Mass Spectrometry-based Plasma Proteomics: Considerations from Sample Collection to Achieving Translatable Data

The proteomicanalysis of human blood and blood-derived products, particularly plasma, offers an attractive avenue to translate researchfrom the laboratory into the clinic. However, due to its particular protein composition, performing proteomicsassays with plasmais challenging. Plasma proteomicshas though regained interest due to recent technological advances, but challenges imposed by both the complications inherent to studying human biology(e.g. sample variability) and the limitations in available technologies and methods remain. As part of the Human Plasma ProteomeProject (HPPP), we bring together key aspects of the plasma proteomicspipeline. We provide considerations and recommendations concerning the study design, plasmacollection and quality metrics, plasma processingworkflows, data acquisition by mass spectrometry (MS), data processing and bioinformatic analysis. With exciting opportunities in studying human health and disease via the plasma proteomicspipeline, a more informed analysis of plasmawill accelerate interest and possibilities for the incorporation of proteomics-scaled assays into clinical practice.