image: In the workflow of AmproCode, each type of the selected residues on peptide or protein samples can be respectively modified by the DNA barcode, and the composition code which is the relative ratio of these residues from each protein can be amplified and quantified by qPCR. Matching the experimentally obtained composition code with the codes in the proteome database library by the database search algorithm allows protein identification of the sample.
Credit: ©Science China Press
In this study led by Prof. Peng R. Chen and Prof. Chu Wang (College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University), the authors developed an amplifiable protein identification method called “AmproCode”.
Ultrasensitive protein identification is very significant but extremely challenging, because unlike the nucleic acids that could rely on the polymerase chain reaction (PCR) for amplification, proteins cannot be directly amplified. However, the authors believe that application of a collection of residue-specific reactions that can selectively label different types of amino acids with the amplifiable DNA barcodes, in conjunction with the innovative proteome database matching method, may ultimately produce a breakthrough technique for turning proteins into amplifiable molecules (see the image below). They validated their idea both computationally and experimentally in this study.
They first designed computational assays for proteome database matching and for theoretical estimation of the identification rate of AmproCode. The computational results showed that 99% proteins in the whole proteome and 93% proteins in the secretome could be identified after quantifying only four residue types, providing the theoretical basis for their method.
They also rationally selected several residue types including Cys, Lys, Met, Asp/Glu and Tyr for AmproCode. They tested their residue-specific chemical reactions on both small molecules and peptides, and designed the DNA barcoding strategy.
Then, the researchers demonstrated AmproCode by the identification of different synthetic peptides including ELA, URP and Aβ found in the secretome. Their technique allows protein identification at an extremely low concentration (fmol/L), which is 10 to 10000 times more sensitive than the common mass spectrometry and ELISA-based approaches. It shows that AmproCode has the capability for amplifiable protein identification from trace samples.
Moreover, they evaluated the performance of AmproCode in different conditions by computational estimations. They found that quantitation of more residue could bring significant improvement to AmproCode in the coverage, accuracy and adaptability.
Although this is only a proof-of-concept study, their novel concept of amplifiable protein fingerprinting provides a new framework towards development of the next generation protein sequencing, which may finally realize single-cell proteomics and may promote the discovery of clinical biomarkers.
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See the article:
Amplifiable protein identification via residue-resolved barcoding and composition code counting
https://doi.org/10.1093/nsr/nwae183
Journal
National Science Review