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Graham RLJ, McMullen AA, Moore G, Dempsey-Hibbert NC, Myers B, Graham C. SWATH-MS identification of CXCL7, LBP, TGFβ1 and PDGFRβ as novel biomarkers in human systemic mastocytosis. Sci Rep 2022; 12:5087. [PMID: 35332176 PMCID: PMC8948255 DOI: 10.1038/s41598-022-08345-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/07/2022] [Indexed: 12/11/2022] Open
Abstract
Mastocytosis is a rare myeloproliferative disease, characterised by accumulation of neoplastic mast cells in one or several organs. It presents as cutaneous or systemic. Patients with advanced systemic mastocytosis have a median survival of 3.5 years. The aetiology of mastocytosis is poorly understood, patients present with a broad spectrum of varying clinical symptoms that lack specificity to point clearly to a definitive diagnosis. Discovery of novel blood borne biomarkers would provide a tractable method for rapid identification of mastocytosis and its sub-types. Moving towards this goal, we carried out a clinical biomarker study on blood from twenty individuals (systemic mastocytosis: n = 12, controls: n = 8), which were subjected to global proteome investigation using the novel technology SWATH-MS. This identified several putative biomarkers for systemic mastocytosis. Orthogonal validation of these putative biomarkers was achieved using ELISAs. Utilising this workflow, we identified and validated CXCL7, LBP, TGFβ1 and PDGF receptor-β as novel biomarkers for systemic mastocytosis. We demonstrate that CXCL7 correlates with neutrophil count offering a new insight into the increased prevalence of anaphylaxis in mastocytosis patients. Additionally, demonstrating the utility of SWATH-MS for the discovery of novel biomarkers in the systemic mastocytosis diagnostic sphere.
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Affiliation(s)
- R L J Graham
- School of Biological Sciences, Queens University Belfast, Chlorine Gardens, Belfast, BT9 5DL, UK
| | - A A McMullen
- Department of Life Sciences, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - G Moore
- School of Biological Sciences, Queens University Belfast, Chlorine Gardens, Belfast, BT9 5DL, UK
| | - N C Dempsey-Hibbert
- Department of Life Sciences, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - B Myers
- University Hospitals of Leicester NHS Trust, Leicester, LE3 9QP, UK
| | - C Graham
- School of Biological Sciences, Queens University Belfast, Chlorine Gardens, Belfast, BT9 5DL, UK.
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2
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The Extracellular Matrix Environment of Clear Cell Renal Cell Carcinoma Determines Cancer Associated Fibroblast Growth. Cancers (Basel) 2021; 13:cancers13235873. [PMID: 34884982 PMCID: PMC8657052 DOI: 10.3390/cancers13235873] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 12/30/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer and is often caused by mutations in the oxygen-sensing machinery of kidney epithelial cells. Due to its pseudo-hypoxic state, ccRCC recruits extensive vasculature and other stromal components. Conventional cell culture methods provide poor representation of stromal cell types in primary cultures of ccRCC, and we hypothesized that mimicking the extracellular environment of the tumor would promote growth of both tumor and stromal cells. We employed proteomics to identify the components of ccRCC extracellular matrix (ECM) and found that in contrast to healthy kidney cortex, laminin, collagen IV, and entactin/nidogen are minor contributors. Instead, the ccRCC ECM is composed largely of collagen VI, fibronectin, and tenascin C. Analysis of single cell expression data indicates that cancer-associated fibroblasts are a major source of tumor ECM production. Tumor cells as well as stromal cells bind efficiently to a nine-component ECM blend characteristic of ccRCC. Primary patient-derived tumor cells bind the nine-component blend efficiently, allowing to us to establish mixed primary cultures of tumor cells and stromal cells. These miniature patient-specific replicas are conducive to microscopy and can be used to analyze interactions between cells in a model tumor microenvironment.
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Serrano-Blesa E, Porter A, Lendrem DW, Pitzalis C, Barton A, Treumann A, Isaacs JD. Robust optimization of SWATH-MS workflow for human blood serum proteome analysis using a quality by design approach. Clin Proteomics 2021; 18:20. [PMID: 34384350 PMCID: PMC8359389 DOI: 10.1186/s12014-021-09323-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Background It is not enough to optimize proteomics assays. It is critical those assays are robust to operating conditions. Without robust assays, proteomic biomarkers are unlikely to translate readily into the clinic. This study outlines a structured approach to the identification of a robust operating window for proteomics assays and applies that method to Sequential Window Acquisition of all Theoretical Spectra Mass Spectroscopy (SWATH-MS). Methods We used a sequential quality by design approach exploiting a fractional screening design to first identify critical SWATH-MS parameters, then using response surface methods to identify a robust operating window with good reproducibility, before validating those settings in a separate validation study. Results The screening experiment identified two critical SWATH-MS parameters. We modelled the number of proteins and reproducibility as a function of those parameters identifying an operating window permitting robust maximization of the number of proteins quantified in human serum. In a separate validation study, these settings were shown to give good proteome-wide coverage and high quantification reproducibility. Conclusions Using design of experiments permits identification of a robust operating window for SWATH-MS. The method gives a good understanding of proteomics assays and greater data-driven confidence in SWATH-MS performance. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09323-z.
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Affiliation(s)
- Edith Serrano-Blesa
- National Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Porter
- Newcastle University Protein and Proteome Facility, Newcastle upon Tyne, UK
| | - Dennis W Lendrem
- National Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, Queen Mary University of London, London, UK
| | - Anne Barton
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre,, The University of Manchester, Manchester, UK
| | - Achim Treumann
- Newcastle University Protein and Proteome Facility, Newcastle upon Tyne, UK
| | - John D Isaacs
- National Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK. .,Musculoskeletal Unit, Freeman Hospital, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK.
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Chantada-Vázquez MDP, García Vence M, Serna A, Núñez C, Bravo SB. SWATH-MS Protocols in Human Diseases. Methods Mol Biol 2021; 2259:105-141. [PMID: 33687711 DOI: 10.1007/978-1-0716-1178-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Identification of molecular biomarkers for human diseases is one of the most important disciplines in translational science as it helps to elucidate their origin and early progression. Thus, it is a key factor in better diagnosis, prognosis, and treatment. Proteomics can help to solve the problem of sample complexity when the most common primary sample specimens were analyzed: organic fluids of easy access. The latest developments in high-throughput and label-free quantitative proteomics (SWATH-MS), together with more advanced liquid chromatography, have enabled the analysis of large sample sets with the sensitivity and depth needed to succeed in this task. In this chapter, we show different sample processing methods (major protein depletion, digestion, etc.) and a micro LC-SWATH-MS protocol to identify/quantify several proteins in different types of samples (serum/plasma, saliva, urine, tears).
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Affiliation(s)
| | - María García Vence
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | | | - Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain.
| | - Susana B Bravo
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain.
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Guo Z, Huang S, Wang J, Feng YL. Recent advances in non-targeted screening analysis using liquid chromatography - high resolution mass spectrometry to explore new biomarkers for human exposure. Talanta 2020; 219:121339. [DOI: 10.1016/j.talanta.2020.121339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/16/2020] [Accepted: 06/09/2020] [Indexed: 12/29/2022]
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Guo Z, Zhu Z, Huang S, Wang J. Non-targeted screening of pesticides for food analysis using liquid chromatography high-resolution mass spectrometry-a review. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2020; 37:1180-1201. [DOI: 10.1080/19440049.2020.1753890] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Zeqin Guo
- College of Bioengineering, Chongqing University, Chongqing, P. R. China
| | - Zhiguo Zhu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, P.R. China
| | - Sheng Huang
- College of Bioengineering, Chongqing University, Chongqing, P. R. China
| | - Jianhua Wang
- College of Bioengineering, Chongqing University, Chongqing, P. R. China
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Oxidative Catabolism of (+)-Pinoresinol Is Initiated by an Unusual Flavocytochrome Encoded by Translationally Coupled Genes within a Cluster of (+)-Pinoresinol-Coinduced Genes in Pseudomonas sp. Strain SG-MS2. Appl Environ Microbiol 2020; 86:AEM.00375-20. [PMID: 32198167 DOI: 10.1128/aem.00375-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/12/2020] [Indexed: 12/19/2022] Open
Abstract
Burkholderia sp. strain SG-MS1 and Pseudomonas sp. strain SG-MS2 have previously been found to mineralize (+)-pinoresinol through a common catabolic pathway. Here, we used comparative genomics, proteomics, protein semipurification, and heterologous expression to identify a flavoprotein from the vanillyl alcohol oxidase/p-cresol methyl hydroxylase (VAO/PCMH) enzyme family in SG-MS2 that carries out the initial hydroxylation of (+)-pinoresinol at the benzylic carbon. The cognate gene is translationally coupled with a downstream cytochrome gene, and the cytochrome is required for activity. The flavoprotein has a unique combination of cofactor binding and cytochrome requirements for the VAO/PCMH family. The heterologously expressed enzyme has a Km of 1.17 μM for (+)-pinoresinol. The enzyme is overexpressed in strain SG-MS2 upon exposure to (+)-pinoresinol, along with 45 other proteins, 22 of which were found to be encoded by genes in an approximately 35.1-kb cluster also containing the flavoprotein and cytochrome genes. Homologs of 18 of these 22 genes, plus the flavoprotein and cytochrome genes, were also found in a 38.7-kb cluster in SG-MS1. The amino acid identities of four of the other proteins within the SG-MS2 cluster suggest they catalyze conversion of hydroxylated pinoresinol to protocatechuate and 2-methoxyhydroquinone. Nine other proteins upregulated in SG-MS2 on exposure to (+)-pinoresinol appear to be homologs of proteins known to comprise the protocatechuate and 2-methoxyhydroquinone catabolic pathways, but only three of the cognate genes lie within the cluster containing the flavoprotein and cytochrome genes.IMPORTANCE (+)-Pinoresinol is an important plant defense compound, a major food lignan for humans and some other animals, and the model compound used to study degradation of the β-β' linkages in lignin. We report a gene cluster, in one strain each of Pseudomonas and Burkholderia, that is involved in the oxidative catabolism of (+)-pinoresinol. The flavoprotein component of the α-hydroxylase which heads the pathway belongs to the 4-phenol oxidizing (4PO) subgroup of the vanillyl alcohol oxidase/p-cresol methyl hydroxylase (VAO/PCMH) enzyme family but constitutes a novel combination of cofactor and electron acceptor properties for the family. It is translationally coupled with a cytochrome gene whose product is also required for activity. The work casts new light on the biology of (+)-pinoresinol and its transformation to other bioactive molecules. Potential applications of the findings include new options for deconstructing lignin into useful chemicals and the generation of new phytoestrogenic enterolactones from lignans.
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Kang Y, Schneider BB, Bedford L, Covey TR. Design Characteristics to Eliminate the Need for Parameter Optimization in Nanoflow ESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2347-2357. [PMID: 31418126 DOI: 10.1007/s13361-019-02301-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/23/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The sampling efficiency in electrospray ionization-mass spectrometry (ESI-MS) can be improved by decreasing the liquid flow rate to the nanoflow regime, where it is possible to draw a large fraction of the ESI plume into the mass spectrometer. This mode of operation is typically more difficult than ESI-MS at higher flow rates because it requires careful optimization of a number of parameters to achieve optimal sampling efficiency. In this work, we screened the relative impact on signal intensity and spray stability of factors that included sprayer position, spray electrode protrusion, sprayer tip shape, spray angle relative to the MS inlet, nebulizer gas flow rate, ESI potential, and means for generating the electric field to initiate electrospray. Based on the screening results, we explore the possibility of providing fixed optimal values for many of the key source parameters to eliminate much of the tuning that is required for conventional nanoflow sources. This approach has potential to greatly simplify nanoflow ESI-MS, while providing optimized sensitivity, stability, and robustness, with decreased variability between analyses.
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Affiliation(s)
- Yang Kang
- SCIEX, 71 Four Valley Drive, Concord, Ontario, L4K 4V8, Canada.
| | | | - Leigh Bedford
- SCIEX, 71 Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
| | - Thomas R Covey
- SCIEX, 71 Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
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Noor Z, Ranganathan S. Bioinformatics approaches for improving seminal plasma proteome analysis. Theriogenology 2019; 137:43-49. [PMID: 31186128 DOI: 10.1016/j.theriogenology.2019.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Reproduction efficiency of male animals is one of the key factors influencing the sustainability of livestock. Mass spectrometry (MS) based proteomics has become an important tool for studying seminal plasma proteomes. In this review, we summarize bioinformatics analysis strategies for current proteomics approaches, for identifying novel biomarkers of reproductive robustness.
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Affiliation(s)
- Zainab Noor
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.
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Selectivity enhancement using sequential mass isolation window acquisition with hybrid quadrupole time-of-flight mass spectrometry for pesticide residues. J Chromatogr A 2019; 1591:99-109. [PMID: 30658912 DOI: 10.1016/j.chroma.2019.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/20/2018] [Accepted: 01/08/2019] [Indexed: 12/29/2022]
Abstract
The introduction of sequential mass isolation window acquisition mode in high-resolution quadrupole time-of-flight analysers undoubtedly represents an important improvement in the MS/MS spectra obtained when working in non-target analysis. However, the advantages and limitations of this approach have not been sufficiently defined and evaluated. The present work seeks to fill this gap by considering its application in non-target multiresidue pesticide analysis. This work focuses on the called SWATH® method, which combines both MS and MS/MS acquisition, dividing the entire mass range into smaller segments for the MS/MS mode. The effect of the number of mass isolation windows, the total cycle-time lapsed, the sensitivity obtained, the MS/MS spectra quality, the ion ratio stability as well as the identification and quantification capabilities has been evaluated. The use of ten mass isolation windows for data acquisition was selected as a compromise between the required points per chromatographic peak and the reduction in interferences achieved. An identification study was carried out on 141 pesticides in 20 vegetable matrices to check the false positives and false identifications found automatically, in accordance with the criteria set out in Document No. SANTE/11945/2015. Furthermore, special attention was given to certain issues that can make correct identification difficult, such as low fragment abundance due using of a generic collision energy, the matrix influence on the collision cell, the effect of the concentration level as well as deconvolution failure and mass window width. Finally, to verify the efficiency of the optimum parameters proposed, two proficiency samples were analysed, obtaining good results. This proved the benefits in terms of identification and quantification purposes.
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Braccia C, Tomati V, Caci E, Pedemonte N, Armirotti A. SWATH label-free proteomics for cystic fibrosis research. J Cyst Fibros 2018; 18:501-506. [PMID: 30348611 DOI: 10.1016/j.jcf.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND Label-free proteomics is a powerful tool for biological investigation. The SWATH protocol, relying on the Pan Human ion library, currently represents the state-of-the-art methodology for this kind of analysis. We recently discovered that this tool is not perfectly suitable for proteomics research in the CF field, as it lacks assays for several proteins crucial for the CF biology, including CFTR. METHODS We extensively investigated the proteome of a very popular model for in vitro research on CF, CFBE41o-, and we used the corresponding data to improve the power of SWATH proteomics for CF investigation. We then used this improved tool to explore in depth the proteome of primary bronchial epithelial (BE) cells deriving from four CF individuals compared with that of four corresponding non-CF controls. By means of advanced bioinformatics tools, we outlined the presence of a number of protein networks being significantly altered by CF. RESULTS Our analysis on patients' BE cells identified 154 proteins dysregulated by the CF pathology (94 upregulated and 60 downregulated). Some known CFTR interactors are present among them, but our analysis also revealed the alteration of other proteins not previously known to be related with CF. CONCLUSIONS The present work outlines the power of SWATH label free proteomics applied to CF research.
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Affiliation(s)
- Clarissa Braccia
- D3Pharmachemistry, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; Dipartimento di Chimica, Università degli Studi di Genova, Via Dodecaneso 31, 16146 Genova, Italy
| | - Valeria Tomati
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Emanuela Caci
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Nicoletta Pedemonte
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Andrea Armirotti
- Analytical Chemistry Lab, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
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Koopmans F, Ho JTC, Smit AB, Li KW. Comparative Analyses of Data Independent Acquisition Mass Spectrometric Approaches: DIA, WiSIM-DIA, and Untargeted DIA. Proteomics 2018; 18:1700304. [PMID: 29134766 PMCID: PMC5817406 DOI: 10.1002/pmic.201700304] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/04/2017] [Indexed: 11/11/2022]
Abstract
Data-independent acquisition (DIA) is an emerging technology for quantitative proteomics. Current DIA focusses on the identification and quantitation of fragment ions that are generated from multiple peptides contained in the same selection window of several to tens of m/z. An alternative approach is WiSIM-DIA, which combines conventional DIA with wide-SIM (wide selected-ion monitoring) windows to partition the precursor m/z space to produce high-quality precursor ion chromatograms. However, WiSIM-DIA has been underexplored; it remains unclear if it is a viable alternative to DIA. We demonstrate that WiSIM-DIA quantified more than 24 000 unique peptides over five orders of magnitude in a single 2 h analysis of a neuronal synapse-enriched fraction, compared to 31 000 in DIA. There is a strong correlation between abundance values of peptides quantified in both the DIA and WiSIM-DIA datasets. Interestingly, the S/N ratio of these peptides is not correlated. We further show that peptide identification directly from DIA spectra identified >2000 proteins, which included unique peptides not found in spectral libraries generated by DDA.
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Affiliation(s)
- Frank Koopmans
- Department of Molecular and Cellular NeurobiologyCNCRAmsterdam NeuroscienceVrije UniversiteitAmsterdamThe Netherlands
| | | | - August B. Smit
- Department of Molecular and Cellular NeurobiologyCNCRAmsterdam NeuroscienceVrije UniversiteitAmsterdamThe Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular NeurobiologyCNCRAmsterdam NeuroscienceVrije UniversiteitAmsterdamThe Netherlands
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Borràs E, Sabidó E. What is targeted proteomics? A concise revision of targeted acquisition and targeted data analysis in mass spectrometry. Proteomics 2017; 17. [PMID: 28719092 DOI: 10.1002/pmic.201700180] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 12/14/2022]
Abstract
Targeted proteomics has gained significant popularity in mass spectrometry-based protein quantification as a method to detect proteins of interest with high sensitivity, quantitative accuracy and reproducibility. However, with the emergence of a wide variety of targeted proteomics methods, some of them with high-throughput capabilities, it is easy to overlook the essence of each method and to determine what makes each of them a targeted proteomics method. In this viewpoint, we revisit the main targeted proteomics methods and classify them in four categories differentiating those methods that perform targeted data acquisition from targeted data analysis, and those methods that are based on peptide ion data (MS1 targeted methods) from those that rely on the peptide fragments (MS2 targeted methods).
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Affiliation(s)
- Eva Borràs
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
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Bade R, White JM, Gerber C. Qualitative and quantitative temporal analysis of licit and illicit drugs in wastewater in Australia using liquid chromatography coupled to mass spectrometry. Anal Bioanal Chem 2017; 410:529-542. [DOI: 10.1007/s00216-017-0747-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/02/2017] [Accepted: 11/05/2017] [Indexed: 11/30/2022]
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