1
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Degl'Innocenti A, Braccia C, Genchi GG, di Leo N, Leoncino L, Catalano F, Armirotti A, Ciofani G. Proteome Alterations and Nucleosome Activation in Rat Myoblasts Treated with Cerium Oxide Nanoparticles. ACS OMEGA 2024; 9:29226-29233. [PMID: 39005815 PMCID: PMC11238203 DOI: 10.1021/acsomega.3c09715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/28/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024]
Abstract
Oxidative stress is a widespread causative agent of disease. Together with its general relevance for biomedicine, such a dynamic is recognizably detrimental to space exploration. Among other solutions, cerium oxide nanoparticles (or nanoceria, NC) display a long-lasting, self-renewable antioxidant activity. In a previous experiment, we evaluated oxidative imbalance in rat myoblasts in space, aboard the International Space Station, and unveiled possible protective effects from NC through RNA sequencing. Here, we focus on the myoblast response to NC on land by means of proteomics, defining a list of proteins that putatively react to NC and confirming nucleosomes/histones as likely mediators of its molecular action. The proteomics data set we present here and its counterpart from the space study share four factors. These are coherently either up- (Hist1h4b) or down-regulated (Gnl3, Mtdh, Trip12) upon NC exposure.
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Affiliation(s)
- Andrea Degl'Innocenti
- Smart Bio-Interfaces, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera, Pisa 56025, Italy
- Department of Medical Biotechnologies, Polyclinic Hospital Santa Maria alle Scotte, Università degli Studi di Siena, Viale Mario Bracci 2, Siena 53100, Italy
| | - Clarissa Braccia
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Giada Graziana Genchi
- Smart Bio-Interfaces, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera, Pisa 56025, Italy
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Università degli Studi di Bari Aldo Moro, Via Edoardo Orabona 4, Bari 70125, Italy
| | - Nicoletta di Leo
- Smart Bio-Interfaces, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera, Pisa 56025, Italy
| | - Luca Leoncino
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Federico Catalano
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Gianni Ciofani
- Smart Bio-Interfaces, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera, Pisa 56025, Italy
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2
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Jin L, Wang F, Wang X, Harvey BP, Bi Y, Hu C, Cui B, Darcy AT, Maull JW, Phillips BR, Kim Y, Jenkins GJ, Sornasse TR, Tian Y. Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized Sequential Window Acquisition of All THeoretical Mass Spectra (SWATH) Proteomics Workflow. Proteomes 2023; 11:32. [PMID: 37873874 PMCID: PMC10594463 DOI: 10.3390/proteomes11040032] [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: 08/16/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/25/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune and inflammatory disease. Plasma biomarkers are critical for understanding disease mechanisms, treatment effects, and diagnosis. Mass spectrometry-based proteomics is a powerful tool for unbiased biomarker discovery. However, plasma proteomics is significantly hampered by signal interference from high-abundance proteins, low overall protein coverage, and high levels of missing data from data-dependent acquisition (DDA). To achieve quantitative proteomics analysis for plasma samples with a balance of throughput, performance, and cost, we developed a workflow incorporating plate-based high abundance protein depletion and sample preparation, comprehensive peptide spectral library building, and data-independent acquisition (DIA) SWATH mass spectrometry-based methodology. In this study, we analyzed plasma samples from both RA patients and healthy donors. The results showed that the new workflow performance exceeded that of the current state-of-the-art depletion-based plasma proteomic platforms in terms of both data quality and proteome coverage. Proteins from biological processes related to the activation of systemic inflammation, suppression of platelet function, and loss of muscle mass were enriched and differentially expressed in RA. Some plasma proteins, particularly acute-phase reactant proteins, showed great power to distinguish between RA patients and healthy donors. Moreover, protein isoforms in the plasma were also analyzed, providing even deeper proteome coverage. This workflow can serve as a basis for further application in discovering plasma biomarkers of other diseases.
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Affiliation(s)
- Liang Jin
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Fei Wang
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Xue Wang
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Bohdan P. Harvey
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Yingtao Bi
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Chenqi Hu
- DMPK, Takeda Development Center Americas Inc., Cambridge, MA 02142, USA; (C.H.)
| | - Baoliang Cui
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Anhdao T. Darcy
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - John W. Maull
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Ben R. Phillips
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Youngjae Kim
- DMPK, Takeda Development Center Americas Inc., Cambridge, MA 02142, USA; (C.H.)
| | - Gary J. Jenkins
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Thierry R. Sornasse
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Yu Tian
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
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3
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Stepler KE, Hannah SC, Taneyhill LA, Nemes P. Deep Proteome of the Developing Chick Midbrain. J Proteome Res 2023; 22:3264-3274. [PMID: 37616547 DOI: 10.1021/acs.jproteome.3c00291] [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: 08/26/2023]
Abstract
The epithelial-to-mesenchymal transition (EMT) and migration of cranial neural crest cells within the midbrain are critical processes that permit proper craniofacial patterning in the early embryo. Disruptions in these processes not only impair development but also lead to various diseases, underscoring the need for their detailed understanding at the molecular level. The chick embryo has served historically as an excellent model for human embryonic development, including cranial neural crest cell EMT and migration. While these developmental events have been characterized transcriptionally, studies at the protein level have not been undertaken to date. Here, we applied mass spectrometry (MS)-based proteomics to establish a deep proteomics profile of the chick midbrain region during early embryonic development. Our proteomics method combines optimal lysis conditions, offline fractionation, separation on a nanopatterned stationary phase (μPAC) using nanoflow liquid chromatography, and detection using quadrupole-ion trap-Orbitrap tribrid high-resolution tandem MS. Identification of >5900 proteins and >450 phosphoproteins in this study marks the deepest coverage of the chick midbrain proteome to date. These proteins have known roles in pathways related to neural crest cell EMT and migration such as signaling, proteolysis/extracellular matrix remodeling, and transcriptional regulation. This study offers valuable insight into important developmental processes occurring in the midbrain region and demonstrates the utility of proteomics for characterization of tissue microenvironments during chick embryogenesis.
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Affiliation(s)
- Kaitlyn E Stepler
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Seth C Hannah
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Lisa A Taneyhill
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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4
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Burton NR, Polasky DA, Shikwana F, Ofori S, Yan T, Geiszler DJ, Veiga Leprevost FD, Nesvizhskii AI, Backus KM. Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics. J Am Chem Soc 2023; 145:21303-21318. [PMID: 37738129 DOI: 10.1021/jacs.3c05797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Mass spectrometry-based chemoproteomics has emerged as an enabling technology for functional biology and drug discovery. To address limitations of established chemoproteomics workflows, including cumbersome reagent synthesis and low throughput sample preparation, here, we established the silane-based cleavable isotopically labeled proteomics (sCIP) method. The sCIP method is enabled by a high yielding and scalable route to dialkoxydiphenylsilane fluorenylmethyloxycarbonyl (DADPS-Fmoc)-protected amino acid building blocks, which enable the facile synthesis of customizable, isotopically labeled, and chemically cleavable biotin capture reagents. sCIP is compatible with both MS1- and MS2-based quantitation, and the sCIP-MS2 method is distinguished by its click-assembled isobaric tags in which the reporter group is encoded in the sCIP capture reagent and balancer in the pan cysteine-reactive probe. The sCIP-MS2 workflow streamlines sample preparation with early stage isobaric labeling and sample pooling, allowing for high coverage and increased sample throughput via customized low cost six-plex sample multiplexing. When paired with a custom FragPipe data analysis workflow and applied to cysteine-reactive fragment screens, sCIP proteomics revealed established and unprecedented cysteine-ligand pairs, including the discovery that mitochondrial uncoupling agent FCCP acts as a covalent-reversible cysteine-reactive electrophile.
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Affiliation(s)
- Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Flowreen Shikwana
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Samuel Ofori
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, United States
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5
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Deng L, Handler DCL, Multari DH, Haynes PA. Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1162:122453. [PMID: 33279813 DOI: 10.1016/j.jchromb.2020.122453] [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: 05/25/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/29/2022]
Abstract
Shotgun proteomics is a high-throughput technology which has been developed with the aim of investigating the maximum number of proteins in cells in a given experiment. However, protein discovery and data generation vary in depth and coverage when different technical strategies are selected. In this study, three different sample preparation approaches, and peptide or protein fractionation methods, were applied to identify and quantify proteins from log-phase yeast lysate: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), filter-aided sample preparation coupled with gas phase fractionation (FASP-GPF), and FASP - high pH reversed phase fractionation (HpH). Fractions were initially analyzed and compared using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS) employing data dependent acquisition on a linear ion trap instrument. The number of fractions and analytical replicates was adjusted so that each experiment used a similar amount of mass spectrometric instrument time. A second set of experiments was performed, comparing FASP-GPF, SDS-PAGE and FASP-HpH using a Q Exactive Orbitrap mass spectrometer. Compared with results from the linear ion trap mass spectrometer, the use of a Q Exactive Orbitrap mass spectrometer enabled a substantial increase in protein identifications, and an even greater increase in peptide identifications. This shows that the main advantage of using the higher resolution instrument is in increased proteome coverage. A total of 1035, 1357 and 2134 proteins were separately identified by FASP-GPF, SDS-PAGE and FASP-HpH. Combining results from the Orbitrap experiments, there were a total of 2269 proteins found, with 94% of them identified using the FASP-HpH method. Therefore, the FASP-HpH method is the optimal choice among these approaches, when applied to this type of sample.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - David C L Handler
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Dylan H Multari
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia.
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6
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Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics. Int J Mol Sci 2020; 21:ijms21041524. [PMID: 32102244 PMCID: PMC7073195 DOI: 10.3390/ijms21041524] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.
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7
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Popov DV, Vinogradova OL, Zgoda VG. Preparation of Human Skeletal Muscle Samples for Proteomic Analysis with Isobaric iTRAQ Labels. Mol Biol 2019. [DOI: 10.1134/s0026893319040095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Liu C, Oveissi S, Downs R, Kirby J, Nedeva C, Puthalakath H, Faou P, Duan M, Chen W. Semiquantitative Proteomics Enables Mapping of Murine Neutrophil Dynamics following Lethal Influenza Virus Infection. THE JOURNAL OF IMMUNOLOGY 2019; 203:1064-1075. [PMID: 31308090 DOI: 10.4049/jimmunol.1900337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 12/31/2022]
Abstract
Neutrophils are rapidly deployed innate immune cells, and excessive recruitment is causally associated with influenza-induced pathologic conditions. Despite this, the complete set of influenza lethality-associated neutrophil effector proteins is currently unknown. Whether the expression of these proteins is predetermined during bone marrow (BM) neutrophil maturation or further modulated by tissue compartment transitions has also not been comprehensively characterized at a proteome-wide scale. In this study, we used high-resolution mass spectrometry to map how the proteomes of murine neutrophils change comparatively across BM, blood, and the alveolar airspaces to deploy an influenza lethality-associated response. Following lethal influenza infection, mature neutrophils undergo two infection-dependent and one context-independent compartmental transitions. Translation of type I IFN-stimulated genes is first elevated in the BM, preceding the context-independent downregulation of ribosomal proteins observed in blood neutrophils. Following alveolar airspace infiltration, the bronchoalveolar lavage (BAL) neutrophil proteome is further characterized by a limited increase in type I IFN-stimulated and metal-sequestering proteins as well as a decrease in degranulation-associated proteins. An influenza-selective and dose-dependent increase in antiviral and lipid metabolism-associated proteins was also observed in BAL neutrophils, indicative of a modest capacity for pathogen response tuning. Altogether, our study provides new and comprehensive evidence that the BAL neutrophil proteome is shaped by BM neutrophil maturation as well as subsequent compartmental transitions following lethal influenza infection.
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Affiliation(s)
- Chuanxin Liu
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Sara Oveissi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Rachael Downs
- La Trobe Comprehensive Proteomics Platform, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia; and
| | - Jason Kirby
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Urrbrae, South Australia 5064, Australia
| | - Christina Nedeva
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Hamsa Puthalakath
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Pierre Faou
- La Trobe Comprehensive Proteomics Platform, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia; and
| | - Mubing Duan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia;
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia;
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Dou M, Tsai CF, Piehowski PD, Wang Y, Fillmore TL, Zhao R, Moore RJ, Zhang P, Qian WJ, Smith RD, Liu T, Kelly RT, Shi T, Zhu Y. Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples. Anal Chem 2019; 91:9707-9715. [PMID: 31241912 DOI: 10.1021/acs.analchem.9b01248] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two-dimensional reversed-phase capillary liquid chromatography (2D RPLC) separations have enabled comprehensive proteome profiling of biological systems. However, milligram sample quantities of proteins are typically required due to significant losses during offline fractionation. Such a large sample requirement generally precludes the application samples in the nanogram to low-microgram range. To achieve in-depth proteomic analysis of such small-sized samples, we have developed the nanoFAC (nanoflow Fractionation and Automated Concatenation) 2D RPLC platform, in which the first dimension high-pH fractionation was performed on a 75-μm i.d. capillary column at a 300 nL/min flow rate with automated fraction concatenation, instead of on a typically used 2.1 mm column at a 200 μL/min flow rate with manual concatenation. Each fraction was then fully transferred to the second-dimension low-pH nanoLC separation using an autosampler equipped with a custom-machined syringe. We have found that using a polypropylene 96-well plate as collection device as well as the addition of n-Dodecyl β-d-maltoside (0.01%) in the collection buffer can significantly improve sample recovery. We have demonstrated the nanoFAC 2D RPLC platform can achieve confident identifications of ∼49,000-94,000 unique peptides, corresponding to ∼6,700-8,300 protein groups using only 100-1000 ng of HeLa tryptic digest (equivalent to ∼500-5,000 cells). Furthermore, by integrating with phosphopeptide enrichment, the nanoFAC 2D RPLC platform can identify ∼20,000 phosphopeptides from 100 μg of MCF-7 cell lysate.
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Affiliation(s)
- Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Chia-Feng Tsai
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Paul D Piehowski
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yang Wang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Pengfei Zhang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Wei-Jun Qian
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Richard D Smith
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Tujin Shi
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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10
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Demmers LC, Heck AJR, Wu W. Pre-fractionation Extends but also Creates a Bias in the Detectable HLA Class Ι Ligandome. J Proteome Res 2019; 18:1634-1643. [PMID: 30784271 PMCID: PMC6456874 DOI: 10.1021/acs.jproteome.8b00821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
HLA
class Ι molecules can communicate a range of cellular
alterations (mutations, changes in protein copy number, aberrant post-translational
modifications, or pathogen proteins) to CD8+ T lymphocytes in the
form of HLA peptide ligands. At any given moment, tens of thousands
of different self and foreign HLA class Ι peptides may be presented
on the cell surface by HLA class Ι complexes. Due to the enormous
biochemical diversity and low abundance of each of these peptides,
HLA ligandome analysis presents unique challenges. Even with advances
in enrichment strategies and MS instrumentation and fragmentation,
sufficient ligandome depth for identification of viral pathogens and
immuno therapeutically important tumor neo-antigens is still not routinely
achievable. In this study, we evaluated two pre-fractionation techniques,
high-pH reversed-phase and strong cation exchange, for the complementary
analyses of HLA class Ι peptide ligands. We observe that pre-fractionation
substantially extends the detectable HLA class Ι ligandome but
also creates an identification bias. We thus advocate a rational choice
between high-pH reversed-phase or strong cation exchange pre-fractionation
for deeper HLA class Ι ligandome analysis, depending on the
HLA locus, allele, or peptide ligand modification in question.
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Affiliation(s)
- Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
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11
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Dou M, Zhu Y, Liyu A, Liang Y, Chen J, Piehowski PD, Xu K, Zhao R, Moore RJ, Atkinson MA, Mathews CE, Qian WJ, Kelly RT. Nanowell-mediated two-dimensional liquid chromatography enables deep proteome profiling of <1000 mammalian cells. Chem Sci 2018; 9:6944-6951. [PMID: 30210768 PMCID: PMC6124911 DOI: 10.1039/c8sc02680g] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/15/2018] [Indexed: 12/14/2022] Open
Abstract
Multidimensional peptide separations can greatly increase the depth of coverage in proteome profiling. However, a major challenge for multidimensional separations is the requirement of large biological samples, often containing milligram amounts of protein. We have developed nanowell-mediated two-dimensional (2D) reversed-phase nanoflow liquid chromatography (LC) separations for in-depth proteome profiling of low-nanogram samples. Peptides are first separated using high-pH LC and the effluent is concatenated into 4 or 12 nanowells. The contents of each nanowell are reconstituted in LC buffer and collected for subsequent separation and analysis by low-pH nanoLC-MS/MS. The nanowell platform minimizes peptide losses to surfaces in offline 2D LC fractionation, enabling >5800 proteins to be confidently identified from just 50 ng of HeLa digest. Furthermore, in combination with a recently developed nanowell-based sample preparation workflow, we demonstrated deep proteome profiling of >6000 protein groups from small populations of cells, including ∼650 HeLa cells and 10 single human pancreatic islet thin sections (∼1000 cells) from a pre-symptomatic type 1 diabetic donor.
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Affiliation(s)
- Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Andrey Liyu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Yiran Liang
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Jing Chen
- Department of Pathology , Immunology and Laboratory Medicine , University of Florida , Gainesville , FL 32611 , USA
| | - Paul D Piehowski
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA 99354 , USA
| | - Kerui Xu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA 99354 , USA
| | - Mark A Atkinson
- Department of Pathology , Immunology and Laboratory Medicine , University of Florida , Gainesville , FL 32611 , USA
| | - Clayton E Mathews
- Department of Pathology , Immunology and Laboratory Medicine , University of Florida , Gainesville , FL 32611 , USA
| | - Wei-Jun Qian
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA 99354 , USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
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12
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Hamid Z, Summa M, Armirotti A. A Swath Label-Free Proteomics insight into the Faah -/- Mouse Liver. Sci Rep 2018; 8:12142. [PMID: 30108271 PMCID: PMC6092373 DOI: 10.1038/s41598-018-30553-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022] Open
Abstract
Fatty acid amide hydrolase (FAAH) is an important enzyme for lipid metabolism and an interesting pharmacological target, given its role in anandamide breakdown. The FAAH−/− genotype is the most widely used mouse model to investigate the effects of a complete pharmacological inhibition of this enzyme. In this paper, we explore, by means of label-free SWATH proteomics, the changes in protein expression occurring in the liver of FAAH−/− knockout (KO) mice. We identified several altered biological processes and pathways, like fatty acid synthesis and glycolysis, which explain the observed phenotype of this mouse. We also observed the alteration of other proteins, like carboxylesterases and S-methyltransferases, apparently not immediately related to FAAH, but known to have important biological roles. Our study, reporting more than 3000 quantified proteins, offers an in-depth analysis of the liver proteome of this model.
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Affiliation(s)
- Zeeshan Hamid
- D3Validation, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163, Genova, Italy.,Scuola Superiore Sant'Anna. via Piazza Martiri della Libertà, 33, 56127, Pisa, Italy
| | - Maria Summa
- Analytical Chemistry and In-vivo Facility, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163, Genova, Italy
| | - Andrea Armirotti
- Analytical Chemistry and In-vivo Facility, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163, Genova, Italy.
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13
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Choi SB, Lombard-Banek C, Muñoz-LLancao P, Manzini MC, Nemes P. Enhanced Peptide Detection Toward Single-Neuron Proteomics by Reversed-Phase Fractionation Capillary Electrophoresis Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:913-922. [PMID: 29147852 DOI: 10.1007/s13361-017-1838-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/12/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
The ability to detect peptides and proteins in single cells is vital for understanding cell heterogeneity in the nervous system. Capillary electrophoresis (CE) nanoelectrospray ionization (nanoESI) provides high-resolution mass spectrometry (HRMS) with trace-level sensitivity, but compressed separation during CE challenges protein identification by tandem HRMS with limited MS/MS duty cycle. Here, we supplemented ultrasensitive CE-nanoESI-HRMS with reversed-phase (RP) fractionation to enhance identifications from protein digest amounts that approximate to a few mammalian neurons. An ~1 to 20 μg neuronal protein digest was fractionated on a RP column (ZipTip), and 1 ng to 500 pg of peptides were analyzed by a custom-built CE-HRMS system. Compared with the control (no fractionation), RP fractionation improved CE separation (theoretical plates ~274,000 versus 412,000 maximum, resp.), which enhanced detection sensitivity (2.5-fold higher signal-to-noise ratio), minimized co-isolation spectral interferences during MS/MS, and increased the temporal rate of peptide identification by up to ~57%. From 1 ng of protein digest (<5 neurons), CE with RP fractionation identified 737 protein groups (1,753 peptides), or ~480 protein groups (~1,650 peptides) on average per analysis. The approach was scalable to 500 pg of protein digest (~a single neuron), identifying 225 protein groups (623 peptides) in technical triplicates, or 141 protein groups on average per analysis. Among identified proteins, 101 proteins were products of genes that are known to be transcriptionally active in single neurons during early development of the brain, including those involved in synaptic transmission and plasticity and cytoskeletal organization. Graphical abstract ᅟ.
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Affiliation(s)
- Sam B Choi
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Camille Lombard-Banek
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Pablo Muñoz-LLancao
- Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University, Washington, DC, 20052, USA
| | - M Chiara Manzini
- Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University, Washington, DC, 20052, USA
| | - Peter Nemes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA.
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
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14
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Ma S, Wang C, Zhao B, Ren X, Tian S, Wang J, Zhang C, Shao Y, Qiu M, Wang X. Tandem mass tags labeled quantitative proteomics to study the effect of tobacco smoke exposure on the rat lung. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:496-506. [PMID: 29307719 DOI: 10.1016/j.bbapap.2018.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 12/24/2017] [Accepted: 01/03/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND The causal link between tobacco smoke exposure (TSE) and numerous severe respiratory system diseases (RSD), including chronic bronchitis, chronic obstructive pulmonary disease, and lung cancer, is well established. However, the pathogenesis of TSE-induced RSD remains incompletely understood. This research aims to detect the pathogenetic mechanisms and potential therapeutic targets of TSE-induced RSD. METHODS This study employed TSE model which rats were exposed to a concentration of 60% tobacco smoke in a toxicant exposure system for four weeks. Tandem mass tags (TMT) labeled quantitative proteomics combined with off-line high pH reversed-phase fractionation, and nano-liquid chromatography-mass spectrometry method (off-line high pH RPF-nano-LC-MS/MS) were adopted to detect differentially expressed proteins (DEPs) in the lung tissues of the TSE model rats and to compare them with those in control. The accuracy of the results was verified by western blot. RESULTS Compared with the control group, 33 proteins in the TSE model group's lung tissues showed significant differential expression. Analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that, several biological pathways, such as the steroid biosynthesis pathway, were involved and played significant roles in the pathogenesis of the experimental group's TSE. CONCLUSIONS These findings make a crucial contribution to the search for a comprehensive understanding of TSE-induced RSD's pathogenesis, and furthermore provide guidance for the diagnosis and treatment of TSE-induced RSD.
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Affiliation(s)
- Shuangshuang Ma
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China; Shandong Analysis and Test Center, Shandong Academy of Sciences, Jinan 250014, China
| | - Chunguo Wang
- Beijing Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Baosheng Zhao
- Beijing Academy of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaolei Ren
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Simin Tian
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Juan Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Chi Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Yuanyang Shao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Minyi Qiu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Xueyong Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
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15
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Braccia C, Espinal MP, Pini M, De Pietri Tonelli D, Armirotti A. A new SWATH ion library for mouse adult hippocampal neural stem cells. Data Brief 2018; 18:1-8. [PMID: 29896482 PMCID: PMC5995750 DOI: 10.1016/j.dib.2018.02.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/07/2018] [Accepted: 02/22/2018] [Indexed: 12/31/2022] Open
Abstract
Over the last years, the SWATH data-independent acquisition protocol (Sequential Window acquisition of All THeoretical mass spectra) has become a cornerstone for the worldwide proteomics community (Collins et al., 2017) [1]. In this approach, a high-resolution quadrupole-ToF mass spectrometer acquires thousands of MS/MS data by selecting not just a single precursor at a time, but by allowing a broad m/z range to be fragmented. This acquisition window is then sequentially moved from the lowest to the highest mass selection range. This technique enables the acquisition of thousands of high-resolution MS/MS spectra per minute in a standard LC–MS run. In the subsequent data analysis phase, the corresponding dataset is searched in a “triple quadrupole-like” mode, thus not considering the whole MS/MS scan spectrum, but by searching for several precursor to fragment transitions that identify and quantify the corresponding peptide. This search is made possible with the use of an ion library, previously acquired in a classical data dependent, full-spectrum mode (Fabre et al., 2017; Wu et al., 2017) [2], [3]. The SWATH protocol, combining the protein identification power of high-resolution MS/MS spectra with the robustness and accuracy in analyte quantification of triple-quad targeted workflows, has become very popular in proteomics research. The major drawback lies in the ion library itself, which is normally demanding and time-consuming to build. Conversely, through the realignment of chromatographic retention times, an ion library of a given proteome can relatively easily be tailored upon “any” proteomics experiment done on the same proteome. We are thus hereby sharing with the worldwide proteomics community our newly acquired ion library of mouse adult hippocampal neural stem cells. Given the growing effort in neuroscience research involving proteomics experiments (Pons-Espinal et al., 2017; Sarnyai and Guest, 2017; Sethi et al., 2015; Bramini et al., 2016) [4,[5], [6], [7], we believe that this data might be of great help for the neuroscience community. All the here reported data (RAW files, results and ion library) can be freely downloaded from the SWATHATLAS (Deutsch et al., 2008) [8] website (http://www.peptideatlas.org/PASS/PASS01110)
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Key Words
- ACN, Acetonitrile
- DDA, Data dependent acquisition
- DTT, Dithiothreitol
- EGF, Epidermal growth factor
- FA, Formic acid
- FGF, Fibroblast growth factor
- IAA, Iodoacetamide
- Neural stem cells
- Neuroscience
- PDL, Poly-D-Lysine
- PSM, Peptide spectrum match
- PTMs, Post translational modifications
- Proteomics
- SWATH
- TEA, Triethylamine
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Affiliation(s)
- Clarissa Braccia
- D3 PharmaChemistry, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Meritxell Pons Espinal
- Neurobiology of miRNA Lab, Neuroscience and Brain Technologies Department, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Mattia Pini
- D3 PharmaChemistry, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Davide De Pietri Tonelli
- Neurobiology of miRNA Lab, Neuroscience and Brain Technologies Department, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Andrea Armirotti
- D3 PharmaChemistry, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Corresponding author.
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16
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High AA, Tan H, Pagala VR, Niu M, Cho JH, Wang X, Bai B, Peng J. Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification. J Vis Exp 2017. [PMID: 29286450 DOI: 10.3791/56474] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep-proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an extensive LC/LC-MS/MS platform, and post-MS computational interference correction to accurately quantitate whole proteomes. This protocol includes the following main steps: protein extraction and digestion, TMT labeling, 2-dimensional (2D) LC, high-resolution mass spectrometry, and computational data processing. Quality control steps are included for troubleshooting and evaluating experimental variation. More than 10,000 proteins in mammalian samples can be confidently quantitated with this protocol. This protocol can also be applied to the quantitation of post translational modifications with minor changes. This multiplexed, robust method provides a powerful tool for proteomic analysis in a variety of complex samples, including cell culture, animal tissues, and human clinical specimens.
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Affiliation(s)
- Anthony A High
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital;
| | - Haiyan Tan
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital
| | | | - Mingming Niu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital; Heilongjiang University of Chinese Medicine
| | - Ji-Hoon Cho
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital
| | - Xusheng Wang
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital
| | - Bing Bai
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital
| | - Junmin Peng
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital; Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital;
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17
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Richard VR, Domanski D, Percy AJ, Borchers CH. An online 2D-reversed-phase – Reversed-phase chromatographic method for sensitive and robust plasma protein quantitation. J Proteomics 2017; 168:28-36. [DOI: 10.1016/j.jprot.2017.07.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/14/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022]
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18
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Zhu MZ, Li N, Wang YT, Liu N, Guo MQ, Sun BQ, Zhou H, Liu L, Wu JL. Acid/Salt/pH Gradient Improved Resolution and Sensitivity in Proteomics Study Using 2D SCX-RP LC–MS. J Proteome Res 2017; 16:3470-3475. [DOI: 10.1021/acs.jproteome.7b00443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ming-Zhi Zhu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Sino-Africa Joint
Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Na Li
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Yi-Tong Wang
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Ning Liu
- Central
Laboratory, Second Hospital of Jilin University, Changchun, China
| | - Ming-Quan Guo
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Sino-Africa Joint
Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Bao-qing Sun
- State
Key Laboratory of Respiratory Disease, National Clinical Center for
Respiratory Diseases, Guangzhou Institute of Respiratory Diseases,
First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hua Zhou
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Liang Liu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Jian-Lin Wu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
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19
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Kulak NA, Geyer PE, Mann M. Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics. Mol Cell Proteomics 2017; 16:694-705. [PMID: 28126900 PMCID: PMC5383787 DOI: 10.1074/mcp.o116.065136] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/25/2017] [Indexed: 01/22/2023] Open
Abstract
Recent advances in mass spectrometry (MS)-based proteomics now allow very deep coverage of cellular proteomes. To achieve near-comprehensive identification and quantification, the combination of a first HPLC-based peptide fractionation orthogonal to the on-line LC-MS/MS step has proven to be particularly powerful. This first dimension is typically performed with milliliter/min flow and relatively large column inner diameters, which allow efficient pre-fractionation but typically require peptide amounts in the milligram range. Here, we describe a novel approach termed "spider fractionator" in which the post-column flow of a nanobore chromatography system enters an eight-port flow-selector rotor valve. The valve switches the flow into different flow channels at constant time intervals, such as every 90 s. Each flow channel collects the fractions into autosampler vials of the LC-MS/MS system. Employing a freely configurable collection mechanism, samples are concatenated in a loss-less manner into 2-96 fractions, with efficient peak separation. The combination of eight fractions with 100 min gradients yields very deep coverage at reasonable measurement time, and other parameters can be chosen for even more rapid or for extremely deep measurements. We demonstrate excellent sensitivity by decreasing sample amounts from 100 μg into the sub-microgram range, without losses attributable to the spider fractionator and while quantifying close to 10,000 proteins. Finally, we apply the system to the rapid automated and in-depth characterization of 12 different human cell lines to a median depth of 11,472 different proteins, which revealed differences recapitulating their developmental origin and differentiation status. The fractionation technology described here is flexible, easy to use, and facilitates comprehensive proteome characterization with minimal sample requirements.
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Affiliation(s)
- Nils A Kulak
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,§PreOmics GmbH, Martinsried, Germany; and
| | - Philipp E Geyer
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,‖Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; .,‖Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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20
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Kuljanin M, Dieters-Castator DZ, Hess DA, Postovit LM, Lajoie GA. Comparison of sample preparation techniques for large-scale proteomics. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600337] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/07/2016] [Accepted: 11/07/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Miljan Kuljanin
- Department of Biochemistry; University of Western Ontario; London ON Canada
| | | | - David A. Hess
- Department of Physiology and Pharmacology; University of Western Ontario; London ON Canada
| | - Lynne-Marie Postovit
- Department of Anatomy and Cell Biology; University of Western Ontario; London ON Canada
- Department of Oncology; University of Alberta; Edmonton AB Canada
| | - Gilles A. Lajoie
- Department of Biochemistry; University of Western Ontario; London ON Canada
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21
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Bai B, Tan H, Pagala VR, High AA, Ichhaporia VP, Hendershot L, Peng J. Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry. Methods Enzymol 2016; 585:377-395. [PMID: 28109439 DOI: 10.1016/bs.mie.2016.10.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry-based proteomics has experienced an unprecedented advance in comprehensive analysis of proteins and posttranslational modifications, with particular technical progress in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an optimized LC-MS/MS platform to quantitate whole proteome and phosphoproteome. The major steps include protein extraction and digestion, TMT labeling, two-dimensional liquid chromatography, TiO2-mediated phosphopeptide enrichment, high-resolution mass spectrometry, and computational data processing. This protocol routinely leads to confident quantification of more than 10,000 proteins and approximately 30,000 phosphosites in mammalian samples. Quality control steps are implemented for troubleshooting and evaluating experimental variation. Such a multiplexed robust method provides a powerful tool for dissecting proteomic signatures at the systems level in a variety of complex samples, ranging from cell culture, animal tissues to human clinical specimens.
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Affiliation(s)
- B Bai
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - H Tan
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - V R Pagala
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - A A High
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - V P Ichhaporia
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - L Hendershot
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - J Peng
- St. Jude Children's Research Hospital, Memphis, TN, United States; St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, United States.
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22
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Wang H, Xie S. Identification ofl-carnitine and its impurities in food supplement formulations by online column-switching liquid chromatography coupled with linear ion trap mass spectrometry. J Sep Sci 2016; 40:431-441. [DOI: 10.1002/jssc.201600652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 10/09/2016] [Accepted: 11/03/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Hang Wang
- Instrumental Analysis Center; Shanghai Jiao Tong University; Shanghai P.R. China
| | - Sijun Xie
- Instrumental Analysis Center; Shanghai Jiao Tong University; Shanghai P.R. China
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23
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Wither MJ, Hansen KC, Reisz JA. Mass Spectrometry-Based Bottom-Up Proteomics: Sample Preparation, LC-MS/MS Analysis, and Database Query Strategies. ACTA ACUST UNITED AC 2016; 86:16.4.1-16.4.20. [PMID: 27801520 DOI: 10.1002/cpps.18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent technological advances in mass spectrometry (MS) have made possible the investigation and quantification of complex mixtures of biomolecules. The exceptional sensitivity and resolving power of today's mass spectrometers allow for the detection of proteins and peptides at low femtomole quantities; however, these attributes demand high sample purity to minimize artifacts and achieve the highest degree of biomolecule identification. Tissue preparation for proteomic studies is particularly challenging due to their heterogeneity in cell type, presence of insoluble biomaterials, and wide diversity of biomolecules. The workflow described herein details sample preparation from tissues through protein extraction, proteolysis, and purification to generate peptides for MS analysis. Increased peptide resolution and a corresponding increase in protein identification is accomplished using polarity-based fractionation (C18 resin) at the peptide level. Additionally, approaches to instrument set up, including the use of nanoscale liquid chromatography and quadrupole Orbitrap MS, along with database searching, are described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Matthew J Wither
- Biological Mass Spectrometry Core, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Kirk C Hansen
- Biological Mass Spectrometry Core, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Julie A Reisz
- Biological Mass Spectrometry Core, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
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24
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Identification of Impurities in 5-Aminolevulinic Acid by Two-Dimensional Column-Switching Liquid Chromatography Coupled with Linear Ion Trap Mass Spectrometry. Chromatographia 2016. [DOI: 10.1007/s10337-016-3165-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Dimayacyac-Esleta BRT, Tsai CF, Kitata RB, Lin PY, Choong WK, Lin TD, Wang YT, Weng SH, Yang PC, Arco SD, Sung TY, Chen YJ. Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling. Anal Chem 2015; 87:12016-23. [PMID: 26554430 DOI: 10.1021/acs.analchem.5b03639] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Membrane proteins are crucial targets for cancer biomarker discovery and drug development. However, in addition to the inherent challenges of hydrophobicity and low abundance, complete membrane proteome coverage of clinical specimen is usually hindered by the requirement of large amount of starting materials. Toward comprehensive membrane proteomic profiling for small amounts of samples (10 μg), we developed high-pH reverse phase (Hp-RP) combined with stop-and-go extraction tip (StageTip) technique, as a fast (∼15 min.), sensitive, reproducible, high-resolution and multiplexed fractionation method suitable for accurate quantification of the membrane proteome. This approach provided almost 2-fold enhanced detection of peptides encompassing transmembrane helix (TMH) domain, as compared with strong anion exchange (SAX) and strong cation exchange (SCX) StageTip techniques. Almost 5000 proteins (∼60% membrane proteins) can be identified in only 10 μg of membrane protein digests, showing the superior sensitivity of the Hp-RP StageTip approach. The method allowed up to 9- and 6-fold increase in the identification of unique hydrophobic and hydrophilic peptides, respectively. The Hp-RP StageTip method enabled in-depth membrane proteome profiling of 11 lung cancer cell lines harboring different EGFR mutation status, which resulted in the identification of 3983 annotated membrane proteins. This provides the largest collection of reference peptide spectral data for lung cancer membrane subproteome. Finally, relative quantification of membrane proteins between Gefitinib-resistant and -sensitive lung cancer cell lines revealed several up-regulated membrane proteins with key roles in lung cancer progression.
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Affiliation(s)
- Baby Rorielyn T Dimayacyac-Esleta
- Institute of Chemistry, University of the Philippines , Diliman Quezon City 1101, Philippines.,Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Chia-Feng Tsai
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wai-Kok Choong
- Institute of Information Science, Academia Sinica , Taipei 115, Taiwan
| | - Tai-Du Lin
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Biochemical Sciences, National Taiwan University , Taipei 10617, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Shao-Hsing Weng
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University , Taipei 10617, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital , Taipei 10617, Taiwan.,National Taiwan University College of Medicine , Taipei 10051, Taiwan.,Institute of Biomedical Science, Academia Sinica , Taipei 115, Taiwan
| | - Susan D Arco
- Institute of Chemistry, University of the Philippines , Diliman Quezon City 1101, Philippines
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica , Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan
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