Summary
Overview
Work History
Education
Publications
Presentations/Workshop
Accomplishments
References
Timeline
Generic

Sofani Gebreyesus

Provo

Summary

A highly driven research scientist specializing in bioanalytical chemistry, with extensive experience in developing innovative analytical techniques for protein and peptide analysis. Skilled in microfluidics, nanoLC, and mass spectrometry, with a strong track record of collaborating within cross-functional research teams and contributing to scientific advancements.

Overview

7
7
years of professional experience

Work History

Postdoctoral Fellow

Brigham Young Unversity
Provo
02.2024 - Current
  • Title: Developing a targeted mass spectrometry method for phosphopeptide quantification from a single cell. Supervisor: Dr. Ryan T. Kelly, department of Chemistry and biochemistry, BYU, Provo, Utah ∗ I built customized nanoLC system on U3000 which is suitable for sensitive phosphopeptide analysis. ∗ Optimized all parts of the nanoLC system including the sample loop size (1ul-to-40nl), LC internal diameter (75um-to-20um), type and size of stationary material (5um-to-1.5um), flow-rate (250nl/min-to-10nl/min), FAIMS compensation voltage (-80 to -20), etc. ∗ Optimized mass spec instrument set-ups including Ion transfer tube temperature, spray voltage(current), normalized collision energy, injection time, AGC, scan rate, Isolation window, etc. ∗ Prepared a scheduled mass spectrometry method using Skyline software to perform Parallel Reaction Monitoring (PRM) runs on the Stellar mass spectrometer. ∗ Performed peak picking and refinement on the mass spec run files imported into Skyline, then collected the peak area and retention time for each precursor for further data analysis. ∗ Using a custom-built script, determined the limit of detection and quantification for heavily-labeled phosphopeptide standards spiked into single-cell lysate (serving as the background matrix) to be between 10 attomoles and 100 zeptomoles

Postdoctoral Fellow

Brigham Young Unversity
Provo
02.2024 - Current
  • Title: Towards improving proteomic separation efficiency by Trap-and-Elute nanochromatography. Supervisor: Dr. Ryan T. Kelly, department of Chemistry and biochemistry, BYU, Provo, Utah ∗ I packed Trap and LC columns using seven different stationary phases from major vendors, varying particle sizes, as well as different length and internal diameters of fused silica capillaries. ∗ Compared the retentivity of these materials by running Pierce HeLa protein digest standard. ∗ Identified the optimal combination for trap-and-elute separations and best experimental conditions to minimize peak dispersion through refocusing (analytes are retained at the column inlet). In trap-and-elute separations, the analytical column should be more retentive than the trap column. ∗ I ran single-cell samples using the optimized separation condition and compared the results with the standard setup, yielding a 100 percent increase in protein identification.

Graduate Student Researcher

Academia Sinica
Taipei
09.2018 - 01.2023
  • Title: Developing highly sensitive methods for single-cell (phospho-)proteomics Taipei, Taiwan Supervisor: Dr. Hsiung Lin Tu, Institute of Chemistry, Academia sinica. ∗ I designed multilayer microfluidic chips using Auto-CAD software accompanied by simulations using COMSOL Multiphysics software. ∗ Fabricated the master molds and their PDMS replica using photolithographic and softlithographic techniques in clean-rooms. ∗ Developed a packing method for C18 stationary phase materials in the integrated trap microcolumns of iProChip and SciProChip for global single-cell proteomics. The efficient desalting process demonstrated by more than 90 percent sample recovery. ∗ Developed a packing method and working protocol for metal oxide affinity chromatography using Titanium Oxide particles in the integrated microcolumns within the iPhosChip for nanoscale-to-single-cell phosphoproteomics studies. The efficient enrichment at nano-litre range showcased by up to 95 percent specificity, enabling phosphopeptide enrichment at single-cell level. ∗ Characterized and validated the performances of the integrated functional modules within the chips (such as; cell capturing, mixing, peptide desalting and/or phosphopeptide enrichment). ∗ Developed Graphic User Interface by MATLAB for various designs of chips to effectively control the devices. ∗ Developed and customized the proteomics workflows to address the reagent-chip incompatibility and workflow complexities. For instance; complete skipping of desalting steps in the phosphoroteomics workflow through carefully selecting compatible reagents that could not lead to precipitation, which simplified the workflow significantly to be executable with a chip. ∗ Conducted (phospho)proteomic workflows on the chips using both adherent and suspension cells, and analysis of LC-MS/MS raw data using Spectronaut™ (for data-independent acquisition) and MaxQuant (using data-dependent acquisition). ∗ The identification of 1,500 proteins from a single mammalian cell was the highest at the time of its publication (Nat. Commun., 2022), while, to the best of my knowledge, the identification of approximately 200 phosphopeptides from single non-small cell lung cancer (PC-9) cells still stands as the highest (Adv. Sci., 2025).

Education

Ph.D. - Chemistry

National Taiwan University
Taipei
01-2023

Master of Science - Chemistry

Arbaminch University
Arbaminch
06-2011

Publications

  • Gul Muneer*, Sofani Tafesse Gebreyesus*, Ciao-Syuan Chen, Tzu-Tsung Lee, Fengchao Yu, Chih-An Lin, Min-Shu Hsieh, Alexey I. Nesvizhskii, Chao-Chi Ho, Sung-Liang Yu, Hsiung-Lin Tu, Yu-Ju Chen, ”Mapping Nanoscale-To-Single-Cell Phosphoproteomic Landscape by Chip-DIA” Advanced Science 12.1 (2025): 2570004.. • Sofani Tafesse Gebreyesus, Gul Muneer, Chih-Cheng Huang, Asad Ali Siyal, Mihir Anand, Yu-Ju Chen and Hsiung-Lin Tu ”Recent advances in microfluidics for single-cell functional proteomics” Lab Chip, 2023,23, 1726-1751. • Narani Rakesh, Hsiung-Lin Tu, Po-Chun Chang, Sofani Tafesse Gebreyesus, Che-Jen Lin* ”A real-time flow sensor based on fluorescent complex emulsions with semi-perfluoroalkyl substituted -cyanostilbene” Advanced Science (2023): 2304108. • Sofani Tafesse Gebreyesus, Gul Muneer, Yu-Ju Chen, Hsiung-Lin Tu. ”High-throughput single-cell proteomics based on highly multiplexed microfluidic chip” (Manuscript preparation). • Sofani Tafesse Gebreyesus, Asad Ali Siyal, Reta Birhanu Kitata, Eric Sheng-Wen Chen, Bayarmaa Enkhbayar, Takashi Angata, Kuo-I. Lin, Yu-Ju Chen, and Hsiung-Lin Tu. ”Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry.” Nat. commun. 13, no. 1 (2022): 1-13. • Sofani Tafesse Gebreyesus, Ali Mohammed Yimer, Masood Akhtar Khan. ”The effect of protonation of a substrate, on a catalytic mechanism of Nicotinate-dehydrogenase” JCBPS, 5, no.1 (2015):120-127. • Sofani Tafesse Gebreyesus, Masood Akhtar Khan.”An overview on metal complexes of selected schiff-bases with their electrochemical and sensor aspects” J. Chem. and Chem. Sci, 5, no.1 (2015):20-26. • Sofani Tafesse Gebreyesus. ”Heavy metals in contaminated soil: sources washing through chemical extractants” ASRJETS, 10, no.1 (2014):54-60.

Presentations/Workshop

  • 2023 Joint 11th AOHUPO and 7th AOAPO congress, Sofani Tafesse Gebreyesus, Gul Muneer, Asad Ali, Ciao Syuan Chen, Yu-Ju Chen, Hsiung-Lin Tu. An integrated strategy for streamlined proteomics analysis, Invited Oral Abstract, (Singapore). • 2022 Chemistry National Meeting, Sofani Tafesse Gebreyesus, Asad Ali Siyal, Yuju Chen and Hsiung-Lin Tu. Streamlined single-cell proteomics by all-in-one microfluidic chip and data-independent acquisition mass spectrometry, poster, National Taiwan Normal University (Taiwan). • 2021 HUPO ReCONNECT, Sofani Tafesse Gebreyesus, Asad Ali Siyal, Dr.Reta Birhanu Kitata, Dr.Eric Sheng Wen Chen, Bayarmaa Enkhbayar, Dr.Takashi Angata, Dr.Kuo-I Lin, Dr.Yuju Chen and Dr.Hsiung-Lin Tu. Streamlined Single-Cell Proteomics by the All-in-One Chip and Data-Independent Acquisition Mass Spectrometry, poster. • 2021 Chemical Society Annual Meeting, Sofani Tafesse Gebreyesus, Asad Ali Siyal, Reta Birhanu Kitata, Eric Sheng Wen Chen, Yuju Chen and Hsiung-Lin Tu. Ultra-streamlined single cell proteomics by all-in-one chip and data independent-acqusition mass spectroscopy, poster, National Central University (Taiwan). • 2021 Virtual Podium Asia Pacific (VPAP), Sofani Tafesse Gebreyesus, Asad Ali Siyal, Reta Birhanu Kitata, Eric Sheng Wen Chen, Yuju Chen and Hsiung-Lin Tu. Streamlined Single-cell Proteomics by All-in-one Chip and Data-independent Acquisition Mass Spectrometry, Oral presentation.

Accomplishments

  • Awarded with Taiwan International Graduate Program (TIGP), Academia Sinica, Taiwan to pursue Graduate studies at Academia sinica (2017). • Awarded with financial support from regional state of southern Ethiopia (SSEBST 5564-RB-001) for grand innovative project on Biodegradable plastics (20014-15). • Awarded with state government scholarship for masters studies at school of graduate studies, Arbaminch university, Arbaminch - Ethiopia (2009-11).

References

References available upon request.

Timeline

Postdoctoral Fellow

Brigham Young Unversity
02.2024 - Current

Postdoctoral Fellow

Brigham Young Unversity
02.2024 - Current

Graduate Student Researcher

Academia Sinica
09.2018 - 01.2023

Ph.D. - Chemistry

National Taiwan University

Master of Science - Chemistry

Arbaminch University

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