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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 method

Analytical technique

Evaluated parameter

Pre-analytical factor

Threshold

Organ

References

Spectrophotometry

DC protein assay

Concentration determined based on standard curve

N/A

N/A

Colon, kidney

[57, 58]

BCA protein assay

Electrophoresis

Western blot

PCNA detection

Fixation

–

Colon

[57]

Comparative evaluation of reactivity of fresh and FFPE using antibodies against GAPDH, tropomyosin, vinculin and myosin

–

–

Sheep tissue from skeletal muscle, liver, human hyperplastic thyroid tissue

[59]

SDS-PAGE and silver staining

Size distribution

Sample age

High quality proteins are feasible to extract from 14 years samples

Liver

[60]

N-cadherin and phospo-ERK detection

2D-PAGE

Comparison of 2D-PAGE gel protein profiles

Time to freeze

30 min

Kidney

[61]

Immunoblotting

P-p27 detection

–

–

Cell culture

[62]

Mass spectrometry

LC–MS/MS analysis

Comparative analysis of peptide hits between fresh-frozen and FFPE samples

Fixation

–

Muscle

[59]

Protein overlap between fresh and FFPE tissue sections

Fixation

–

Kidney

[58]

Capillary isoelectric focusing coupled with RP LC–MS/MS

–

Storage time

From 7 years fewer distinct peptides and proteins were identified but the normalised expression values of actin, desmin and progesterone receptor were consistent until 12 years

Mesenchyme

[63]

Protein microarray

RPPAs

Evaluation of increase and decrease percentage of phosphoproteins

Time to fixation

20 min

Uterus, colon, lung, ovary, breast, lymph node

[64]