HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples

TLDR

Blood‑derived sample analysis is affected by many pre‑analytical variables, and the diversity of sample types and analytical methods in the HUPO PPP makes it impossible to prescribe a single standard set of pre‑analytical conditions. The paper compiles observations from experiments and clinical theory to guide plasma proteome sample handling. The authors studied sample type selection, storage stability, protease inhibitor use, and clinical standardization to evaluate pre‑analytical impacts. The study recommends platelet‑depleted plasma over serum for peptidomics, aliquoting and liquid‑nitrogen storage, early judicious use of protease inhibitors, diligent tracking of pre‑analytical variables, and reference materials for QC/QA, emphasizing awareness of all variables as a prerequisite for proteomic studies.

Abstract

There is a substantial list of pre-analytical variables that can alter the analysis of blood-derived samples. We have undertaken studies on some of these issues including choice of sample type, stability during storage, use of protease inhibitors, and clinical standardization. As there is a wide range of sample variables and a broad spectrum of analytical techniques in the HUPO PPP effort, it is not possible to define a single list of pre-analytical standards for samples or their processing. We present here a compendium of observations, drawing on actual results and sound clinical theories and practices. Based on our data, we find that (1) platelet-depleted plasma is preferable to serum for certain peptidomic studies; (2) samples should be aliquoted and stored preferably in liquid nitrogen; (3) the addition of protease inhibitors is recommended, but should be incorporated early and used judiciously, as some form non specific protein adducts and others interfere with peptide studies. Further, (4) the diligent tracking of pre-analytical variables and (5) the use of reference materials for quality control and quality assurance, are recommended. These findings help provide guidance on sample handling issues, with the overall suggestion being to be conscious of all possible pre-analytical variables as a prerequisite of any proteomic study.