Artifactual isoform profile modification following treatment of human plasma or serum with protease inhibitor, monitored by 2-dimensional electrophoresis and mass spectrometry.

The inclusion of protease inhibitors in serum or plasma samples has been found to significantly impact the isoform profile of selected plasma proteins as seen on 2-dimensional electrophoresis (2-DE) gels. With the addition of a protease inhibitor cocktail, several human plasma protein trains [depleted of albumin and immunoglobulin G (IgG)] exhibited higher isoelectric point (pI) isoforms. This shift was especially apparent for apolipoprotein A1 (apo A1), a relatively high abundance protein. The six protease inhibitor components of the cocktail were individually investigated with albumin and IgG depleted human plasma, and it was shown that the observed effects were caused by 4-(2-aminoethyl) benzenesulfonyl fluoride (AEBSF), a serine protease inhibitor that covalently modifies proteins and/or peptides. Several serine-and/or tyrosine-containing peptides of apo A1 were modified with a concomitant mass increase of 183 Da, which is consistent with the mass increase expected following reaction with AEBSF. These modifications were observed with increasing propensity in the higher pI spots. An increase in both the number and proportion of modified peptides with increasing pI was also observed. A model is proposed for the random or stochastic coupling of AEBSF-derived moieties to serine and/or tyrosine residues throughout apo A1 and potentially other plasma proteins.

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

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.