Benoit Fatou, PhD and Hanno Steen, PhD
Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA.
High throughput proteomics-based sample processing workflows have been developed, allowing for analysis of hundreds of individual neat plasma or serum samples randomized in multi-well micro plates. However, the LC/MS-based analytical pipeline requires an excellent robustness and reproducibility of the short gradients to be compatible with such large cohort studies, and to limit potential technical biases and batch effects. Given these constraints, we have been developing robust sample-sparing high throughput sample processing methods in combination with state-of-the-art instrumentation to enable large scale plasma/serum proteomic studies using submicroliter volumes of sample. We have developed a targeted and multiplexed LC/MS method, on a Shimadzu LCMS8060 triple quadrupole mass spectrometer to monitor the human classical plasma proteome in a high throughput manner (<15 min per sample). We are focusing on those classical plasma proteins needed for a comprehensive description of the immunophenotype of humans under a wide range of immune challenges such as bacterial and viral infection, inflammation on adult and newborn cohort and/or vaccination. These studies have resulted in the successful processing and analysis of ~9,000 plasma samples (and counting).