Highly Sensitive Proteomic Methods to Probe Protein Interactions

Bottom-up proteomics has increasingly assumed a critical role in drug discovery due to its ability to provide a comprehensive analysis of the proteome. Throughout various stages in drug discovery, bottom-up proteomics has shown immense utility in drug target identification, biomarker discovery, drug effect profiling, and precise medicine. However, advancements in proteomics could further enable more comprehensive analyses, thereby aiding the development of new or more effective drugs. This thesis delineates our efforts towards the development of proteomic methods to probe protein interactions. Chapter one provides a general review of three aspects. The first part focuses on methods used for small molecule target identification in the proteomics field. The second part examines HR+/HER2- breast cancer therapies and discusses the emerging diagnostic and prognostic roles of exosomes in cancer disease. The third part discusses challenges in nanoproteomics or single-cell proteomics, encompassing issues such as sample loss in the containers and the utilization time of mass spectrometry instruments. Chapter two describes our efforts to develop high-throughput methods for LC-MS/MS analysis. The first half of this chapter evaluates the non-negligible sample loss from microtubes in nanoproteomics. The second half describes our development of a dual column system to maximize the instrument utilization of LC-MS/MS for high-throughput analysis. Chapter three presents a prediction model based on the exosome proteome of HR+/HER2- patients to predict their responses to combination therapy. We evaluated several exosome isolation methods and employed six machine learning methods to xiii ABSTRACT (continued) construct the prediction model. This approach could predict the treatment outcomes for patients, which contributes to the advancement of precision medicine. Chapter four describes two strategies we employed to identify small molecule binding targets. It is well established that upon binding to a small molecule, a protein undergoes an energy change and experiences an induced conformational change. By employing the energy-based method DiffPOP and the conformation-based method SETI, we can assess binding events from two different perspectives, thereby gaining a comprehensive understanding of small molecule binding targets. DiffPOP detects changes in protein chemical resistance upon binding to identify targets. The SETI method, when supplementing small molecules in the mobile phase, could combine the conformational change and affinity method advantages to enhance the identification of binding targets

Additional file 1 of Clinical diagnostic value of American College of Radiology thyroid imaging report and data system in different kinds of thyroid nodules

Additional file 1

Additional file 2 of Clinical diagnostic value of American College of Radiology thyroid imaging report and data system in different kinds of thyroid nodules

Additional file 2

Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation

Nonspecific binding between the protein and the container is an often-neglected cause of sample loss in large-scale proteomics sample preparation. In nanoproteomics, due to the small sample size, this absorption loss is no longer negligible, and researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences in microtube performance on reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well understood. Here, we investigated the protein/peptide loss during the nanoproteomics experiment process. Our results showed that there are significant differences in nonspecific binding among the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. Interestingly, we found that the storage temperature could also be one of the key factors that contribute to protein recovery from the plastic container. In addition, we investigated the binding preferences of different microtubes by the physical characteristics of the identified proteins and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings help to better understand protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample

Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation

Nonspecific binding between the protein and the container is an often-neglected cause of sample loss in large-scale proteomics sample preparation. In nanoproteomics, due to the small sample size, this absorption loss is no longer negligible, and researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences in microtube performance on reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well understood. Here, we investigated the protein/peptide loss during the nanoproteomics experiment process. Our results showed that there are significant differences in nonspecific binding among the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. Interestingly, we found that the storage temperature could also be one of the key factors that contribute to protein recovery from the plastic container. In addition, we investigated the binding preferences of different microtubes by the physical characteristics of the identified proteins and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings help to better understand protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample

Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation

Nonspecific binding between the protein and the container is an often-neglected cause of sample loss in large-scale proteomics sample preparation. In nanoproteomics, due to the small sample size, this absorption loss is no longer negligible, and researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences in microtube performance on reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well understood. Here, we investigated the protein/peptide loss during the nanoproteomics experiment process. Our results showed that there are significant differences in nonspecific binding among the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. Interestingly, we found that the storage temperature could also be one of the key factors that contribute to protein recovery from the plastic container. In addition, we investigated the binding preferences of different microtubes by the physical characteristics of the identified proteins and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings help to better understand protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample

Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation

Nonspecific binding between the protein and the container is an often-neglected cause of sample loss in large-scale proteomics sample preparation. In nanoproteomics, due to the small sample size, this absorption loss is no longer negligible, and researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences in microtube performance on reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well understood. Here, we investigated the protein/peptide loss during the nanoproteomics experiment process. Our results showed that there are significant differences in nonspecific binding among the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. Interestingly, we found that the storage temperature could also be one of the key factors that contribute to protein recovery from the plastic container. In addition, we investigated the binding preferences of different microtubes by the physical characteristics of the identified proteins and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings help to better understand protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample

sj-dta-2-sgo-10.1177_21582440231206626 – for Emission Reduction Effect, Influencing Factors and Economic Impact of China’s Carbon Market

sj-dta-2-sgo-10.1177_21582440231206626 for Emission Reduction Effect, Influencing Factors and Economic Impact of China’s Carbon Market by Heng Zhang, Ziwei Zhang, Keyuan Sun and Yutong Zou in SAGE Open</p

sj-do-1-sgo-10.1177_21582440231206626 – Supplemental material for Emission Reduction Effect, Influencing Factors and Economic Impact of China’s Carbon Market

Supplemental material, sj-do-1-sgo-10.1177_21582440231206626 for Emission Reduction Effect, Influencing Factors and Economic Impact of China’s Carbon Market by Heng Zhang, Ziwei Zhang, Keyuan Sun and Yutong Zou in SAGE Open</p

The role of private equity when portfolio firms go public: Evidence from ChiNext board

We probe into the question of why entrepreneurial firms choose to obtain private equity finance (PE) shortly before going public on the ChiNext Board (the Chinese alternative stock market for smaller firms, part of the Shenzhen Stock Exchange, SZSE). Using unique hand-collected data we find that, compared with non-PE-backed firms, firms with PE equity stakes introduced shortly before the IPO did not reduce IPO underpricing or decrease the offering cost. However PE investors increased the probability of approval when the firms applied to the China Securities Regulatory Commission (CSRC) for listing. We suggest the stock issuance rules for the ChiNext should be reformed to lower entrepreneurial firms’ financing cost and to encourage PE firms to undertake more value-adding activities