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Wang J, Tan H, Fu Y, Mishra A, Sun H, Wang Z, Wu Z, Wang X, Serrano GE, Beach TG, Peng J, High AA. Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1253-1260. [PMID: 38754071 DOI: 10.1021/jasms.4c00067] [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: 05/18/2024]
Abstract
Accurate and precise quantification is crucial in modern proteomics, particularly in the context of exploring low-amount samples. While the innovative 4D-data-independent acquisition (DIA) quantitative proteomics facilitated by timsTOF mass spectrometers gives enhanced sensitivity and selectivity for protein identification, the diaPASEF (parallel accumulation-serial fragmentation combined with data-independent acquisition) parameters have not been systematically optimized, and a comprehensive evaluation of the quantification is currently lacking. In this study, we conducted a thorough optimization of key parameters on a timsTOF SCP instrument, including sample loading amount (50 ng), ramp/accumulation time (140 ms), isolation window width (20 m/z), and gradient time (60 min). To further improve the identification of proteins in low-amount samples, we utilized different column settings and introduced 0.02% n-dodecyl-β-d-maltoside (DDM) in the sample reconstitution solution, resulting in a remarkable 19-fold increase in protein identification at the single-cell-equivalent level. Moreover, a comprehensive comparison of protein quantification using a tandem mass tag reporter (TMT-reporter), complement TMT ions (TMTc), and diaPASEF revealed a strong correlation between these methods. Both diaPASEF and TMTc have effectively addressed the issue of ratio compression, highlighting the diaPASEF method's effectiveness in achieving accurate quantification data compared to TMT reporter quantification. Additionally, an in-depth analysis of in-group variation positioned diaPASEF between the TMT-reporter and TMTc methods. Therefore, diaPASEF quantification on the timsTOF SCP instrument emerges as a precise and accurate methodology for quantitative proteomics, especially for samples with small amounts.
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Affiliation(s)
- Ju Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yingxue Fu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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2
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Gao Y, Li J, Hu K, Wang S, Yang S, Ai Q, Yan J. Phosphoproteomic analysis of APP/PS1 mice of Alzheimer's disease by DIA based mass spectrometry analysis with PRM verification. J Proteomics 2024; 299:105157. [PMID: 38462170 DOI: 10.1016/j.jprot.2024.105157] [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: 12/04/2023] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
Traditional Chinese medicine has been utilized in China for approximately thousands of years in clinical settings to prevent Alzheimer's disease (AD) and enhance memory, despite the lack of a systematic exploration of its biological underpinnings. Exciting research has corroborated the beneficial effects of tetrahydroxy stilbene glycoside (TSG), an extract derived from Polygonum multiflorum, in delaying learning and memory impairment in a model that mimics AD. Therefore, the primary objective of this study is to investigate the major function of TSG upon protein regulation in AD. Herein, a novel approach, encompassing data independent acquisition (DIA), DIA phosphorylated proteomics, and parallel reaction monitoring (PRM), was utilized to integrate quantitative proteomic data collected from APP/PS1 mouse model exhibiting toxic intracellular aggregation of Aβ. Initially, we deliberated upon both single and multi-dimensional data pertaining to AD model mice. Furthermore, we authenticated disparities in protein phosphorylation quantity and expression, phosphorylation function, and ultimately phosphorylation kinase analysis. In order to validate the results, we utilized PRM ion monitoring technology to identify potential protein or peptide biomarkers. In the mixed samples, targeted detection of 50 target proteins revealed that 26 to 33 target proteins were stably detected by PRM. In summary, our findings provide new candidates for AD biomarker, which have been identified and validated through protein researches conducted on mouse brains. This offers a wealth of potential resources for extensive biomarker validation in neurodegenerative diseases. SIGNIFICANCE: DIA phosphorylated proteomics technique was used to detect and analyze phosphorylated proteins in brain tissues of mice with AD. Data were analyzed by various bioinformatics tools to explore the phosphorylation events and characterize them related to TSG. The results of DIA were further verified by PRM. Besides, we mapped the major metabolite classes emerging from the analyses to key biological pathways implicated in AD to understand the potential roles of the molecules and the interactions in triggering symptom onset and progression of AD. Meanwhile, we clarified that in the context of AD onset and TSG intervention, the changes in proteins, protein phosphorylation, phosphorylation kinases, and the internal connections.
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Affiliation(s)
- Yan Gao
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China; Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China.
| | - Juntong Li
- Nanjing University of Chinese Medicine, Nanjing, 210023, China; Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Kaichao Hu
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Changchun University of Chinese Medicine, Changchun 130117, China
| | - Shasha Wang
- Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Songwei Yang
- Hunan University of Chinese Medicine, Changsha 410208, China
| | - Qidi Ai
- Hunan University of Chinese Medicine, Changsha 410208, China
| | - Jiaqing Yan
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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3
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Murfuni MS, Prestagiacomo LE, Giuliano A, Gabriele C, Signoretti S, Cuda G, Gaspari M. Evaluation of PAC and FASP Performance: DIA-Based Quantitative Proteomic Analysis. Int J Mol Sci 2024; 25:5141. [PMID: 38791181 PMCID: PMC11121386 DOI: 10.3390/ijms25105141] [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: 03/20/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
The aim of this study was to compare filter-aided sample preparation (FASP) and protein aggregation capture (PAC) starting from a three-species protein mix (Human, Soybean and Pisum sativum) and two different starting amounts (1 and 10 µg). Peptide mixtures were analyzed by data-independent acquisition (DIA) and raw files were processed by three commonly used software: Spectronaut, MaxDIA and DIA-NN. Overall, the highest number of proteins (mean value of 5491) were identified by PAC (10 µg), while the lowest number (4855) was identified by FASP (1 µg). The latter experiment displayed the worst performance in terms of both specificity (0.73) and precision (0.24). Other tested conditions showed better diagnostic accuracy, with specificity values of 0.95-0.99 and precision values between 0.61 and 0.86. In order to provide guidance on the data analysis pipeline, the accuracy diagnostic of three software was investigated: (i) the highest sensitivity was obtained with Spectronaut (median of 0.67) highlighting the ability of Spectronaut to quantify low-abundance proteins, (ii) the best precision value was obtained by MaxDIA (median of 0.84), but with a reduced number of identifications compared to Spectronaut and DIA-NN data, and (iii) the specificity values were similar (between 0.93 and 0.99). The data are available on ProteomeXchange with the identifier PXD044349.
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Chiang Y, Welker F, Collins MJ. Spectra without stories: reporting 94% dark and unidentified ancient proteomes. OPEN RESEARCH EUROPE 2024; 4:71. [PMID: 38903702 PMCID: PMC11187534 DOI: 10.12688/openreseurope.17225.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 06/22/2024]
Abstract
Background Data-dependent, bottom-up proteomics is widely used for identifying proteins and peptides. However, one key challenge is that 70% of fragment ion spectra consistently fail to be assigned by conventional database searching. This 'dark matter' of bottom-up proteomics seems to affect fields where non-model organisms, low-abundance proteins, non-tryptic peptides, and complex modifications may be present. While palaeoproteomics may appear as a niche field, understanding and reporting unidentified ancient spectra require collaborative innovation in bioinformatics strategies. This may advance the analysis of complex datasets. Methods 14.97 million high-impact ancient spectra published in Nature and Science portfolios were mined from public repositories. Identification rates, defined as the proportion of assigned fragment ion spectra, were collected as part of deposited database search outputs or parsed using open-source python packages. Results and Conclusions We report that typically 94% of the published ancient spectra remain unidentified. This phenomenon may be caused by multiple factors, notably the limitations of database searching and the selection of user-defined reference data with advanced modification patterns. These 'spectra without stories' highlight the need for widespread data sharing to facilitate methodological development and minimise the loss of often irreplaceable ancient materials. Testing and validating alternative search strategies, such as open searching and de novo sequencing, may also improve overall identification rates. Hence, lessons learnt in palaeoproteomics may benefit other fields grappling with challenging data.
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Affiliation(s)
- Yun Chiang
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- The Nice Institute of Chemistry, Universite Cote d'Azur, Nice, France
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew James Collins
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, England, UK
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Fu Q, Vegesna M, Sundararaman N, Damoc E, Arrey TN, Pashkova A, Mengesha E, Debbas P, Joung S, Li D, Cheng S, Braun J, McGovern DPB, Murray C, Xuan Y, Eyk JEV. Paradigm shift in biomarker translation: a pipeline to generate clinical grade biomarker candidates from DIA-MS discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.586018. [PMID: 38562888 PMCID: PMC10983901 DOI: 10.1101/2024.03.20.586018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Clinical biomarker development has been stymied by inaccurate protein quantification from mass spectrometry (MS) discovery data and a prolonged validation process. To mitigate these issues, we created the Targeted Extraction Assessment of Quantification (TEAQ) software package. This innovative tool uses the discovery cohort analysis to select precursors, peptides, and proteins that adhere to established targeted assay criteria. TEAQ was applied to Data-Independent Acquisition MS data from plasma samples acquired on an Orbitrap™ Astral™ MS. Identified precursors were evaluated for linearity, specificity, repeatability, reproducibility, and intra-protein correlation from 11-point loading curves under three throughputs, to develop a resource for clinical-grade targeted assays. From a clinical cohort of individuals with inflammatory bowel disease (n=492), TEAQ successfully identified 1116 signature peptides for 327 quantifiable proteins from 1180 identified proteins. Embedding stringent selection criteria adaptable to targeted assay development into the analysis of discovery data will streamline the transition to validation and clinical studies.
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6
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Bianco M, Calvano CD, Ventura G, Losito I, Cataldi TRI. Proteomics for Microalgae Extracts by High-Resolution Mass Spectrometry. Methods Mol Biol 2024; 2820:67-88. [PMID: 38941016 DOI: 10.1007/978-1-0716-3910-8_8] [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: 06/29/2024]
Abstract
Two protocols of protein extraction from Arthrospira platensis (spirulina) microalgae to study their proteome by mass spectrometry (MS) are here presented. The first is based on an aqueous buffer solution of Tris-HCl and the second on cold acetone. The identification of proteins was carried out by a bottom-up approach, which involves enzymatic digestion of extracted proteins followed by either matrix-assisted laser desorption ionization with time-of-flight (MALDI-TOF) MS or liquid chromatography (LC) coupled with electrospray ionization (ESI) and Fourier-transform tandem MS. While MALDI-TOF MS allowed for a fast peptide mass fingerprinting (PMF) check yet identifying less than 20 proteins in the extracted samples, the data-dependent acquisitions (DDA) mode of reversed-phase (RP) LC-ESI tandem FTMS/MS separations allowed us to recognize more than one hundred proteins by searching into dedicated spectral libraries. The application of MALDI-TOF MS analysis was found, however, of great support for preliminary investigations of cyanobacteria samples before proceeding with the RPLC-ESI-MS/MS DDA investigation, which definitively allows for a qualitative proteome analysis also of minor spirulina proteins in processed foodstuffs. Although the protein content in spirulina can be influenced by cultivation and environmental conditions, e.g., light intensity, climate, and water/air quality, here the qualitative chemical profiles of the examined samples were characterized by similar composition in high-quality proteins as phycocyanins and phycoerythrins.
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Affiliation(s)
- Mariachiara Bianco
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Cosima D Calvano
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy.
- Centro Interdipartimentale di Ricerca SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy.
| | - Giovanni Ventura
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro Interdipartimentale di Ricerca SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Ilario Losito
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro Interdipartimentale di Ricerca SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Tommaso R I Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro Interdipartimentale di Ricerca SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
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7
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Postoenko VI, Garibova LA, Levitsky LI, Bubis JA, Gorshkov MV, Ivanov MV. IQMMA: Efficient MS1 Intensity Extraction Pipeline Using Multiple Feature Detection Algorithms for DDA Proteomics. J Proteome Res 2023; 22:2827-2835. [PMID: 37579078 DOI: 10.1021/acs.jproteome.3c00075] [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: 08/16/2023]
Abstract
One of the key steps in data dependent acquisition (DDA) proteomics is detection of peptide isotopic clusters, also called "features", in MS1 spectra and matching them to MS/MS-based peptide identifications. A number of peptide feature detection tools became available in recent years, each relying on its own matching algorithm. Here, we provide an integrated solution, the intensity-based Quantitative Mix and Match Approach (IQMMA), which integrates a number of untargeted peptide feature detection algorithms and returns the most probable intensity values for the MS/MS-based identifications. IQMMA was tested using available proteomic data acquired for both well-characterized (ground truth) and real-world biological samples, including a mix of Yeast and E. coli digests spiked at different concentrations into the Human K562 digest used as a background, and a set of glioblastoma cell lines. Three open-source feature detection algorithms were integrated: Dinosaur, biosaur2, and OpenMS FeatureFinder. None of them was found optimal when applied individually to all the data sets employed in this work; however, their combined use in IQMMA improved efficiency of subsequent protein quantitation. The software implementing IQMMA is freely available at https://github.com/PostoenkoVI/IQMMA under Apache 2.0 license.
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Affiliation(s)
- Valeriy I Postoenko
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, National Research University, G. Dolgoprudny, Institutsky Lane 9, Dolgoprudny 141701, Russia
| | - Leyla A Garibova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, National Research University, G. Dolgoprudny, Institutsky Lane 9, Dolgoprudny 141701, Russia
| | - Lev I Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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8
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Révész Á, Hevér H, Steckel A, Schlosser G, Szabó D, Vékey K, Drahos L. Collision energies: Optimization strategies for bottom-up proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1261-1299. [PMID: 34859467 DOI: 10.1002/mas.21763] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 06/07/2023]
Abstract
Mass-spectrometry coupled to liquid chromatography is an indispensable tool in the field of proteomics. In the last decades, more and more complex and diverse biochemical and biomedical questions have arisen. Problems to be solved involve protein identification, quantitative analysis, screening of low abundance modifications, handling matrix effect, and concentrations differing by orders of magnitude. This led the development of more tailored protocols and problem centered proteomics workflows, including advanced choice of experimental parameters. In the most widespread bottom-up approach, the choice of collision energy in tandem mass spectrometric experiments has outstanding role. This review presents the collision energy optimization strategies in the field of proteomics which can help fully exploit the potential of MS based proteomics techniques. A systematic collection of use case studies is then presented to serve as a starting point for related further scientific work. Finally, this article discusses the issue of comparing results from different studies or obtained on different instruments, and it gives some hints on methodology transfer between laboratories based on measurement of reference species.
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Affiliation(s)
- Ágnes Révész
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Helga Hevér
- Chemical Works of Gedeon Richter Plc, Budapest, Hungary
| | - Arnold Steckel
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
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9
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Fabian O, Bajer L, Drastich P, Harant K, Sticova E, Daskova N, Modos I, Tichanek F, Cahova M. A Current State of Proteomics in Adult and Pediatric Inflammatory Bowel Diseases: A Systematic Search and Review. Int J Mol Sci 2023; 24:ijms24119386. [PMID: 37298338 DOI: 10.3390/ijms24119386] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are systemic immune-mediated conditions with predilection for the gastrointestinal tract and include Crohn's disease and ulcerative colitis. Despite the advances in the fields of basic and applied research, the etiopathogenesis remains largely unknown. As a result, only one third of the patients achieve endoscopic remission. A substantial portion of the patients also develop severe clinical complications or neoplasia. The need for novel biomarkers that can enhance diagnostic accuracy, more precisely reflect disease activity, and predict a complicated disease course, thus, remains high. Genomic and transcriptomic studies contributed substantially to our understanding of the immunopathological pathways involved in disease initiation and progression. However, eventual genomic alterations do not necessarily translate into the final clinical picture. Proteomics may represent a missing link between the genome, transcriptome, and phenotypical presentation of the disease. Based on the analysis of a large spectrum of proteins in tissues, it seems to be a promising method for the identification of new biomarkers. This systematic search and review summarize the current state of proteomics in human IBD. It comments on the utility of proteomics in research, describes the basic proteomic techniques, and provides an up-to-date overview of available studies in both adult and pediatric IBD.
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Affiliation(s)
- Ondrej Fabian
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Department of Pathology and Molecular Medicine, 3rd Faculty of Medicine, Charles University and Thomayer Hospital, 140 59 Prague, Czech Republic
| | - Lukas Bajer
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Pavel Drastich
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Karel Harant
- Proteomics Core Facility, Faculty of Science, Charles University, 252 50 Vestec, Czech Republic
| | - Eva Sticova
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Department of Pathology, Royal Vinohrady Teaching Hospital, Srobarova 1150/50, 100 00 Prague, Czech Republic
| | - Nikola Daskova
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Istvan Modos
- Department of Informatics, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Filip Tichanek
- Department of Informatics, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Monika Cahova
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
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10
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Prokai L, Zaman K, Prokai-Tatrai K. Mass spectrometry-based retina proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1032-1062. [PMID: 35670041 PMCID: PMC9730434 DOI: 10.1002/mas.21786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
A subfield of neuroproteomics, retina proteomics has experienced a transformative growth since its inception due to methodological advances in enabling chemical, biochemical, and molecular biology techniques. This review focuses on mass spectrometry's contributions to facilitate mammalian and avian retina proteomics to catalog and quantify retinal protein expressions, determine their posttranslational modifications, as well as its applications to study the proteome of the retina in the context of biology, health and diseases, and therapy developments.
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Affiliation(s)
- Laszlo Prokai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Khadiza Zaman
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Katalin Prokai-Tatrai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
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11
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Higgins L, Gerdes H, Cutillas PR. Principles of phosphoproteomics and applications in cancer research. Biochem J 2023; 480:403-420. [PMID: 36961757 PMCID: PMC10212522 DOI: 10.1042/bcj20220220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation capabilities and sensitivity, in biochemical methods for sample preparation and in computational pipelines are enabling an increasingly deep analysis of the phosphoproteome, where previous bottlenecks in data acquisition, processing and interpretation are being relieved. These powerful hardware and algorithmic innovations are not only providing exciting new mechanistic insights into tumour biology, from where new drug targets may be derived, but are also leading to the discovery of phosphoproteins as mediators of drug sensitivity and resistance and as classifiers of disease subtypes. These studies are, therefore, uncovering phosphoproteins as a new generation of disruptive biomarkers to improve personalised anti-cancer therapies.
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Affiliation(s)
- Luke Higgins
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Henry Gerdes
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Pedro R. Cutillas
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
- Alan Turing Institute, The British Library, London, U.K
- Digital Environment Research Institute, Queen Mary University of London, London, U.K
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12
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Li C, Xiao J, Wu S, Liu L, Zeng X, Zhao Q, Zhang Z. Clinical application of serum-based proteomics technology in human tumor research. Anal Biochem 2023; 663:115031. [PMID: 36580994 DOI: 10.1016/j.ab.2022.115031] [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: 10/28/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 12/27/2022]
Abstract
The rapid development of proteomics technology in the past decades has led to further human understanding of tumor research, and in some ways, the technology plays a very important supporting role in the early detection of tumors. Human serum has been shown to contain a variety of proteins closely related to life activities, and the dynamic change in proteins can often reflect the physiological and pathological conditions of the body. Serum has the advantage of easy extraction, so the application of proteomics technology in serum has become a hot spot and frontier area for the study of malignant tumors. However, there are still many difficulties in the standardized use of proteomic technologies, which inevitably limit the clinical application of proteomic technologies due to the heterogeneity of human proteins leading to incomplete whole proteome populations, in addition to most serum protein markers being now not highly specific in aiding the early detection of tumors. Nevertheless, further development of proteomics technologies will greatly increase our understanding of tumor biology and help discover more new tumor biomarkers with specificity that will enable medical technology.
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Affiliation(s)
- Chen Li
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Juan Xiao
- Department of Otorhinolaryngology, The Second Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Shihua Wu
- Department of Pathology, The Second Hospital of Shaoyang College, Hunan, Shaoyang, 422000, Hunan Province, China
| | - Lu Liu
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Xuemei Zeng
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang, 421001, China
| | - Qiang Zhao
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China.
| | - Zhiwei Zhang
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China; Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang, 421001, China.
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13
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Bersching K, Michna T, Tenzer S, Jacob S. Data-Independent Acquisition (DIA) Is Superior for High Precision Phospho-Peptide Quantification in Magnaporthe oryzae. J Fungi (Basel) 2022; 9:jof9010063. [PMID: 36675884 PMCID: PMC9863866 DOI: 10.3390/jof9010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
The dynamic interplay of signaling networks in most major cellular processes is characterized by the orchestration of reversible protein phosphorylation. Consequently, analytic methods such as quantitative phospho-peptidomics have been pushed forward from a highly specialized edge-technique to a powerful and versatile platform for comprehensively analyzing the phosphorylation profile of living organisms. Despite enormous progress in instrumentation and bioinformatics, a high number of missing values caused by the experimental procedure remains a major problem, due to either a random phospho-peptide enrichment selectivity or borderline signal intensities, which both cause the exclusion for fragmentation using the commonly applied data dependent acquisition (DDA) mode. Consequently, an incomplete dataset reduces confidence in the subsequent statistical bioinformatic processing. Here, we successfully applied data independent acquisition (DIA) by using the filamentous fungus Magnaporthe oryzae as a model organism, and could prove that while maintaining data quality (such as phosphosite and peptide sequence confidence), the data completeness increases dramatically. Since the method presented here reduces the LC-MS/MS analysis from 3 h to 1 h and increases the number of phosphosites identified up to 10-fold in contrast to published studies in Magnaporthe oryzae, we provide a refined methodology and a sophisticated resource for investigation of signaling processes in filamentous fungi.
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Affiliation(s)
- Katharina Bersching
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55131 Mainz, Germany
| | - Thomas Michna
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Helmholtz-Institute for Translational Oncology Mainz (HI-TRON), 55131 Mainz, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan Jacob
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55131 Mainz, Germany
- Correspondence:
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14
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Kong W, Hui HWH, Peng H, Goh WWB. Dealing with missing values in proteomics data. Proteomics 2022; 22:e2200092. [PMID: 36349819 DOI: 10.1002/pmic.202200092] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022]
Abstract
Proteomics data are often plagued with missingness issues. These missing values (MVs) threaten the integrity of subsequent statistical analyses by reduction of statistical power, introduction of bias, and failure to represent the true sample. Over the years, several categories of missing value imputation (MVI) methods have been developed and adapted for proteomics data. These MVI methods perform their tasks based on different prior assumptions (e.g., data is normally or independently distributed) and operating principles (e.g., the algorithm is built to address random missingness only), resulting in varying levels of performance even when dealing with the same dataset. Thus, to achieve a satisfactory outcome, a suitable MVI method must be selected. To guide decision making on suitable MVI method, we provide a decision chart which facilitates strategic considerations on datasets presenting different characteristics. We also bring attention to other issues that can impact proper MVI such as the presence of confounders (e.g., batch effects) which can influence MVI performance. Thus, these too, should be considered during or before MVI.
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Affiliation(s)
- Weijia Kong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Harvard Wai Hann Hui
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hui Peng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Wilson Wen Bin Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Centre for Biomedical Informatics, Nanyang Technological University, Singapore, Singapore
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15
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Solovyeva EM, Bubis JA, Tarasova IA, Lobas AA, Ivanov MV, Nazarov AA, Shutkov IA, Gorshkov MV. On the Feasibility of Using an Ultra-Fast DirectMS1 Method of Proteome-Wide Analysis for Searching Drug Targets in Chemical Proteomics. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1342-1353. [PMID: 36509723 DOI: 10.1134/s000629792211013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Protein quantitation in tissue cells or physiological fluids based on liquid chromatography/mass spectrometry is one of the key sources of information on the mechanisms of cell functioning during chemotherapeutic treatment. Information on significant changes in protein expression upon treatment can be obtained by chemical proteomics and requires analysis of the cellular proteomes, as well as development of experimental and bioinformatic methods for identification of the drug targets. Low throughput of whole proteome analysis based on liquid chromatography and tandem mass spectrometry is one of the main factors limiting the scale of these studies. The method of direct mass spectrometric identification of proteins, DirectMS1, is one of the approaches developed in recent years allowing ultrafast proteome-wide analyses employing minute-scale gradients for separation of proteolytic mixtures. Aim of this work was evaluation of both possibilities and limitations of the method for identification of drug targets at the level of whole proteome and for revealing cellular processes activated by the treatment. Particularly, the available literature data on chemical proteomics obtained earlier for a large set of onco-pharmaceuticals using multiplex quantitative proteome profiling were analyzed. The results obtained were further compared with the proteome-wide data acquired by the DirectMS1 method using ultrashort separation gradients to evaluate efficiency of the method in identifying known drug targets. Using ovarian cancer cell line A2780 as an example, a whole-proteome comparison of two cell lysis techniques was performed, including the freeze-thaw lysis commonly employed in chemical proteomics and the one based on ultrasonication for cell disruption, which is the widely accepted as a standard in proteomic studies. Also, the proteome-wide profiling was performed using ultrafast DirectMS1 method for A2780 cell line treated with lonidamine, followed by gene ontology analyses to evaluate capabilities of the method in revealing regulation of proteins in the cellular processes associated with drug treatment.
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Affiliation(s)
- Elizaveta M Solovyeva
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Irina A Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Anna A Lobas
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alexey A Nazarov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ilya A Shutkov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
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16
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Gurke R, Bendes A, Bowes J, Koehm M, Twyman RM, Barton A, Elewaut D, Goodyear C, Hahnefeld L, Hillenbrand R, Hunter E, Ibberson M, Ioannidis V, Kugler S, Lories RJ, Resch E, Rüping S, Scholich K, Schwenk JM, Waddington JC, Whitfield P, Geisslinger G, FitzGerald O, Behrens F, Pennington SR. Omics and Multi-Omics Analysis for the Early Identification and Improved Outcome of Patients with Psoriatic Arthritis. Biomedicines 2022; 10:2387. [PMID: 36289648 PMCID: PMC9598654 DOI: 10.3390/biomedicines10102387] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
The definitive diagnosis and early treatment of many immune-mediated inflammatory diseases (IMIDs) is hindered by variable and overlapping clinical manifestations. Psoriatic arthritis (PsA), which develops in ~30% of people with psoriasis, is a key example. This mixed-pattern IMID is apparent in entheseal and synovial musculoskeletal structures, but a definitive diagnosis often can only be made by clinical experts or when an extensive progressive disease state is apparent. As with other IMIDs, the detection of multimodal molecular biomarkers offers some hope for the early diagnosis of PsA and the initiation of effective management and treatment strategies. However, specific biomarkers are not yet available for PsA. The assessment of new markers by genomic and epigenomic profiling, or the analysis of blood and synovial fluid/tissue samples using proteomics, metabolomics and lipidomics, provides hope that complex molecular biomarker profiles could be developed to diagnose PsA. Importantly, the integration of these markers with high-throughput histology, imaging and standardized clinical assessment data provides an important opportunity to develop molecular profiles that could improve the diagnosis of PsA, predict its occurrence in cohorts of individuals with psoriasis, differentiate PsA from other IMIDs, and improve therapeutic responses. In this review, we consider the technologies that are currently deployed in the EU IMI2 project HIPPOCRATES to define biomarker profiles specific for PsA and discuss the advantages of combining multi-omics data to improve the outcome of PsA patients.
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Affiliation(s)
- Robert Gurke
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Annika Bendes
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - John Bowes
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WU, UK
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Michaela Koehm
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Division of Rheumatology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | | | - Anne Barton
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WU, UK
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Dirk Elewaut
- VIB-UGent Center for Inflammation Research, Ghent University, 9052 Ghent, Belgium
| | - Carl Goodyear
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8QQ, UK
| | - Lisa Hahnefeld
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | | | - Ewan Hunter
- Oxford BioDynamics Limited, Oxford OX4 2JZ, UK
| | - Mark Ibberson
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Vassilios Ioannidis
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Sabine Kugler
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer IAIS, Institute for Intelligent Analysis and Information Systems, Schloss Birlinghoven 1, 53757 Sankt Augustin, Germany
| | - Rik J. Lories
- Department of Development and Regeneration, KU Leuven, Skeletal Biology and Engineering Research Centre, P.O. Box 813 O&N, Herestraat 49, 3000 Leuven, Belgium
| | - Eduard Resch
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Stefan Rüping
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer IAIS, Institute for Intelligent Analysis and Information Systems, Schloss Birlinghoven 1, 53757 Sankt Augustin, Germany
| | - Klaus Scholich
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jochen M. Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - James C. Waddington
- Atturos Ltd., c/o UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Phil Whitfield
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, Garscube Campus, University of Glasgow, Glasgow G61 1QH, UK
| | - Gerd Geisslinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Oliver FitzGerald
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Frank Behrens
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Division of Rheumatology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Stephen R. Pennington
- Atturos Ltd., c/o UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
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17
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Ivanov MV, Bubis JA, Gorshkov V, Tarasova IA, Levitsky LI, Solovyeva EM, Lipatova AV, Kjeldsen F, Gorshkov MV. DirectMS1Quant: Ultrafast Quantitative Proteomics with MS/MS-Free Mass Spectrometry. Anal Chem 2022; 94:13068-13075. [PMID: 36094425 DOI: 10.1021/acs.analchem.2c02255] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, we presented the DirectMS1 method of ultrafast proteome-wide analysis based on minute-long LC gradients and MS1-only mass spectra acquisition. Currently, the method provides the depth of human cell proteome coverage of 2500 proteins at a 1% false discovery rate (FDR) when using 5 min LC gradients and 7.3 min runtime in total. While the standard MS/MS approaches provide 4000-5000 protein identifications within a couple of hours of instrumentation time, we advocate here that the higher number of identified proteins does not always translate into better quantitation quality of the proteome analysis. To further elaborate on this issue, we performed a one-on-one comparison of quantitation results obtained using DirectMS1 with three popular MS/MS-based quantitation methods: label-free (LFQ) and tandem mass tag quantitation (TMT), both based on data-dependent acquisition (DDA) and data-independent acquisition (DIA). For comparison, we performed a series of proteome-wide analyses of well-characterized (ground truth) and biologically relevant samples, including a mix of UPS1 proteins spiked at different concentrations into an Echerichia coli digest used as a background and a set of glioblastoma cell lines. MS1-only data was analyzed using a novel quantitation workflow called DirectMS1Quant developed in this work. The results obtained in this study demonstrated comparable quantitation efficiency of 5 min DirectMS1 with both TMT and DIA methods, yet the latter two utilized a 10-20-fold longer instrumentation time.
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Affiliation(s)
- Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Irina A Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Lev I Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elizaveta M Solovyeva
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anastasiya V Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
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18
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Baba T, Zhang Z, Liu S, Burton L, Ryumin P, Le Blanc JCY. Localization of Multiple O-Linked Glycans Exhibited in Isomeric Glycopeptides by Hot Electron Capture Dissociation. J Proteome Res 2022; 21:2462-2471. [PMID: 36074808 DOI: 10.1021/acs.jproteome.2c00378] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a method to obtain a comprehensive profile of multiple glycosylations in glycopeptide isoforms. We detected a wide range of abundances of various O-glycoforms in isomeric glycopeptides using hot electron capture dissociation (hot ECD) in liquid chromatography-tandem mass spectrometry. To capture low abundant glycosylated species, a prototype of a ZenoTOF 7600 system incorporating an efficient electron-activated dissociation device to perform hot ECD was operated in targeted or scheduled high-resolution multiple reaction monitoring workflows. In addition, Zeno trap pulsing was activated to enhance the sensitivity of the time-of-flight mass spectrometer. Sixty-nine O-glycopeptides of the long O-glycopeptides in tryptic bovine fetuin digest were obtained with a relative abundance range from 100 to 0.2%, which included sialylated glycans with Neu5Ac and Neu5Gc.
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Affiliation(s)
- Takashi Baba
- Sciex, 71 Four Valley Dr., Concord, Ontario L4K 4V8, Canada
| | - Zoe Zhang
- Sciex, 1201 Radio Rd., Redwood City, California 94065, United States
| | - Suya Liu
- Sciex, 71 Four Valley Dr., Concord, Ontario L4K 4V8, Canada
| | - Lyle Burton
- Sciex, 71 Four Valley Dr., Concord, Ontario L4K 4V8, Canada
| | - Pavel Ryumin
- Sciex, 71 Four Valley Dr., Concord, Ontario L4K 4V8, Canada
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19
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Clostridium novyi’s Alpha-Toxin Changes Proteome and Phosphoproteome of HEp-2 Cells. Int J Mol Sci 2022; 23:ijms23179939. [PMID: 36077344 PMCID: PMC9456407 DOI: 10.3390/ijms23179939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
C. novyi type A produces the alpha-toxin (TcnA) that belongs to the large clostridial glucosylating toxins (LCGTs) and is able to modify small GTPases by N-acetylglucosamination on conserved threonine residues. In contrast, other LCGTs including Clostridioides difficile toxin A and toxin B (TcdA; TcdB) modify small GTPases by mono-o-glucosylation. Both modifications inactivate the GTPases and cause strong effects on GTPase-dependent signal transduction pathways and the consequent reorganization of the actin cytoskeleton leading to cell rounding and finally cell death. However, the effect of TcnA on target cells is largely unexplored. Therefore, we performed a comprehensive screening approach of TcnA treated HEp-2 cells and analyzed their proteome and their phosphoproteome using LC-MS-based methods. With this data-dependent acquisition (DDA) approach, 5086 proteins and 9427 phosphosites could be identified and quantified. Of these, 35 proteins were found to be significantly altered after toxin treatment, and 1832 phosphosites were responsive to TcnA treatment. By analyzing the TcnA-induced proteomic effects of HEp-2 cells, 23 common signaling pathways were identified to be altered, including Actin Cytoskeleton Signaling, Epithelial Adherens Junction Signaling, and Signaling by Rho Family GTPases. All these pathways are also regulated after application of TcdA or TcdB of C. difficile. After TcnA treatment the regulation on phosphorylation level was much stronger compared to the proteome level, in terms of both strength of regulation and the number of regulated phosphosites. Interestingly, various signaling pathways such as Signaling by Rho Family GTPases or Integrin Signaling were activated on proteome level while being inhibited on phosphorylation level or vice versa as observed for the Role of BRCA1 in DNA Damage Response. ZIP kinase, as well as Calmodulin-dependent protein kinases IV & II, were observed as activated while Aurora-A kinase and CDK kinases tended to be inhibited in cells treated with TcnA based on their substrate regulation pattern.
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20
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Jeong K, Babović M, Gorshkov V, Kim J, Jensen ON, Kohlbacher O. FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts. Nat Commun 2022; 13:4407. [PMID: 35906205 PMCID: PMC9338294 DOI: 10.1038/s41467-022-31922-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
The detailed analysis and structural characterization of proteoforms by top-down proteomics (TDP) has gained a lot of interest in biomedical research. Data-dependent acquisition (DDA) of intact proteins is non-trivial due to the diversity and complexity of proteoforms. Dedicated acquisition methods thus have the potential to greatly improve TDP. Here, we present FLASHIda, an intelligent online data acquisition algorithm for TDP that ensures the real-time selection of high-quality precursors of diverse proteoforms. FLASHIda combines fast charge deconvolution algorithms and machine learning-based quality assessment for optimal precursor selection. In an analysis of E. coli lysate, FLASHIda increases the number of unique proteoform level identifications from 800 to 1500 or generates a near-identical number of identifications in one third of the instrument time when compared to standard DDA mode. Furthermore, FLASHIda enables sensitive mapping of post-translational modifications and detection of chemical adducts. As a software extension module to the instrument, FLASHIda can be readily adopted for TDP studies of complex samples to enhance proteoform identification rates.
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Affiliation(s)
- Kyowon Jeong
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
| | - Maša Babović
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Odense, Denmark
| | - Vladimir Gorshkov
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Odense, Denmark
| | - Jihyung Kim
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Sand 14, 72076, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Odense, Denmark
| | - Oliver Kohlbacher
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
- Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Str. 9, 72076, Tübingen, Germany.
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21
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Fasimoye RY, Spencer R, Soto-Martin E, Eijlers P, Elmassoudi H, Brivio S, Mangana C, Sabele V, Rechtorikova R, Wenzel M, Connolly B, Pettitt J, Müller B. A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex. Nucleic Acids Res 2022; 50:7591-7607. [PMID: 35736244 PMCID: PMC9303266 DOI: 10.1093/nar/gkac534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022] Open
Abstract
Spliced leader trans-splicing is essential for gene expression in many eukaryotes. To elucidate the molecular mechanism of this process, we characterise the molecules associated with the Caenorhabditis elegans major spliced leader snRNP (SL1 snRNP), which donates the spliced leader that replaces the 5' untranslated region of most pre-mRNAs. Using a GFP-tagged version of the SL1 snRNP protein SNA-1 created by CRISPR-mediated genome engineering, we immunoprecipitate and identify RNAs and protein components by RIP-Seq and mass spectrometry. This reveals the composition of the SL1 snRNP and identifies associations with spliceosome components PRP-8 and PRP-19. Significantly, we identify a novel, nematode-specific protein required for SL1 trans-splicing, which we designate SNA-3. SNA-3 is an essential, nuclear protein with three NADAR domains whose function is unknown. Mutation of key residues in NADAR domains inactivates the protein, indicating that domain function is required for activity. SNA-3 interacts with the CBC-ARS2 complex and other factors involved in RNA metabolism, including SUT-1 protein, through RNA or protein-mediated contacts revealed by yeast two-hybrid assays, localisation studies and immunoprecipitations. Our data are compatible with a role for SNA-3 in coordinating trans-splicing with target pre-mRNA transcription or in the processing of the Y-branch product of the trans-splicing reaction.
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Affiliation(s)
- Rotimi Yemi Fasimoye
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Rosie Elizabeth Barker Spencer
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Eva Soto-Martin
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Peter Eijlers
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Haitem Elmassoudi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Sarah Brivio
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Carolina Mangana
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Viktorija Sabele
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Radoslava Rechtorikova
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Marius Wenzel
- Centre of Genome-Enabled Biology and Medicine, University of Aberdeen, 23 St Machar Drive, Aberdeen AB24 3RY, Scotland, UK
| | - Bernadette Connolly
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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22
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Yan L, Yan N, Gao XY, Liu Y, Liu ZP. Degradation of amoxicillin by newly isolated Bosea sp. Ads-6. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154411. [PMID: 35288139 DOI: 10.1016/j.scitotenv.2022.154411] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/15/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Amoxicillin (AMX), one of the micro-amount hazardous pollutants, was frequently detected in environments, and of great risks to environments and human health. Microbial degradation is a promising method to eliminate pollutants. In this study, an efficient AMX-degrading strain, Ads-6, was isolated and characterized. Strain Ads-6, belonging to the genus Bosea, was also able to grow on AMX as the sole carbon and nitrogen source, with a removal of ~60% TOC. Ads-6 exhibited strong AMX-degrading ability at initial concentrations of 0.5-2 mM and pH 6-8. Addition of yeast extract could significantly enhance its degrading ability. Many degradation intermediates were identified by HPLC-MS, including new ones such as two phosphorylated products which were firstly defined in AMX degradation. A new AMX degradation pathway was proposed accordingly. Moreover, the results of comparative transcriptomes and proteomes revealed that β-lactamase, L, D-transpeptidase or its homologous enzymes were responsible for the initial degradation of AMX. Protocatechuate branch of the beta-ketoadipate pathway was confirmed as the downstream degradation pathway. These results in the study suggested that Ads-6 is great potential in biodegradation of antibiotics as well as in the bioremediation of contaminated environments.
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Affiliation(s)
- Lei Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Yan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xi-Yan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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23
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Gong S, Hu X, Chen S, Sun B, Wu JL, Li N. Dual roles of drug or its metabolite-protein conjugate: Cutting-edge strategy of drug discovery using shotgun proteomics. Med Res Rev 2022; 42:1704-1734. [PMID: 35638460 DOI: 10.1002/med.21889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 11/11/2022]
Abstract
Many drugs can bind directly to proteins or be bioactivated by metabolizing enzymes to form reactive metabolites (RMs) that rapidly bind to proteins to form drug-protein conjugates or metabolite-protein conjugates (DMPCs). The close relationship between DMPCs and idiosyncratic adverse drug reactions (IADRs) has been recognized; drug discovery teams tend to avoid covalent interactions in drug discovery projects. Covalent interactions in DMPCs can provide high potency and long action duration and conquer the intractable targets, inspiring drug design, and development. This forms the dual role feature of DMPCs. Understanding the functional implications of DMPCs in IADR control and therapeutic applications requires precise identification of these conjugates from complex biological samples. While classical biochemical methods have contributed significantly to DMPC detection in the past decades, the low abundance and low coverage of DMPCs have become a bottleneck in this field. An emerging transformation toward shotgun proteomics is on the rise. The evolving shotgun proteomics techniques offer improved reproducibility, throughput, specificity, operability, and standardization. Here, we review recent progress in the systematic discovery of DMPCs using shotgun proteomics. Furthermore, the applications of shotgun proteomics supporting drug development, toxicity mechanism investigation, and drug repurposing processes are also reviewed and prospected.
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Affiliation(s)
- Shilin Gong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Xiaolan Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Shengshuang Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Respiratory Medical Center, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
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24
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Fortuin S, Soares NC. The Integration of Proteomics and Metabolomics Data Paving the Way for a Better Understanding of the Mechanisms Underlying Microbial Acquired Drug Resistance. Front Med (Lausanne) 2022; 9:849838. [PMID: 35602483 PMCID: PMC9120609 DOI: 10.3389/fmed.2022.849838] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Due to an increase in the overuse of antimicrobials and accelerated incidence of drug resistant pathogens, antimicrobial resistance has become a global health threat. In particular, bacterial antimicrobial resistance, in both hospital and community acquired transmission, have been found to be the leading cause of death due to infectious diseases. Understanding the mechanisms of bacterial drug resistance is of clinical significance irrespective of hospital or community acquired since it plays an important role in the treatment strategy and controlling infectious diseases. Here we highlight the advances in mass spectrometry-based proteomics impact in bacterial proteomics and metabolomics analysis- focus on bacterial drug resistance. Advances in omics technologies over the last few decades now allows multi-omics studies in order to obtain a comprehensive understanding of the biochemical alterations of pathogenic bacteria in the context of antibiotic exposure, identify novel biomarkers to develop new drug targets, develop time-effectively screen for drug susceptibility or resistance using proteomics and metabolomics.
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Affiliation(s)
- Suereta Fortuin
- African Microbiome Institute, General Internal Medicine, Stellenbosch University, Cape Town, South Africa
- *Correspondence: Suereta Fortuin
| | - Nelson C. Soares
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Nelson C. Soares
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25
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Lorenzo-Pouso AI, Bravo SB, Carballo J, Del Pilar Chantada-Vázquez M, Bagán J, Bagán L, Chamorro-Petronacci CM, Conde-Amboage M, López-López R, García-García A, Pérez-Sayáns M. Quantitative proteomics in medication-related osteonecrosis of the jaw: a proof-of-concept study. Oral Dis 2022. [PMID: 35377498 DOI: 10.1111/odi.14201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/23/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Medication-related osteonecrosis of the jaw (MRONJ) is a paradoxical effect associated with bone modifying agents (BMAs) and other drugs. Currently no valuable diagnostic or prognosis biomarkers exist. This goal of this research was to study MRONJ related salivary proteome. MATERIALS AND METHODS This case-control aimed to study salivary proteome in MRONJ versus control groups i) formed from BMAs consumers and ii) healthy individuals to unravel biomarkers. 38 samples of unstimulated whole saliva (18 MRONJ patients, 10 BMA consumers, and 10 healthy controls) were collected. Proteomic analysis by SWATH-MS coupled to bioinformatics analysis was executed. RESULTS 586 proteins were identified, 175 proteins showed significant differences among MRONJ versus controls. SWATH-MS revealed differentially expressed proteins among three groups, which have never isolated. These proteins had distinct roles including cell envelope organization, positive regulation of vesicle fusion, positive regulation of receptor binding, or regulation of low-density lipoprotein particle clearance. Integrative analysis prioritised 3 proteins (MMP9, AACT and HBD). Under receiver operating characteristic analysis, this panel discriminated MRONJ with a sensitivity of 90% and a specificity of 78.9%. CONCLUSION These findings may inform of a novel biomarker panel for MRONJ prediction or diagnosis. Nonetheless, further research is needed to validate this panel.
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Affiliation(s)
- Alejandro I Lorenzo-Pouso
- Oral Medicine, Oral Surgery and Implantology Unit, MedOralRes Group, University of Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Spain
| | - Susana B Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Spain
| | - Javier Carballo
- Department of Food Technology, Faculty of Sciences, University of Vigo-Ourense Campus, Spain
| | - María Del Pilar Chantada-Vázquez
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Spain
| | - José Bagán
- Department of Stomatology and Maxillofacial Surgery, University General Hospital of Valencia, Spain
| | - Leticia Bagán
- Department of Stomatology and Maxillofacial Surgery, University General Hospital of Valencia, Spain
| | - Cintia M Chamorro-Petronacci
- Oral Medicine, Oral Surgery and Implantology Unit, MedOralRes Group, University of Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Spain
| | - Mercedes Conde-Amboage
- Models of Optimization, Decision, Statistics and Applications Reseach Group (MODESTYA), Department of Statistics, Mathematical Analysis and Optimization, University of Santiago de Compostela, Spain
| | - Rafael López-López
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Hospital Complex of Santiago de Compostela (SERGAS), Spain
| | - Abel García-García
- Oral Medicine, Oral Surgery and Implantology Unit, MedOralRes Group, University of Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Spain
| | - Mario Pérez-Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit, MedOralRes Group, University of Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Spain
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26
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Lin Z, Wang L, Chen M, Zheng X, Chen J. Proteome and microbiota analyses characterizing dynamic coral-algae-microbe tripartite interactions under simulated rapid ocean acidification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152266. [PMID: 34896508 DOI: 10.1016/j.scitotenv.2021.152266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/29/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Ocean acidification (OA) is a pressing issue currently and in the future for coral reefs. The importance of maintenance interactions among partners of the holobiont association in the stress response is well appreciated; however, the candidate molecular and microbial mechanisms that underlie holobiont stress resilience or susceptibility remain unclear. Here, to assess the effects of rapid pH change on coral holobionts at both the protein and microbe levels, combined proteomics and microbiota analyses of the scleractinian coral Galaxea fascicularis exposed to three relevant OA scenarios, including current (pHT = 8.15), preindustrial (pHT = 8.45) and future IPCC-2100 scenarios (pHT = 7.85), were conducted. The results demonstrated that pH changes had no significant effect on the physiological calcification rate of G. fascicularis in a 10-day experiment; however, significant differences were recorded in the proteome and 16S profiling. Proteome variance analysis identified some of the core biological pathways in coral holobionts, including coral host infection and immune defence, and maintaining metabolic compatibility involved in energy homeostasis, nutrient cycling, antibiotic activity and carbon budgets of coral-Symbiodiniaceae interactions were key mechanisms in the early OA stress response. Furthermore, microbiota changes indicate substantial microbial community and functional disturbances in response to OA stress, potentially compromising holobiont health and fitness. Our results may help to elucidate many complex mechanisms to describe scleractinian coral holobiont responses to OA and raise interesting questions for future studies.
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Affiliation(s)
- Zhenyue Lin
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China.
| | - Liuying Wang
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Mingliang Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China.
| | - Xinqing Zheng
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian 361005, China
| | - Jianming Chen
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China.
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27
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Ravuri HG, Noor Z, Mills PC, Satake N, Sadowski P. Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma. Proteomes 2022; 10:9. [PMID: 35324581 PMCID: PMC8953371 DOI: 10.3390/proteomes10010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 02/22/2022] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry-based plasma proteomics offers a major advance for biomarker discovery in the veterinary field, which has traditionally been limited to quantification of a small number of proteins using biochemical assays. The development of foundational data and tools related to sequential window acquisition of all theoretical mass spectra (SWATH)-mass spectrometry has allowed for quantitative profiling of a significant number of plasma proteins in humans and several animal species. Enabling SWATH in dogs enhances human biomedical research as a model species, and significantly improves diagnostic and disease monitoring capability. In this study, a comprehensive peptide spectral library specific to canine plasma proteome was developed and evaluated using SWATH for protein quantification in non-depleted dog plasma. Specifically, plasma samples were subjected to various orthogonal fractionation and digestion techniques, and peptide fragmentation data corresponding to over 420 proteins was collected. Subsequently, a SWATH-based assay was introduced that leveraged the developed resource and that enabled reproducible quantification of 400 proteins in non-depleted plasma samples corresponding to various disease conditions. The ability to profile the abundance of such a significant number of plasma proteins using a single method in dogs has the potential to accelerate biomarker discovery studies in this species.
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Affiliation(s)
- Halley Gora Ravuri
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (H.G.R.); (P.C.M.)
| | - Zainab Noor
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia;
| | - Paul C. Mills
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (H.G.R.); (P.C.M.)
| | - Nana Satake
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (H.G.R.); (P.C.M.)
| | - Pawel Sadowski
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD 4000, Australia
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28
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Casado P, Hijazi M, Gerdes H, Cutillas PR. Implementation of Clinical Phosphoproteomics and Proteomics for Personalized Medicine. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:87-106. [PMID: 34905168 DOI: 10.1007/978-1-0716-1936-0_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The identification of biomarkers for companion diagnostics is revolutionizing the development of treatments tailored to individual patients in different disease areas including cancer. Precision medicine is most frequently based on the detection of genomic markers that correlate with the efficacy of selected targeted therapies. However, since nongenetic mechanisms also contribute to disease biology, there is a considerable interest of using proteomic techniques as additional source of biomarkers to personalize therapies. In this chapter, we describe label-free mass spectrometry methods for proteomic and phosphoproteomic analysis compatible with routine analysis of clinical samples. We also outline bioinformatic pipelines based on statistical learning that use these proteomics datasets as input to quantify kinase activities and predict drug responses in cancer cells.
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Affiliation(s)
- Pedro Casado
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Maruan Hijazi
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Henry Gerdes
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Pedro R Cutillas
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK.
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29
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Nättinen J, Aapola U, Nukareddy P, Uusitalo H. Looking deeper into ocular surface health: an introduction to clinical tear proteomics analysis. Acta Ophthalmol 2021; 100:486-498. [PMID: 34750985 DOI: 10.1111/aos.15059] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022]
Abstract
Ocular surface diseases are becoming more prevalent worldwide. Reasons for this include the ongoing population ageing and increasing use of digital displays, although ophthalmologists have a wide selection of tools, which can be implemented in the evaluation of the ocular surface health, methods, which enable the in-depth study of biological functions are gaining more interest. These new approaches are needed, since the individual responses to ocular surface diseases and treatments can vary from person to person, and the correlations between clinical signs and symptoms are often low. Modern mass spectrometry (MS) methods can produce information on hundreds of tear proteins, which in turn can provide valuable information on the biological effects occurring on the ocular surface. In this review article, we will provide an overview of the different aspects, which are part of a successful tear proteomics study design and equip readers with a better understanding of the methods most suited for their MS-based tear proteomics study in the field of ophthalmology and ocular surface.
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Affiliation(s)
- Janika Nättinen
- SILK Department of Ophthalmology Faculty of Medicine and Health Technology Tampere University Tampere Finland
| | - Ulla Aapola
- SILK Department of Ophthalmology Faculty of Medicine and Health Technology Tampere University Tampere Finland
| | - Praveena Nukareddy
- SILK Department of Ophthalmology Faculty of Medicine and Health Technology Tampere University Tampere Finland
| | - Hannu Uusitalo
- SILK Department of Ophthalmology Faculty of Medicine and Health Technology Tampere University Tampere Finland
- Tays Eye Centre Tampere University Hospital Tampere Finland
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30
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Liu W, Cheng X, Kang R, Wang Y, Guo X, Jing W, Wei F, Ma S. Systematic Characterization and Identification of Saikosaponins in Extracts From Bupleurum marginatum var. stenophyllum Using UPLC-PDA-Q/TOF-MS. Front Chem 2021; 9:747987. [PMID: 34660539 PMCID: PMC8514958 DOI: 10.3389/fchem.2021.747987] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Saikosaponins comprise a large group of chemical components present in the Bupleurum species that have attracted attention in the field of medicine because of their significant biological activities. Due to the high polarity, structural similarity, and the presence of several isomers of this class of components, their structural identification is extremely challenging. In this study, the mass spectrometric fragmentation pathways, UV spectral features, and chromatographic behavior of different types of saikosaponins were investigated using 24 standard substances. Saikosaponins containing carbonyl groups (C=O) in the aglycone produced fragment ions by loss of 30 Da, and in addition, type IV saikosaponins could produce [aglycone−CH2OH−OH−H]− and [aglycone−H2O−H]− fragment ions through neutral losses at positions C16 and C17. The above characteristic ions can be used to identify saikosaponins. More notably, the identification process of saikosaponins was systematically summarized, and using this method, 109 saikosaponins were identified or tentatively characterized from the saikosaponins extract of Bupleurum marginatum var. stenophyllum (BMS) using UPLC-PDA-Q/TOF-MS with both data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes, of which 25 were new compounds and 60 were first discovered from BMS. Further studies revealed that the saikosaponins profiles of BMS, Bupleurum chinense DC (BC), and Bupleurum marginatum Wall. ex DC (BMW) were very similar. This work is of great significance for the basic research of the Bupleurum species and provides strong technical support to solve the resource problems associated with Radix Bupleuri.
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Affiliation(s)
- Wenxi Liu
- Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Xianlong Cheng
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Rong Kang
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Yadan Wang
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Xiaohan Guo
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Wenguang Jing
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Feng Wei
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Shuangcheng Ma
- Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
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31
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Das B, Saviola AJ, Mukherjee AK. Biochemical and Proteomic Characterization, and Pharmacological Insights of Indian Red Scorpion Venom Toxins. Front Pharmacol 2021; 12:710680. [PMID: 34650430 PMCID: PMC8505525 DOI: 10.3389/fphar.2021.710680] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/16/2021] [Indexed: 12/16/2022] Open
Abstract
The Indian red scorpion (Mesobuthus tamulus) is one of the world's deadliest scorpions, with stings representing a life-threatening medical emergency. This species is distributed throughout the Indian sub-continent, including eastern Pakistan, eastern Nepal, and Sri Lanka. In India, Indian red scorpions are broadly distributed in western Maharashtra, Saurashtra, Kerala, Andhra Pradesh, Tamil Nadu, and Karnataka; however, fatal envenomations have been recorded primarily in the Konkan region of Maharashtra. The Indian red scorpion venom proteome comprises 110 proteins belonging to 13 venom protein families. The significant pharmacological activity is predominantly caused by the low molecular mass non-enzymatic Na+ and K+ ion channel toxins. Other minor toxins comprise 15.6% of the total venom proteome. Indian red scorpion stings induce the release of catecholamine, which leads to pathophysiological abnormalities in the victim. A strong correlation has been observed between venom proteome composition and local (swelling, redness, heat, and regional lymph node involvement) and systemic (tachycardia, mydriasis, hyperglycemia, hypertension, toxic myocarditis, cardiac failure, and pulmonary edema) manifestations. Immediate administration of antivenom is the preferred treatment for Indian red scorpion stings. However, scorpion-specific antivenoms have exhibited poor immunorecognition and neutralization of the low molecular mass toxins. The proteomic analysis also suggests that Indian red scorpion venom is a rich source of pharmacologically active molecules that may be envisaged as drug prototypes. The following review summarizes the progress made towards understanding the venom proteome of the Indian red scorpion and addresses the current understanding of the pathophysiology associated with its sting.
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Affiliation(s)
- Bhabana Das
- Department of Molecular Biology and Biotechnology, School of Sciences, Tezpur University, Tezpur, India
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ashis K. Mukherjee
- Department of Molecular Biology and Biotechnology, School of Sciences, Tezpur University, Tezpur, India
- Institute of Advanced Study in Science and Technology, Guwahati, India
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32
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Bahmani M, O’Lone CE, Juhász A, Nye-Wood M, Dunn H, Edwards IB, Colgrave ML. Application of Mass Spectrometry-Based Proteomics to Barley Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8591-8609. [PMID: 34319719 PMCID: PMC8389776 DOI: 10.1021/acs.jafc.1c01871] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Barley (Hordeum vulgare) is the fourth most cultivated crop in the world in terms of production volume, and it is also the most important raw material of the malting and brewing industries. Barley belongs to the grass (Poaceae) family and plays an important role in food security and food safety for both humans and livestock. With the global population set to reach 9.7 billion by 2050, but with less available and/or suitable land for agriculture, the use of biotechnology tools in breeding programs are of considerable importance in the quest to meet the growing food gap. Proteomics as a member of the "omics" technologies has become popular for the investigation of proteins in cereal crops and particularly barley and its related products such as malt and beer. This technology has been applied to study how proteins in barley respond to adverse environmental conditions including abiotic and/or biotic stresses, how they are impacted during food processing including malting and brewing, and the presence of proteins implicated in celiac disease. Moreover, proteomics can be used in the future to inform breeding programs that aim to enhance the nutritional value and broaden the application of this crop in new food and beverage products. Mass spectrometry analysis is a valuable tool that, along with genomics and transcriptomics, can inform plant breeding strategies that aim to produce superior barley varieties. In this review, recent studies employing both qualitative and quantitative mass spectrometry approaches are explored with a focus on their application in cultivation, manufacturing, processing, quality, and the safety of barley and its related products.
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Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Clare E. O’Lone
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Mitchell Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Hugh Dunn
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Ian B. Edwards
- Edstar
Genetics Pty Ltd, SABC - Loneragan Building, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
- Phone: +61-7-3214-2697. . Fax: +61-7-3214-2900
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33
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Borotto NB, Graham KA. Fragmentation and Mobility Separation of Peptide and Protein Ions in a Trapped-Ion Mobility Device. Anal Chem 2021; 93:9959-9964. [PMID: 34258993 DOI: 10.1021/acs.analchem.1c01188] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ion mobility separations (IMS) have increasingly been coupled with mass spectrometry to increase peak capacity and deconvolute complex mass spectra in proteomics workflows. IMS separations can be integrated prior to or following the collisional activation step. Post-activation IMS separations have demonstrated many advantages, yet few instrument platforms are capable of this feat. Here, we present the fragmentation of peptide ions within a commercially available trapped-ion mobility spectrometry device. Fragmentation is initiated prior to mobility analysis enabling the separation of generated product ions. The added separation step deconvolutes product ion spectra and permits improved annotation of product ions. Furthermore, we demonstrate the isolation and fragmentation of mobility separated product ions with the downstream quadrupole and collisional cell. When applied to melittin and ubiquitin, this ion mobility assisted pseudo-MS3 fragmentation approach generates sequence coverage ∼50% greater than that of typical MS2 analyses. We envision this ion-mobility-assisted fragmentation technique as the foundation of a powerful new pseudo-MS3 workflow for application toward middle- or top-down proteomics.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Katherine A Graham
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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34
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Rozanova S, Barkovits K, Nikolov M, Schmidt C, Urlaub H, Marcus K. Quantitative Mass Spectrometry-Based Proteomics: An Overview. Methods Mol Biol 2021; 2228:85-116. [PMID: 33950486 DOI: 10.1007/978-1-0716-1024-4_8] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent decades, mass spectrometry has moved more than ever before into the front line of protein-centered research. After being established at the qualitative level, the more challenging question of quantification of proteins and peptides using mass spectrometry has become a focus for further development. In this chapter, we discuss and review actual strategies and problems of the methods for the quantitative analysis of peptides, proteins, and finally proteomes by mass spectrometry. The common themes, the differences, and the potential pitfalls of the main approaches are presented in order to provide a survey of the emerging field of quantitative, mass spectrometry-based proteomics.
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Affiliation(s)
- Svitlana Rozanova
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Miroslav Nikolov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.,Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany.,Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany. .,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany.
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35
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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36
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Identification of potential peptide markers for the shelf-life of Pacific oysters (Crassostrea gigas) during anhydrous preservation via mass spectrometry-based peptidomics. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109922] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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37
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Xuan Y, Bateman NW, Gallien S, Goetze S, Zhou Y, Navarro P, Hu M, Parikh N, Hood BL, Conrads KA, Loosse C, Kitata RB, Piersma SR, Chiasserini D, Zhu H, Hou G, Tahir M, Macklin A, Khoo A, Sun X, Crossett B, Sickmann A, Chen YJ, Jimenez CR, Zhou H, Liu S, Larsen MR, Kislinger T, Chen Z, Parker BL, Cordwell SJ, Wollscheid B, Conrads TP. Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies. Nat Commun 2020; 11:5248. [PMID: 33067419 PMCID: PMC7568553 DOI: 10.1038/s41467-020-18904-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/16/2020] [Indexed: 02/02/2023] Open
Abstract
Cancer has no borders: Generation and analysis of molecular data across multiple centers worldwide is necessary to gain statistically significant clinical insights for the benefit of patients. Here we conceived and standardized a proteotype data generation and analysis workflow enabling distributed data generation and evaluated the quantitative data generated across laboratories of the international Cancer Moonshot consortium. Using harmonized mass spectrometry (MS) instrument platforms and standardized data acquisition procedures, we demonstrate robust, sensitive, and reproducible data generation across eleven international sites on seven consecutive days in a 24/7 operation mode. The data presented from the high-resolution MS1-based quantitative data-independent acquisition (HRMS1-DIA) workflow shows that coordinated proteotype data acquisition is feasible from clinical specimens using such standardized strategies. This work paves the way for the distributed multi-omic digitization of large clinical specimen cohorts across multiple sites as a prerequisite for turning molecular precision medicine into reality.
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Affiliation(s)
- Yue Xuan
- Thermo Fisher Scientific GmbH, Hanna-Kunath Str. 11, Bremen, 28199, Germany.
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, 20889, MD, USA
| | - Sebastien Gallien
- Thermo Fisher Scientific, Paris, France.,Thermo Fisher Scientific, Precision Medicine Science Center, Cambridge, MA, USA
| | - Sandra Goetze
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yue Zhou
- Thermo Fisher Scientific Co. Ltd, Shanghai, China
| | - Pedro Navarro
- Thermo Fisher Scientific GmbH, Hanna-Kunath Str. 11, Bremen, 28199, Germany
| | - Mo Hu
- Thermo Fisher Scientific Co. Ltd, Shanghai, China
| | - Niyati Parikh
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, 20889, MD, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, 20889, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, 20889, MD, USA
| | - Christina Loosse
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
| | - Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Sander R Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Davide Chiasserini
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.,Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Hongwen Zhu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Guixue Hou
- BGI-SHENZHEN, Beishan Road, Yantian District, Shenzhen, 518083, Guangdong, China
| | - Muhammad Tahir
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK-5230, Denmark
| | - Andrew Macklin
- Princess Margaret Cancer Centre, 101 College Street PMCRT 9-807, Toronto, ON, M5G 1L7, Canada
| | - Amanda Khoo
- Princess Margaret Cancer Centre, 101 College Street PMCRT 9-807, Toronto, ON, M5G 1L7, Canada
| | - Xiuxuan Sun
- National Translational Science Center for Molecular Medicine, Xi'an, 710032, China.,Department of Cell Biology, School of Basic Medicine, Air Force Medical University, Xi'an, 710032, China
| | - Ben Crossett
- Sydney Mass Spectrometry, The University of Sydney, NSW, 2006, Sydney, Australia
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany.,Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, 44801, Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, AB243FX, Scotland, UK
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Connie R Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Hu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Siqi Liu
- BGI-SHENZHEN, Beishan Road, Yantian District, Shenzhen, 518083, Guangdong, China
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK-5230, Denmark
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, 101 College Street PMCRT 9-807, Toronto, ON, M5G 1L7, Canada
| | - Zhinan Chen
- National Translational Science Center for Molecular Medicine, Xi'an, 710032, China.,Department of Cell Biology, School of Basic Medicine, Air Force Medical University, Xi'an, 710032, China
| | - Benjamin L Parker
- School of Life and Environmental Science, The University of Sydney, NSW, 2006, Sydney, Australia
| | - Stuart J Cordwell
- School of Life and Environmental Science, The University of Sydney, NSW, 2006, Sydney, Australia
| | - Bernd Wollscheid
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, 3289 Woodburn Bldg, Annandale, VA, 22003, USA.
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38
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Sebald K, Dunkel A, Hofmann T. Mapping Taste-Relevant Food Peptidomes by Means of Sequential Window Acquisition of All Theoretical Fragment Ion-Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10287-10298. [PMID: 31508943 DOI: 10.1021/acs.jafc.9b04581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
During the last few years, key taste-active compounds have been isolated and identified by means of a combination of a time- and lab-consuming successive fractionation and sensory characterization. Because the peptidome of fermented, protein-rich food is very complex, new strategies are necessary to accelerate the identification of taste-active peptides. In this study, two advanced mass spectrometric approaches were developed to comprehensively map the bitter tasting peptidome of fermented foods by data-independent acquisition (DIA) using sequential window acquisition of all theoretical fragment ion-mass spectrometry (SWATH-MS) and an in silico-assisted triple quadrupole (QQQ)-based targeted proteomics approach, separately. Application of both techniques on two fresh cheese samples as well as on crude medium-pressure liquid chromatography fractions exhibiting intense bitter taste, followed by filtering the hydrophobic target peptides (Q value of ≥1200 cal/mol) showing a signal-to-noise ratio of ≥10 and a fold change of ≥3 when comparing the less bitter to the more bitter cheese sample, revealed the candidate bitter peptides, which were then validated by means of synthetic reference peptides and human sensory evaluation. The bitter peptides were then quantitated in the fresh cheese samples as well as in a series of dairy products by means of QQQ-MS and SWATH-MS, separately. Although the QQQ-MS method showed 2-80-fold lower limits of quantitation (LOQ), the SWATH-MS method could be shown for the first time to enable the comprehensive quantitation of all sensorially relevant key bitter peptides with LOQs far below the bitter taste recognition concentration of each peptide.
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Affiliation(s)
- Karin Sebald
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner Straße 34, D-85354 Freising, Germany
| | - Andreas Dunkel
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner Straße 34, D-85354 Freising, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner Straße 34, D-85354 Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner Straße 34, D-85354 Freising, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner Straße 34, D-85354 Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel Straße 4, D-85354 Freising, Germany
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39
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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40
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A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of this Field. Proteomes 2020; 8:proteomes8030014. [PMID: 32640657 PMCID: PMC7564415 DOI: 10.3390/proteomes8030014] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023] Open
Abstract
Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future.
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41
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Martano G, Leone M, D'Oro P, Matafora V, Cattaneo A, Masseroli M, Bachi A. SMfinder: Small Molecules Finder for Metabolomics and Lipidomics Analysis. Anal Chem 2020; 92:8874-8882. [PMID: 32501676 DOI: 10.1021/acs.analchem.0c00585] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Metabolomics and lipidomics studies are becoming increasingly popular but available tools for automated data analysis are still limited. The major issue in untargeted metabolomics is linked to the lack of efficient ranking methods allowing accurate identification of metabolites. Herein, we provide a user-friendly open-source software, named SMfinder, for the robust identification and quantification of small molecules. The software introduces an MS2 false discovery rate approach, which is based on single spectral permutation and increases identification accuracy. SMfinder can be efficiently applied to shotgun and targeted analysis in metabolomics and lipidomics without requiring extensive in-house acquisition of standards as it provides accurate identification by using available MS2 libraries in instrument independent manner. The software, downloadable at www.ifom.eu/SMfinder, is suitable for untargeted, targeted, and flux analysis.
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Affiliation(s)
- Giuseppe Martano
- IFOM, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Michele Leone
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20129 Milan, Italy
| | - Pierluca D'Oro
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20129 Milan, Italy
| | | | - Angela Cattaneo
- IFOM, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Marco Masseroli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20129 Milan, Italy
| | - Angela Bachi
- IFOM, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy
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42
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Guan S, Taylor PP, Han Z, Moran MF, Ma B. Data Dependent-Independent Acquisition (DDIA) Proteomics. J Proteome Res 2020; 19:3230-3237. [PMID: 32539411 DOI: 10.1021/acs.jproteome.0c00186] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Data dependent acquisition (DDA) and data independent acquisition (DIA) are traditionally separate experimental paradigms in bottom-up proteomics. In this work, we developed a strategy combining the two experimental methods into a single LC-MS/MS run. We call the novel strategy data dependent-independent acquisition proteomics, or DDIA for short. Peptides identified from DDA scans by a conventional and robust DDA identification workflow provide useful information for interrogation of DIA scans. Deep learning based LC-MS/MS property prediction tools, developed previously, can be used repeatedly to produce spectral libraries facilitating DIA scan extraction. A complete DDIA data processing pipeline, including the modules for iRT vs RT calibration curve generation, DIA extraction classifier training, and false discovery rate control, has been developed. Compared to another spectral library-free method, DIA-Umpire, the DDIA method produced a similar number of peptide identifications, but nearly twice as many protein group identifications. The primary advantage of the DDIA method is that it requires minimal information for processing its data.
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Affiliation(s)
- Shenheng Guan
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Program in Cell Biology and SPARC BioCentre, Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - Paul P Taylor
- Rapid Novor Inc., Unit 450, 137 Glasgow Street, Kitchener, Ontario N2G 4X8, Canada
| | - Ziwei Han
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Michael F Moran
- Program in Cell Biology and SPARC BioCentre, Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - Bin Ma
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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43
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Hijazi M, Smith R, Rajeeve V, Bessant C, Cutillas PR. Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring. Nat Biotechnol 2020; 38:493-502. [PMID: 31959955 DOI: 10.1038/s41587-019-0391-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
Abstract
Understanding how oncogenic mutations rewire regulatory-protein networks is important for rationalizing the mechanisms of oncogenesis and for individualizing anticancer treatments. We report a chemical phosphoproteomics method to elucidate the topology of kinase-signaling networks in mammalian cells. We identified >6,000 protein phosphorylation sites that can be used to infer >1,500 kinase-kinase interactions and devised algorithms that can reconstruct kinase network topologies from these phosphoproteomics data. Application of our methods to primary acute myeloid leukemia and breast cancer tumors quantified the relationship between kinase expression and activity, and enabled the identification of hitherto unknown kinase network topologies associated with drug-resistant phenotypes or specific genetic mutations. Using orthogonal methods we validated that PIK3CA wild-type cells adopt MAPK-dependent circuitries in breast cancer cells and that the kinase TTK is important in acute myeloid leukemia. Our phosphoproteomic signatures of network circuitry can identify kinase topologies associated with both phenotypes and genotypes of cancer cells.
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Affiliation(s)
- Maruan Hijazi
- Signalling and Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ryan Smith
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Vinothini Rajeeve
- Signalling and Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Conrad Bessant
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- The Alan Turing Institute, British Library, London, UK
| | - Pedro R Cutillas
- Signalling and Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, UK.
- The Alan Turing Institute, British Library, London, UK.
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44
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Yee WLS, Drum CL. Increasing Complexity to Simplify Clinical Care: High Resolution Mass Spectrometry as an Enabler of AI Guided Clinical and Therapeutic Monitoring. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wei Loong Sherman Yee
- Yong Loo Lin School of MedicineDepartment of MedicineNational University of Singapore Singapore 119077 Singapore
- Cardiovascular Research Institute (CVRI)National University Health System Singapore 119228 Singapore
| | - Chester Lee Drum
- Yong Loo Lin School of MedicineDepartment of MedicineNational University of Singapore Singapore 119077 Singapore
- Cardiovascular Research Institute (CVRI)National University Health System Singapore 119228 Singapore
- Yong Loo Lin School of MedicineDepartment of BiochemistryNational University of Singapore Singapore 119077 Singapore
- The N.1 Institute for Health (N.1)National University of Singapore Singapore 119077 Singapore
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45
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Ang MY, Low TY, Lee PY, Wan Mohamad Nazarie WF, Guryev V, Jamal R. Proteogenomics: From next-generation sequencing (NGS) and mass spectrometry-based proteomics to precision medicine. Clin Chim Acta 2019; 498:38-46. [DOI: 10.1016/j.cca.2019.08.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022]
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46
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Developing Well-Annotated Species-Specific Protein Databases Using Comparative Proteogenomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:389-400. [PMID: 31347060 DOI: 10.1007/978-3-030-15950-4_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proteomics is a mass spectrometry-based discipline that aims to analyze proteomes and their functions. Many proteomic studies require well-developed protein databases for reference. However, most proteomes are not well-annotated, aside from model organisms. Techniques like six-frame translation, ab initio gene prediction, and EST databases can aid in maximizing the amount of proteins identified in proteomics experiments, however, each of these has its downfalls. Proteogenomics is a term used to describe the union of proteomics, genomics and transcriptomics to assist in the identification of peptides which would help build better annotated proteome databases. Here, current proteomic and proteogenomic methods will be reviewed, and an example of a comparative proteomics method using lake trout liver samples will be described.
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47
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Chu F, Mason KE, Anex DS, Jones AD, Hart BR. Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification. Sci Rep 2019; 9:7641. [PMID: 31113963 PMCID: PMC6529471 DOI: 10.1038/s41598-019-44007-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/16/2019] [Indexed: 11/10/2022] Open
Abstract
Human hair contains minimal intact nuclear DNA for human identification in forensic and archaeological applications. In contrast, proteins offer a pathway to exploit hair evidence for human identification owing to their persistence, abundance, and derivation from DNA. Individualizing single nucleotide polymorphisms (SNPs) are often conserved as single amino acid polymorphisms in genetically variant peptides (GVPs). Detection of GVP markers in the hair proteome via high-resolution tandem mass spectrometry permits inference of SNPs with known statistical probabilities. To adopt this approach for forensic investigations, hair proteomic variation and its effects on GVP identification must first be characterized. This research aimed to assess variation in single-inch head, arm, and pubic hair, and discover body location-invariant GVP markers to distinguish individuals. Comparison of protein profiles revealed greater body location-specific variation in keratin-associated proteins and intracellular proteins, allowing body location differentiation. However, robust GVP markers derive primarily from keratins that do not exhibit body location-specific differential expression, supporting GVP identification independence from hair proteomic variation at the various body locations. Further, pairwise comparisons of GVP profiles with 8 SNPs demonstrated greatest interindividual variation and high intraindividual consistency, enabling similar differentiative potential of individuals using single hairs irrespective of body location origin.
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Affiliation(s)
- Fanny Chu
- Forensic Science Center, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550, USA.,Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA
| | - Katelyn E Mason
- Forensic Science Center, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550, USA
| | - Deon S Anex
- Forensic Science Center, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550, USA.
| | - A Daniel Jones
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI, 48824, USA
| | - Bradley R Hart
- Forensic Science Center, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550, USA
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48
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An Y, Zhou L, Huang Z, Nice EC, Zhang H, Huang C. Molecular insights into cancer drug resistance from a proteomics perspective. Expert Rev Proteomics 2019; 16:413-429. [PMID: 30925852 DOI: 10.1080/14789450.2019.1601561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Resistance to chemotherapy and development of specific and effective molecular targeted therapies are major obstacles facing current cancer treatment. Comparative proteomic approaches have been employed for the discovery of putative biomarkers associated with cancer drug resistance and have yielded a number of candidate proteins, showing great promise for both novel drug target identification and personalized medicine for the treatment of drug-resistant cancer. Areas covered: Herein, we review the recent advances and challenges in proteomics studies on cancer drug resistance with an emphasis on biomarker discovery, as well as understanding the interconnectivity of proteins in disease-related signaling pathways. In addition, we highlight the critical role that post-translational modifications (PTMs) play in the mechanisms of cancer drug resistance. Expert opinion: Revealing changes in proteome profiles and the role of PTMs in drug-resistant cancer is key to deciphering the mechanisms of treatment resistance. With the development of sensitive and specific mass spectrometry (MS)-based proteomics and related technologies, it is now possible to investigate in depth potential biomarkers and the molecular mechanisms of cancer drug resistance, assisting the development of individualized therapeutic strategies for cancer patients.
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Affiliation(s)
- Yao An
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Li Zhou
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Zhao Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Edouard C Nice
- c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Canhua Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
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49
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Wu X, Xing X, Dowlut D, Zeng Y, Liu J, Liu X. Integrating phosphoproteomics into kinase-targeted cancer therapies in precision medicine. J Proteomics 2019; 191:68-79. [DOI: 10.1016/j.jprot.2018.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/20/2018] [Accepted: 03/31/2018] [Indexed: 12/12/2022]
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50
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Doblmann J, Dusberger F, Imre R, Hudecz O, Stanek F, Mechtler K, Dürnberger G. apQuant: Accurate Label-Free Quantification by Quality Filtering. J Proteome Res 2018; 18:535-541. [PMID: 30351950 DOI: 10.1021/acs.jproteome.8b00113] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results. We employ Percolator to assess the quality of quantified peptides. This allows to extract accurate and reliable quantitative results based on false discovery rate. Benchmarking our approach on previously published public data shows that it considerably outperforms currently available algorithms. apQuant is available free of charge as a node for Proteome Discoverer.
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Affiliation(s)
- Johannes Doblmann
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria
| | - Frederico Dusberger
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria
| | - Richard Imre
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Otto Hudecz
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Florian Stanek
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Gerhard Dürnberger
- Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria.,Gregor Mendel Institute of Molecular Plant Biology (GMI) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
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