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Li W, Guo L, Ding XL, Ding Y, Ji LN, Xia XH, Wang K. High-Throughput Single-Molecule Surface-Enhanced Raman Spectroscopic Profiling of Single-Amino Acid Substitutions in Peptides by a Gold Plasmonic Nanopore. ACS NANO 2024; 18:19200-19207. [PMID: 38996344 DOI: 10.1021/acsnano.4c04775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Simultaneous detection and structural characterization of protein variants on a single platform are highly desirable but technically challenging. Herein, we present a single-molecule spectral system based on a gold plasmonic nanopore for analyzing two peptides and their single-point mutated variants. The gold plasmonic nanopore enabled the high-throughput acquisition of surface-enhanced Raman scattering (SERS) spectra at the single-molecule level by electrically driving analytes into hot spots. Furthermore, a statistical method based on Boolean operations was developed to extract prominent features from fluctuated single-molecule SERS spectra. The effects of the single-amino acid substitutions on both the intramolecular interactions and the peptide conformations were directly characterized by the nanopore system, and the results agreed with the predictions by AlphaFold2. This study highlights the mutual benefits of spectroscopy and nanopore technology, whereby the gold plasmonic nanopore offers a powerful tool for the structural analysis of single-molecule proteins.
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Affiliation(s)
- Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Linru Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yanru Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Wu Z, Bonneil É, Belford M, Boeser C, Dunyach JJ, Thibault P. Targeted Mass Spectrometry Analyses of Somatic Mutations in Colorectal Cancer Specimens Using Differential Ion Mobility. J Proteome Res 2024; 23:644-652. [PMID: 38153093 DOI: 10.1021/acs.jproteome.3c00444] [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] [Indexed: 12/29/2023]
Abstract
Identification of K-Ras and B-Raf mutations in colorectal cancer (CRC) is essential to predict patients' response to anti-EGFR therapy and formulate appropriate therapeutic strategies to improve prognosis and survival. Here, we combined parallel reaction monitoring (PRM) with high-field asymmetric waveform ion mobility (FAIMS) to enhance mass spectrometry sensitivity and improve the identification of low-abundance K-Ras and B-Raf mutations in biological samples without immunoaffinity enrichment. In targeted LC-MS/MS analyses, FAIMS reduced the occurrence of interfering ions and enhanced precursor ion purity, resulting in a 3-fold improvement in the detection limit for K-Ras and B-Raf mutated peptides. In addition, the ion mobility separation of isomeric peptides using FAIMS facilitated the unambiguous identification of K-Ras G12D and G13D peptides. The application of targeted LC-MS/MS analyses using FAIMS is demonstrated for the detection and quantitation of B-Raf V600E, K-Ras G12D, G13D, and G12V in CRC cell lines and primary specimens.
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Affiliation(s)
- Zhaoguan Wu
- Institute for Research in Immunology and Cancer (IRIC) Université de Montréal, Montréal H3T 1J4, Canada
- Department of Chemistry, Université de Montréal, MIL Campus, Montréal H2 V 0B3, Canada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer (IRIC) Université de Montréal, Montréal H3T 1J4, Canada
| | - Michael Belford
- ThermoFisher Scientific, San Jose, California 95134, United States
| | - Cornelia Boeser
- ThermoFisher Scientific, San Jose, California 95134, United States
| | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC) Université de Montréal, Montréal H3T 1J4, Canada
- Department of Chemistry, Université de Montréal, MIL Campus, Montréal H2 V 0B3, Canada
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Kotimoole C, Antil N, Kasaragod S, Behera S, Arvind A, Reiling N, Flo T, Prasad T. Development of a spectral library for the discovery of altered genomic events in Mycobacterium avium associated with virulence using mass spectrometry-based proteogenomic analysis. Mol Cell Proteomics 2023; 22:100533. [PMID: 36948415 PMCID: PMC10149365 DOI: 10.1016/j.mcpro.2023.100533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 02/02/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
Mycobacterium avium is one of the prominent disease-causing bacteria in humans. It causes lymphadenitis, chronic and extrapulmonary, and disseminated infections in adults, children, and immunocompromised patients. M. avium has ∼4,500 predicted protein-coding regions on average, which can help discover several variants at the proteome level. Many of them are potentially associated with virulence; thus, identifying such proteins can be a helpful feature in developing panel-based theranostics. In line with such a long-term goal, we carried out an in-depth proteomic analysis of M. avium with both data-dependent and data-independent acquisition methods. Further, a set of proteogenomic investigations were carried out using i) a protein database for Mycobacterium tuberculosis, ii) a M. avium genome six-frame translated database, and iii) a variant protein database of M. avium. A search of mass spectrometry data against M. avium protein database resulted in identifying 2,954 proteins. Further, proteogenomic analyses aided in identifying 1,301 novel peptide sequences and correcting translation start sites for 15 proteins. Ultimately, we created a spectral library of M. avium proteins, including novel genome search-specific peptides and variant peptides detected in this study. We validated the spectral library by a data-independent acquisition of the M. avium proteome. Thus, we present an M. avium spectral library of 29,033 peptide precursors supported by 0.4 million fragment ions for further use by the biomedical community.
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Affiliation(s)
- ChinmayaNarayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Neelam Antil
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Sandeep Kasaragod
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - SantoshKumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Anjana Arvind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Parkallee 22, D-23845 Borstel, Germany; German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany
| | - TrudeHelen Flo
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Kunnskapssenteret, 424.04.035, Øya, Norway
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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. MASS SPECTROMETRY REVIEWS 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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Vitorino R, Choudhury M, Guedes S, Ferreira R, Thongboonkerd V, Sharma L, Amado F, Srivastava S. Peptidomics and proteogenomics: background, challenges and future needs. Expert Rev Proteomics 2021; 18:643-659. [PMID: 34517741 DOI: 10.1080/14789450.2021.1980388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION With available genomic data and related information, it is becoming possible to better highlight mutations or genomic alterations associated with a particular disease or disorder. The advent of high-throughput sequencing technologies has greatly advanced diagnostics, prognostics, and drug development. AREAS COVERED Peptidomics and proteogenomics are the two post-genomic technologies that enable the simultaneous study of peptides and proteins/transcripts/genes. Both technologies add a remarkably large amount of data to the pool of information on various peptides associated with gene mutations or genome remodeling. Literature search was performed in the PubMed database and is up to date. EXPERT OPINION This article lists various techniques used for peptidomic and proteogenomic analyses. It also explains various bioinformatics workflows developed to understand differentially expressed peptides/proteins and their role in disease pathogenesis. Their role in deciphering disease pathways, cancer research, and biomarker discovery using biofluids is highlighted. Finally, the challenges and future requirements to overcome the current limitations for their effective clinical use are also discussed.
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Affiliation(s)
- Rui Vitorino
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manisha Choudhury
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Powai, India
| | - Sofia Guedes
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rita Ferreira
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Francisco Amado
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Powai, India
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Salz R, Bouwmeester R, Gabriels R, Degroeve S, Martens L, Volders PJ, 't Hoen PAC. Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection. J Proteome Res 2021; 20:3353-3364. [PMID: 33998808 PMCID: PMC8280751 DOI: 10.1021/acs.jproteome.1c00264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Indexed: 12/30/2022]
Abstract
Discovery of variant peptides such as a single amino acid variant (SAAV) in shotgun proteomics data is essential for personalized proteomics. Both the resolution of shotgun proteomics methods and the search engines have improved dramatically, allowing for confident identification of SAAV peptides. However, it is not yet known if these methods are truly successful in accurately identifying SAAV peptides without prior genomic information in the search database. We studied this in unprecedented detail by exploiting publicly available long-read RNA sequences and shotgun proteomics data from the gold standard reference cell line NA12878. Searching spectra from this cell line with the state-of-the-art open modification search engine ionbot against carefully curated search databases resulted in 96.7% false-positive SAAVs and an 85% lower true positive rate than searching with peptide search databases that incorporate prior genetic information. While adding genetic variants to the search database remains indispensable for correct peptide identification, inclusion of long-read RNA sequences in the search database contributes only 0.3% new peptide identifications. These findings reveal the differences in SAAV detection that result from various approaches, providing guidance to researchers studying SAAV peptides and developers of peptide spectrum identification tools.
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Affiliation(s)
- Renee Salz
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Pieter-Jan Volders
- VIB-UGent Center for Medical Biotechnology VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Peter A C 't Hoen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
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Low TY, Mohtar MA, Ang MY, Jamal R. Connecting Proteomics to Next‐Generation Sequencing: Proteogenomics and Its Current Applications in Biology. Proteomics 2018; 19:e1800235. [DOI: 10.1002/pmic.201800235] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/09/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
| | - M. Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
| | - Mia Yang Ang
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
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Salvianti F, Pinzani P. The diagnostic potential of mutation detection from single circulating tumor cells in cancer patients. Expert Rev Mol Diagn 2017; 17:975-981. [PMID: 28931314 DOI: 10.1080/14737159.2017.1381561] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Circulating tumor cells (CTCs) have gained importance in the oncology field as biomarkers of tumor development. The most relevant observation that emerged from the recent studies on CTCs is their heterogeneity, which can be investigated by new technologies for single cell analysis. Areas covered: This review considers the most recent advances (limited to the last two years) in the mutational analysis of single CTCs with a critical point of view on the technical challenges still to be faced and the steps needed to reach a standardization of the procedures able to translate these new approaches into clinical practice. Expert commentary: CTCs represent a surrogate tumor sample obtained by a minimally invasive procedure allowing the serial monitoring of the patient during the follow-up period or after treatment. Notwithstanding that, the analysis of CTCs is not so widespread; in fact, a limited number of centers can be equipped and possess the expertise for the development of workflows able to identify, enrich and isolate CTCs from blood. Moreover, the lack of standardized procedures and guidelines limits the study of CTCs to 'research use only' approaches.
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Affiliation(s)
- Francesca Salvianti
- a Department of Clinical and Experimental Biomedical Sciences 'Mario Serio' , University of Florence , Florence , Italy
| | - Pamela Pinzani
- a Department of Clinical and Experimental Biomedical Sciences 'Mario Serio' , University of Florence , Florence , Italy
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