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Konno R, Ishikawa M, Nakajima D, Endo Y, Ohara O, Kawashima Y. Universal Pretreatment Development for Low-input Proteomics Using Lauryl Maltose Neopentyl Glycol. Mol Cell Proteomics 2024; 23:100745. [PMID: 38447790 PMCID: PMC10999711 DOI: 10.1016/j.mcpro.2024.100745] [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: 09/25/2023] [Revised: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
In recent years, there has been a growing demand for low-input proteomics, particularly in the context of single-cell proteomics (SCP). In this study, we have developed a lauryl maltose neopentyl glycol (LMNG)-assisted sample preparation (LASP) method. This method effectively reduces protein and peptide loss in samples by incorporating LMNG, a surfactant, into the digestion solution and subsequently removing the LMNG simply via reversed phase solid-phase extraction. The advantage of removing LMNG during sample preparation for general proteomic analysis is the prevention of mass spectrometry (MS) contamination. When we applied the LASP method to the low-input SP3 method and on-bead digestion in coimmunoprecipitation-MS, we observed a significant improvement in the recovery of the digested peptides. Furthermore, we have established a simple and easy sample preparation method for SCP based on the LASP method and identified a median of 1175 proteins from a single HEK239F cell using liquid chromatography (LC)-MS/MS with a throughput of 80 samples per day.
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Affiliation(s)
- Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Yusuke Endo
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan; Graduate School of Science, Kitasato University, Sagamihara, Kanagawa, Japan.
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Nakajima D, Konno R, Miyashita Y, Ishikawa M, Ohara O, Kawashima Y. Proteome Analysis of Serum Purified Using Solanum tuberosum and Lycopersicon esculentum Lectins. Int J Mol Sci 2024; 25:1315. [PMID: 38279312 PMCID: PMC10816257 DOI: 10.3390/ijms25021315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Serum and plasma exhibit a broad dynamic range of protein concentrations, posing challenges for proteome analysis. Various technologies have been developed to reduce this complexity, including high-abundance depletion methods utilizing antibody columns, extracellular vesicle enrichment techniques, and trace protein enrichment using nanobead cocktails. Here, we employed lectins to address this, thereby extending the scope of biomarker discovery in serum or plasma using a novel approach. We enriched serum proteins using 37 different lectins and subjected them to LC-MS/MS analysis with data-independent acquisition. Solanum tuberosum lectin (STL) and Lycopersicon esculentum lectin (LEL) enabled the detection of more serum proteins than the other lectins. STL and LEL bind to N-acetylglucosamine oligomers, emphasizing the significance of capturing these oligomer-binding proteins when analyzing serum trace proteins. Combining STL and LEL proved more effective than using them separately, allowing us to identify over 3000 proteins from serum through single-shot proteome analysis. We applied the STL/LEL trace-protein enrichment method to the sera of systemic lupus erythematosus model mice. This revealed differences in >1300 proteins between the systemic lupus erythematosus model and control mouse sera, underscoring the utility of this method for biomarker discovery.
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Affiliation(s)
- Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
| | - Yasuomi Miyashita
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
- Department of Developmental Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Chiba, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
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