Comparison of Different Buffers for Protein Extraction from Formalin-Fixed and Paraffin-Embedded Tissue Specimens

<div><p>We determined the best extraction buffer for proteomic investigation using formalin-fixation and paraffin-embedded (FFPE) specimens. A Zwittergent 3–16 based buffer, sodium dodecyl sulfate (SDS)-containing buffer with/without polyethylene glycol 20000 (PEG20000), urea-containing buffer, and FFPE-FASP protein preparation kit were compared for protein extraction from different types of rat FFPE tissues, including the heart, brain, liver, lung, and kidney. All of the samples were divided into two groups of laser microdissected (LMD) and non-LMD specimens. For both kinds of specimens, Zwittergent was the most efficient buffer for identifying peptides and proteins, was broadly applicable to different tissues without impairing the enzymatic digestion, and was well compatible with mass spectrometry analysis. As a high molecular weight carrier substance, PEG20000 improved the identification of peptides and proteins; however, such an advantage is limited to tissues containing submicrograms to micrograms of protein. Considering its low lytic strength, urea-containing buffer would not be the first alternative for protein recovery. In conclusion, Zwittergent 3–16 is an effective buffer for extracting proteins from FFPE specimens for downstream proteomics analysis.</p></div

Characteristics of cohort studies enrolled in the meta-analysis.

<p>Abbreviations: M, male; F, female; MM, multiple myeloma; SIR, standardized incidence ratio; CI, confidence intervals; PY, person years.</p><p>–: Not mentioned.</p

Characteristics of case-control studies enrolled in the meta-analysis.

<p>Abbreviations: RA, rheumatoid arthritis; OR, odds ratio; CI, confidence intervals; M, male; F, female.</p

Funnel plot for case-control and cohort studies (dots: original data; squares: filled data).

<p>Funnel plot for case-control and cohort studies (dots: original data; squares: filled data).</p

Comparison of proteins identified using five different extraction buffers after LMD/MS analysis.

<p>*: Extraction buffers 2–5 compared to extraction buffer 1.</p><p>Comparison of proteins identified using five different extraction buffers after LMD/MS analysis.</p

Forest plot of studies on multiple myeloma development risk in pernicious anemia and AS.

<p>Forest plot of studies on multiple myeloma development risk in pernicious anemia and AS.</p

Forest plot of studies on multiple myeloma development risk in rheumatoid arthritis.

<p>Forest plot of studies on multiple myeloma development risk in rheumatoid arthritis.</p

Meta-analysis of multiple myeloma incidence by subgroup.

<p>Abbreviations: N, number; M, male; F, female; RR, relative risk; NOS, Newcastle-Ottawa Scale.</p>a<p>One case-control study conducted in New Zealand was excluded from analysis.</p>b<p>One study with unknown mean follow-up duration was excluded from analysis.</p><p>–: Cannot be calculated.</p

Workflow of the current study.

<p>Workflow of the current study.</p

Flow diagram depicting the identification and selection of eligible case-control and cohort studies.

<p>Flow diagram depicting the identification and selection of eligible case-control and cohort studies.</p