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Table 3 Summary of publications of quality control tools used in proteomics for evaluating the impact of pre-analytical factors

From: In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network

Measurement methodAnalytical techniqueEvaluated parameterPre-analytical factorThresholdOrganReferences
SpectrophotometryDC protein assayConcentration determined based on standard curveN/AN/AColon, kidney[57, 58]
BCA protein assay
ElectrophoresisWestern blotPCNA detectionFixationColon[57]
Comparative evaluation of reactivity of fresh and FFPE using antibodies against GAPDH, tropomyosin, vinculin and myosinSheep tissue from skeletal muscle, liver, human hyperplastic thyroid tissue[59]
SDS-PAGE and silver stainingSize distributionSample ageHigh quality proteins are feasible to extract from 14 years samplesLiver[60]
N-cadherin and phospo-ERK detection
2D-PAGEComparison of 2D-PAGE gel protein profilesTime to freeze30 minKidney[61]
ImmunoblottingP-p27 detectionCell culture[62]
Mass spectrometryLC–MS/MS analysisComparative analysis of peptide hits between fresh-frozen and FFPE samplesFixationMuscle[59]
Protein overlap between fresh and FFPE tissue sectionsFixationKidney[58]
Capillary isoelectric focusing coupled with RP LC–MS/MSStorage timeFrom 7 years fewer distinct peptides and proteins were identified but the normalised expression values of actin, desmin and progesterone receptor were consistent until 12 yearsMesenchyme[63]
Protein microarrayRPPAsEvaluation of increase and decrease percentage of phosphoproteinsTime to fixation20 minUterus, colon, lung, ovary, breast, lymph node[64]