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Article summary:
1. Formaldehyde-fixed and paraffin-embedded tissues have been created in the past decades and stored in pathological depositories.
2. Protein extraction from formaldehyde-fixed tissues is hampered by the Schiff base formation between the amino groups of proteins and formaldehyde.
3. Tris(hydroxymethyl)aminomethane concentration affects the protein extraction efficiency, and higher concentrations are recommended for efficient protein extraction from FFPE tissue samples.
Article analysis:
The article provides a detailed overview of the challenges associated with extracting proteins from formalin-fixed paraffin-embedded (FFPE) tissues, as well as an analysis of how varying concentrations of tris(hydroxymethyl)aminomethane can affect protein extraction efficiency. The authors provide evidence to support their claims, including references to previous studies that have demonstrated successful protein extraction from FFPE tissues using gel-based proteome analysis approaches such as 2-D PAGE, 2-D DIGE, and 1-D PAGE followed by LC–MS/MS (GeLC–MS/MS). The article also includes a discussion of how formaldehyde fixation can lead to crosslinking between proteins and other molecules in the tissue through Schiff base formation, which can hamper molecular investigation of these samples.
The article appears to be reliable and trustworthy overall; however, there are some potential biases that should be noted. For example, while the authors discuss how formaldehyde fixation can lead to crosslinking between proteins and other molecules in the tissue through Schiff base formation, they do not explore any potential counterarguments or alternative explanations for this phenomenon. Additionally, while they provide evidence to support their claims regarding tris(hydroxymethyl)aminomethane concentration affecting protein extraction efficiency, they do not provide any evidence for potential risks associated with using higher concentrations of this compound for protein extraction. Furthermore, while they discuss how FFPE tissues can serve as a source for invaluable materials for proteomics analysis for the molecular characterization of disease processes aimed at improving diagnosis, prognosis, and therapy, they do not explore any potential drawbacks or limitations associated with this approach.
In conclusion, while this article appears to be reliable overall due to its inclusion of evidence supporting its claims and discussion of relevant topics related to FFPE tissue sample preparation for proteomics analysis, it does contain some potential biases that should be noted when evaluating its trustworthiness and reliability.
Topics for further research:
Formaldehyde fixation risks
Alternative explanations for Schiff base formation
Potential drawbacks of FFPE tissue sample preparation
Limitations of proteomics analysis for molecular characterization
Effects of higher tris(hydroxymethyl)aminomethane concentrations
Gel-based proteome analysis approaches