Optimized proteomic analysis of preserved biological tissue samples
Formalin-fixed paraffin-embedded tissue, or FFPE, is a valuable resource for proteomic studies needed to drive clinically relevant insights. However, obtaining patient-derived samples in sufficient numbers to represent different disease subtypes while also accounting for variables such as age and sex, poses a significant challenge.
To meet this challenge, Moe Haines, John Thorup, Michael Gillette, Shankha Satpathy and others in the Carr lab at the Broad Institute of MIT and Harvard presented an optimized workflow for enhanced proteomic analysis of FFPE samples. They published their findings in Molecular & Cellular Proteomics. In this workflow, they use a combination of pathology, guided dissection, Adaptive Focused Acoustics sonication, digestion and liquid chromatography-tandem mass spectrometry to identify up to 10,000 unique proteins and 11,000 fully localized phosphorylation sites in FFPE tissue. This work demonstrates the ability to derive biologically relevant results from clinically derived tumor samples and offers a significantly reduced overall processing time, thus widening the scope of analysis. This provides a useful avenue for more thorough proteomic analysis of preserved biological samples.
Enjoy reading ASBMB Today?
Become a member to receive the print edition four times a year and the digital edition monthly.
Learn moreGet the latest from ASBMB Today
Enter your email address, and we’ll send you a weekly email with recent articles, interviews and more.
Latest in Science
Science highlights or most popular articles
Heat shock proteins as a promising breast cancer therapeutic
Researchers unveiled isoform-specific targets on heat shock protein 90 which may be beneficial in therapeutic development.
Blood proteomics reveals fungal infection signatures for faster diagnosis
Whole-blood proteomics identifies more than 3,000 host and 160 fungal proteins during cryptococcal infection, offering potential biomarkers for faster diagnosis and improved monitoring without invasive spinal taps.
When things get SAPpy: Novel insights into complement
Researchers have defined interactions between an innate immune protein and two of its known binding partners. They identified potential areas of crosstalk between the two binding interactions.
Glutathione pathway implicated in rare disease
Researchers found that glutathione metabolism plays a central role in the pathogenesis of rare disease methylmalonic aciduria using a novel multiomics approach.
A p-value for proteins
Kyoto University researchers developed UniScore, a new tool that uses a target-decoy method to filter false positives in proteomic searches, helping scientists set thresholds and improve reliability when analyzing complex protein data.
Novel way to uncover tumor microenvironment proteomics
Researchers at the Weizmann Institute of Science developed a novel single-cell approach that facilitates the study of proteins surrounding lung cancer cells.