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Mi W, Zhang X, Wang B, Sun R, Ma S, Hu Z, Dai X. Absolute protein quantification based on calibrated particle counting using electrospray-differential mobility analysis. Anal Chim Acta 2024; 1304:342534. [PMID: 38637035 DOI: 10.1016/j.aca.2024.342534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
The traceability of in vitro diagnostics or drug products is based on the accurate quantification of proteins. In this study, we developed an absolute quantification approach for proteins. This method is based on calibrated particle counting using electrospray-differential mobility analysis (ES-DMA) coupled with a condensation particle counter (CPC). The absolute concentration of proteins was quantified with the observed protein particle number measured with ES-DMA-CPC, and the detection efficiency was determined by calibrators. The measurement performance and quantitative level were verified using two certificated reference materials, BSA and NIMCmAb. The linear regression fit for the detection efficiency values of three reference materials and one highly purified protein (myoglobin, BSA, NIMCmAb and fibrinogen) indicated that the detection efficiency and the particle size distribution of these proteins exhibited a linear relationship. Moreover, to explore the suitability of the detection efficiency-particle size curve for protein quantification, the concentrations of three typical proteinaceous particles, including two high molecular weight proteins (NIST reference material 8671 and D-dimer) and one protein complex (glutathione S-transferase dimer), were determined. This work suggests that this calibrated particle counting method is an efficient approach for nondestructive, rapid and accurate quantification of proteins, especially for measuring proteinaceous particles with tremendous size and without reference standards.
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Affiliation(s)
- Wei Mi
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China.
| | - Xinyi Zhang
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China
| | - Bin Wang
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China
| | - Ruixue Sun
- College of Life Sciences, China Jiliang University, Xueyuan Street 258, Hangzhou, 310018, China
| | - Shangying Ma
- College of Life Sciences, China Jiliang University, Xueyuan Street 258, Hangzhou, 310018, China
| | - Zhishang Hu
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China.
| | - Xinhua Dai
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China.
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Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Vuylsteke M, Stadler C, Eyckerman S, Spirohn K, Hao T, Calderwood MA, Gevaert K. N-terminal proteoforms may engage in different protein complexes. Life Sci Alliance 2023; 6:e202301972. [PMID: 37316325 PMCID: PMC10267514 DOI: 10.26508/lsa.202301972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
Alternative translation initiation and alternative splicing may give rise to N-terminal proteoforms, proteins that differ at their N-terminus compared with their canonical counterparts. Such proteoforms can have altered localizations, stabilities, and functions. Although proteoforms generated from splice variants can be engaged in different protein complexes, it remained to be studied to what extent this applies to N-terminal proteoforms. To address this, we mapped the interactomes of several pairs of N-terminal proteoforms and their canonical counterparts. First, we generated a catalogue of N-terminal proteoforms found in the HEK293T cellular cytosol from which 22 pairs were selected for interactome profiling. In addition, we provide evidence for the expression of several N-terminal proteoforms, identified in our catalogue, across different human tissues, as well as tissue-specific expression, highlighting their biological relevance. Protein-protein interaction profiling revealed that the overlap of the interactomes for both proteoforms is generally high, showing their functional relation. We also showed that N-terminal proteoforms can be engaged in new interactions and/or lose several interactions compared with their canonical counterparts, thus further expanding the functional diversity of proteomes.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tessa Van de Steene
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Charlotte Stadler
- Department of Protein Science, KTH Royal Institute of Technology and Science for Life Laboratories, Stockholm, Sweden
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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Swamy KBS, Schuyler SC, Leu JY. Protein Complexes Form a Basis for Complex Hybrid Incompatibility. Front Genet 2021; 12:609766. [PMID: 33633780 PMCID: PMC7900514 DOI: 10.3389/fgene.2021.609766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/20/2021] [Indexed: 12/20/2022] Open
Abstract
Proteins are the workhorses of the cell and execute many of their functions by interacting with other proteins forming protein complexes. Multi-protein complexes are an admixture of subunits, change their interaction partners, and modulate their functions and cellular physiology in response to environmental changes. When two species mate, the hybrid offspring are usually inviable or sterile because of large-scale differences in the genetic makeup between the two parents causing incompatible genetic interactions. Such reciprocal-sign epistasis between inter-specific alleles is not limited to incompatible interactions between just one gene pair; and, usually involves multiple genes. Many of these multi-locus incompatibilities show visible defects, only in the presence of all the interactions, making it hard to characterize. Understanding the dynamics of protein-protein interactions (PPIs) leading to multi-protein complexes is better suited to characterize multi-locus incompatibilities, compared to studying them with traditional approaches of genetics and molecular biology. The advances in omics technologies, which includes genomics, transcriptomics, and proteomics can help achieve this end. This is especially relevant when studying non-model organisms. Here, we discuss the recent progress in the understanding of hybrid genetic incompatibility; omics technologies, and how together they have helped in characterizing protein complexes and in turn multi-locus incompatibilities. We also review advances in bioinformatic techniques suitable for this purpose and propose directions for leveraging the knowledge gained from model-organisms to identify genetic incompatibilities in non-model organisms.
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Affiliation(s)
- Krishna B. S. Swamy
- Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Scott C. Schuyler
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Head and Neck Surgery, Department of Otolaryngology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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Proteomic-Based Approaches for the Study of Cytokines in Lung Cancer. DISEASE MARKERS 2016; 2016:2138627. [PMID: 27445423 PMCID: PMC4944034 DOI: 10.1155/2016/2138627] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/12/2016] [Indexed: 02/06/2023]
Abstract
Proteomic techniques are currently used to understand the biology of different human diseases, including studies of the cell signaling pathways implicated in cancer progression, which is important in knowing the roles of different proteins in tumor development. Due to its poor prognosis, proteomic approaches are focused on the identification of new biomarkers for the early diagnosis, prognosis, and targeted treatment of lung cancer. Cytokines are proteins involved in inflammatory processes and have been proposed as lung cancer biomarkers and therapeutic targets because it has been reported that some cytokines play important roles in tumor development, invasion, and metastasis. In this review, we aim to summarize the different proteomic techniques used to discover new lung cancer biomarkers and therapeutic targets. Several cytokines have been identified as important players in lung cancer using these techniques. We underline the most important cytokines that are useful as biomarkers and therapeutic targets. We also summarize some of the therapeutic strategies targeted for these cytokines in lung cancer.
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