Quality Control, Preparation, and Protein Stability Issues for Blood Serum and Plasma Used In Biomarker Discovery and Proteomic Profiling Assays

The “omics” Haystack: Defining Sources of Sample Bias in Expression Profiling

“…The test samples were processed by use of various affinity-activated surfaces immediately before mass spectral analysis. As has been suggested elsewhere (9 ), plasma types and serum separator tube choice appeared to have a profound impact on the spectra observed. This variability was further confounded by the selected affinity surface, confirming a phenomenon that has been observed before but never demonstrated under controlled conditions (10 ).…”

Influence of clotting time on the protein composition of serum samples based on LC–MS data☆

“…Some authors have noted that clotting time affects the resulting serum proteome, and that these effects are most pronounced in the low-molecular-weight portion, the socalled peptidome [1,3].…”

“…It has notably been argued that the time and conditions under which blood is allowed to clot (clotting time) are important parameters that must be controlled and kept constant in order to compare protein and peptide profiles [1][2][3][4][5]. However, most existing sample collections have not been obtained with subsequent proteomics analyses in mind and clotting time and conditions have often not been rigorously controlled.…”

Laboratory methods to improve SELDI peak detection and quantitation

“…EAM was applied in two smaller volumes with a constant drying time before the EAM application to increase the number of peaks [6]. Reagent variability was minimized by using reagents from the same manufacturing lot [11] and the possible effects of freezing and thawing and length of time in storage [12] was considered for the serum and fractionated products.…”