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

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.

Thrombin induces broad spectrum proteolysis in human serum samples

“…on analytical outcome, particularly for protein and proteomic studies (3,(8)(9)(10)(11). A recent perspective on the subject has been put forward with specific focus on proteome analyses of blood (12). Variations in cytokine levels within serum vs. plasma have also been demonstrated (13).…”

Enhancing translational research in paediatric rheumatology through standardization

“…13 Variables that may impact analytic outcomes include: 1) the type of blood collection tube and additive, 2) sample processing protocols, times and temperatures, 3) hemolysis, 4) transport conditions, 5) storage parameters (temperatures and freeze-thaw cycles). [14][15][16] These types of differences between samples have a significant impact on the stability of analytes causing deterioration in data quality. The challenge to harmonization of SOPs is to move forward with SOPs developed from the current state of the science and based on empirical evidence and not on ritual.…”

“…19 The HUPO Plasma Proteome project noted that plasma is the noncellular fraction of choice for interrogation of the proteome, with meticulous documentation of preanalytical steps to aid in decision-making for suitable downstream applications. 16 The recommendations from all these international organizations, however, focus exclusively on biospecimen collection from adult subjects. There are relatively few published biospecimen collection guidelines dealing with variables unique to children.…”

Variations pré-analytiques des biomarqueursprotéiques

“…Il inhibe l'activité de la phosphatase alcaline, pourtant c'est lui qui provoque le moins d'interférences. Il peut cependant causer des problèmes en spectrométrie de masse : c'est une molé-cule fortement chargée qui peut empêcher la liaison des molécules à la surface des chips fonctionnalisées utilisées lors de profiling de type SELDI-TOF [8]. De plus, pour certains coffrets de dosage de TNFα et d'IL-6 par technique ELISA, il n'est pas recommandé d'utiliser l'héparine.…”