95134, United States., Boeser CL; Thermo Scientific, San Jose, California 95134, United States., Huguet R; Thermo Scientific, San Jose, California 95134, United States., Fellers RT; Proteinaceous, Inc., Evanston, Illinois 60204, United States., Greer JB; Proteinaceous, Inc., Evanston, Illinois 60204, United States., Greer SM; Thermo Scientific, San Jose, California 95134, United States., Horn DM; Thermo Scientific, San Jose, California 95134, United States., Durbin KR; Proteinaceous, Inc., Evanston, Illinois 60204, United States., Dunyach JJ; Thermo Scientific, San Jose, California 95134, United States., Ahsan N; Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States.; Mass Spectrometry, Proteomics and Metabolomics Core Facility, University of Oklahoma, Norman, Oklahoma 73019, United States., Fornelli L; Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States.; Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States. |
| Abstrakt: |
Blood serum and plasma are arguably the most commonly analyzed clinical samples, with dozens of proteins serving as validated biomarkers for various human diseases. Top-down proteomics may provide additional insights into disease etiopathogenesis since this approach focuses on protein forms, or proteoforms, originally circulating in blood, potentially providing access to information about relevant post-translational modifications, truncations, single amino acid substitutions, and many other sources of protein variation. However, the vast majority of proteomic studies on serum and plasma are carried out using peptide-centric, bottom-up approaches that cannot recapitulate the original proteoform content of samples. Clinical laboratories have been slow to adopt top-down analysis, also due to higher sample handling requirements. In this study, we describe a straightforward protocol for intact proteoform sample preparation based on the depletion of albumin and immunoglobulins, followed by simplified protein fractionation via polyacrylamide gel electrophoresis. After molecular weight-based fractionation, we supplemented the traditional liquid chromatography-tandem mass spectrometry (LC-MS 2 ) data acquisition with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to further simplify serum proteoform mixtures. This LC-FAIMS-MS 2 method led to the identification of over 1000 serum proteoforms < 30 kDa, outperforming traditional LC-MS 2 data acquisition and more than doubling the number of proteoforms identified in previous studies. |
