1
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Xing S, Pai A, Wu R, Lu Y. NHS-Ester Tandem Labeling in One Pot Enables 48-Plex Quantitative Proteomics. Anal Chem 2021; 93:12827-12832. [PMID: 34529408 DOI: 10.1021/acs.analchem.1c01314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stable-isotope labeling strategies are extensively used for multiplex quantitative proteomics. Hybrid-isotope labeling strategies that combine the use of isotopic mass difference labeling and isobaric tags can greatly increase sample multiplexity. In this work, we present a novel hybrid-isotope labeling approach that we termed NHS-ester tandem labeling in one pot (NETLOP). We first optimized 16-plex isobaric TMTpro labeling of lysine residues followed by 2-plex or 3-plex isotopic mTRAQ labeling of peptide N-termini, both of which with commercially available NHS-ester reactive reagents. We then demonstrated the utility of the NETLOP approach by labeling HeLa cell samples and performing proof-of-principle quantitative 32-plex and 48-plex proteomic analyses, each in a single LC-MS/MS experiment. Compared to current hybrid-isotope labeling methods, our NETLOP approach requires no sample cleanup between different labeling steps to minimize sample loss, induces no retention time shifts that compromise quantification accuracy, can be adapted to other NHS-ester isotopic labeling reagents to further increase multiplexity, and is compatible with samples from any origin in a wide array of biological and clinical proteomics applications.
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Affiliation(s)
- Sansi Xing
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Akshat Pai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Ruilin Wu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Yu Lu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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2
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Quantitative determination of osteopontin in bovine, buffalo, yak, sheep and goat milk by Ultra-high performance liquid chromatography-tandem mass spectrometry and stable isotope dimethyl labeling. Food Chem 2020; 343:128489. [PMID: 33153809 DOI: 10.1016/j.foodchem.2020.128489] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/16/2020] [Accepted: 10/23/2020] [Indexed: 11/20/2022]
Abstract
Osteopontin (OPN) is a multifunctional protein present in different tissues, body fluids and milk. Different milk has different level of OPN content. To determine the amount of osteopontin in bovine, buffalo, yak, sheep and goat milk, we developed an ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method to detect an osteopontin signature peptide. The signature peptides selected by searching Uniprot database for trypsin digested osteopontin. The sample preparation procedure includes trypsin digestion, dimethyl labeling of tryptic peptides, purification and concentration of labeled tryptic peptide with solid phase extraction. The limit of detection and limit of quantification are 0.5 mg L-1 and 2.0 mg L-1, respectively. The method has satisfactory analytical performance with a linearity of R2 ≥ 0.998, recoveries of 103.7-111.0%, and precision of 1.8-6.2%. It is also validated and successfully applied to quantifying osteopontin content in bovine, buffalo, yak, sheep and goat milk.
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3
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Frost DC, Feng Y, Li L. 21-plex DiLeu Isobaric Tags for High-Throughput Quantitative Proteomics. Anal Chem 2020; 92:8228-8234. [PMID: 32401496 DOI: 10.1021/acs.analchem.0c00473] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Isobaric tags enable multiplexed quantitative analysis of many biological samples in a single LC-MS/MS experiment. As a cost-effective alternative to expensive commercial isobaric tagging reagents, we developed our own custom N,N-dimethylleucine "DiLeu" isobaric tags for quantitative proteomics. Here, we present a new generation of DiLeu tags that achieves 21-plex quantification in high-resolution HCD MS/MS spectra via distinct reporter ions that differ in mass from each other by a minimum of 3 mDa. The 21-plex set retains the compact tag structure and existing isotopologues of the 12-plex set but includes nine new reporter variants formulated with unique configurations of 13C, 15N, and 2H stable isotopes, each synthesized in-house via a stepwise N-monomethylation synthesis strategy using readily available reagents. Thus, multiplexing capacity is expanded significantly, while preserving the performance and low cost of the previous implementation. We show that 21-plex DiLeu tags generate strong reporter ions following HCD fragmentation of labeled peptides acquired on Orbitrap platforms at a minimum of 60,000 resolving power (at 400 m/z), and we demonstrate accurate 21-plex quantification of labeled K562 human cell line protein digests via single-shot nanoLC-MS/MS analysis on a Q Exactive HF system.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yu Feng
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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4
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Matthiesen R, Carvalho AS. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry. Methods Mol Biol 2020; 2051:161-197. [PMID: 31552629 DOI: 10.1007/978-1-4939-9744-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.
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Affiliation(s)
- Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal.
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5
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Sun M, Liang Y, Li Y, Yang K, Zhao B, Yuan H, Li X, Zhang X, Liang Z, Shan Y, Zhang L, Zhang Y. Comprehensive Analysis of Protein N-Terminome by Guanidination of Terminal Amines. Anal Chem 2019; 92:567-572. [DOI: 10.1021/acs.analchem.9b04141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mingwei Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong 510005, China
| | - Yu Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Huiming Yuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Xiao Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Xiaodan Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yichu Shan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
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6
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Zhang J, Jia S, Lu W, Li W, Jiang R, Liu Y, Yang X, Zou S, Zou X, Zhong H. Real-time laser induced chemical derivatizations of peptide N-Terminus for in-situ mass spectrometric sequencing at sub-picomole and nanosecond scale. Anal Chim Acta 2019; 1100:1-11. [PMID: 31987129 DOI: 10.1016/j.aca.2019.12.029] [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: 10/10/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 11/30/2022]
Abstract
Distinguishing b- and y-ions is essential to compute amino acid sequences from either N- or C-terminus in mass spectrometry. We described herein a solvent free and real time on-plate derivatization approach that can tag N-terminus of peptides at microliter level with p-chlorobenzaldehyde or 2-hydroxy-5-methylisophthalaldehyde for matrix assisted laser desorption ionization mass spectrometry (MALDI MS). Less than 1 μL of sample solutions can be directly mixed with equal volumes of p-chlorobenzaldehyde or 2-hydroxy-5-methylisophthalaldehyde and α-cyano-4-hydroxycinnamic acid (CHCA), a matrix compound to co-crystalize with analytes for efficient absorption of laser energy and peptide ionization. When the mixture spotted on the sample plate is irradiated with the 3rd harmonic (355 nm) of Nd3+:YAG laser pulses (3 ns width), N-terminal amine groups of peptides instantly react with carbonyl groups of chlorobenzaldehyde or 2-hydroxy-5-methylisophthalaldehyde. Resultant peptides carrying with on-plate formed azomethine group (-CN-) are simultaneously protonated and isolated as precursor ions for subsequent collision-activated dissociation. The mass shift with unique Cl isotopic signature unambiguously distinguishes b ions from y ions and other ions. This method does not need extensive sample preparation and is useful for those samples with limited quantities down to sub-picomole level in sub-microliter volumes. The efficiency was demonstrated with synthetic peptides and tryptic peptides of model proteins. It was found that 2-hydroxy-5-methylisophthalaldehyde provides improved yield for peptides containing lysine residues. Unknown proteins of human saliva and bovine milk as well as phosphopeptides have been identified.
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Affiliation(s)
- Juan Zhang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Shanshan Jia
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Wenting Lu
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Weidan Li
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Ruowei Jiang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Yanping Liu
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Xiaojie Yang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Si Zou
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Xuekun Zou
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Hongying Zhong
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China.
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7
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Liao R, Gao Y, Chen M, Li L, Hu X. A Ubiquitous but Overlooked Side Reaction in Dimethyl Labeling of Peptides. Anal Chem 2018; 90:13533-13540. [PMID: 30372036 DOI: 10.1021/acs.analchem.8b03570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Reductive dimethylation using formaldehyde and NaBH3CN to label peptides or proteins on their N-termini and lysine residues is one of the most widely used labeling methods in the quantitative proteomics field. In this study, we characterized a ubiquitous side reaction in dimethylation labeling, causing mass increments of 26 Da on the N-termini of peptides. It can occur extensively on most peptides, which significantly compromises data quality in terms of sensitivity, dynamic range, and peptide- and protein-identification rates. Nevertheless, this side reaction was so-far overlooked, largely because the current database search algorithms limited the detection of unknown modifications. In order to illustrate the chemical nature of this side reaction, 1D and 2D nuclear magnetic resonance (NMR) was performed to elucidate the exact structure of the modification formed through this side reaction, revealing that the side reaction produced an N-methyl-4-imidazolidinone moiety between the first two residues of the undesirably labeled peptides. On the basis of the mechanism proposed for the side reaction, we optimized the reaction conditions for dimethyl-labeling. Compared with the current typical labeling method, our approach can dramatically suppress the side reactions at both the standard protein and proteome levels. As a result, with our optimal labeling method, peptide- and protein-identification rates were significantly increased compared with those from the traditional labeling method.
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Affiliation(s)
- Rijing Liao
- Shanghai Institute of Precision Medicine, The Ninth People's Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai 200125 , China
| | | | - Ming Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Lulu Li
- Shanghai Institute of Precision Medicine, The Ninth People's Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai 200125 , China
| | - Xuye Hu
- Shanghai Clinical Center , Chinese Academy of Sciences , Shanghai 200031 , China
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8
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Muth T, Hartkopf F, Vaudel M, Renard BY. A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics. Proteomics 2018; 18:e1700150. [PMID: 29968278 DOI: 10.1002/pmic.201700150] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/23/2018] [Indexed: 01/15/2023]
Abstract
In shotgun proteomics, peptide and protein identification is most commonly conducted using database search engines, the method of choice when reference protein sequences are available. Despite its widespread use the database-driven approach is limited, mainly because of its static search space. In contrast, de novo sequencing derives peptide sequence information in an unbiased manner, using only the fragment ion information from the tandem mass spectra. In recent years, with the improvements in MS instrumentation, various new methods have been proposed for de novo sequencing. This review article provides an overview of existing de novo sequencing algorithms and software tools ranging from peptide sequencing to sequence-to-protein mapping. Various use cases are described for which de novo sequencing was successfully applied. Finally, limitations of current methods are highlighted and new directions are discussed for a wider acceptance of de novo sequencing in the community.
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Affiliation(s)
- Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Felix Hartkopf
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Marc Vaudel
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020, Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5020, Bergen, Norway
| | - Bernhard Y Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
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9
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Randles MJ, Humphries MJ, Lennon R. Proteomic definitions of basement membrane composition in health and disease. Matrix Biol 2017; 57-58:12-28. [PMID: 27553508 DOI: 10.1016/j.matbio.2016.08.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/01/2016] [Accepted: 08/17/2016] [Indexed: 12/11/2022]
Abstract
Basement membranes are formed from condensed networks of extracellular matrix (ECM) proteins. These structures underlie all epithelial, mesothelial and endothelial sheets and provide an essential structural scaffold. Candidate-based investigations have established that predominant components of basement membranes are laminins, collagen type IV, nidogens and heparan sulphate proteoglycans. More recently, global proteomic approaches have been applied to investigate ECM and these analyses confirm tissue-specific ECM proteomes with a high degree of complexity. The proteomes consist of structural as well as regulatory ECM proteins such as proteases and growth factors. This review is focused on the proteomic analysis of basement membranes and illustrates how this approach can be used to build our understanding of ECM regulation in health and disease.
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Affiliation(s)
- Michael J Randles
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, UK; Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Rachel Lennon
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, UK; Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK; Department of Paediatric Nephrology, Central Manchester University Hospitals NHS Foundation Trust (CMFT), Manchester Academic Health Science Centre (MAHSC), Manchester, UK.
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10
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Fang H, Xiao K, Li Y, Yu F, Liu Y, Xue B, Tian Z. Intact Protein Quantitation Using Pseudoisobaric Dimethyl Labeling. Anal Chem 2016; 88:7198-205. [PMID: 27359340 DOI: 10.1021/acs.analchem.6b01388] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein structural and functional studies rely on complete qualitative and quantitative information on protein species (proteoforms); thus, it is important to quantify differentially expressed proteins at their molecular level. Here we report our development of universal pseudoisobaric dimethyl labeling (pIDL) of amino groups at both the N-terminal and lysine residues for relative quantitation of intact proteins. Initial proof-of-principle study was conducted on standard protein myoglobin and hepatocellular proteomes (HepG2 vs LO2). The amino groups from both the N-terminal and lysine were dimethylated with HXHO (X = (13)C or C) and NaBY3CN (Y = H or D). At the standard protein level, labeling efficiency, effect of product ion size, and mass resolution on quantitation accuracy were explored; and a good linear quantitation dynamic range up to 50-fold was obtained. For the hepatocellular proteome samples, 33 proteins were quantified with RSD ≤ 10% from one-dimensional reversed phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) analysis of the 1:1 mixed samples. The method in this study can be extended to quantitation of other intact proteome systems. The universal "one-pot" dimethyl labeling of all the amino groups in a protein without the need of preblocking of those on the lysine residues is made possible by protein identification and quantitation analysis using ProteinGoggle 2.0 with customized databases of both precursor and product ions containing heavy isotopes.
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Affiliation(s)
- Houqin Fang
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Kaijie Xiao
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Yunhui Li
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Fan Yu
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Yan Liu
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Bingbing Xue
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
| | - Zhixin Tian
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University , Shanghai 200092, China
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11
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Dik E, Naamati A, Asraf H, Lehming N, Pines O. Human Fumarate Hydratase Is Dual Localized by an Alternative Transcription Initiation Mechanism. Traffic 2016; 17:720-32. [DOI: 10.1111/tra.12397] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/29/2016] [Accepted: 03/29/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Ekaterina Dik
- Department of Microbiology Molecular Genetics, IMRIC, Faculty of Medicine; Hebrew University of Jerusalem; Jerusalem Israel
| | - Adi Naamati
- Department of Microbiology Molecular Genetics, IMRIC, Faculty of Medicine; Hebrew University of Jerusalem; Jerusalem Israel
| | - Hadar Asraf
- Department of Microbiology Molecular Genetics, IMRIC, Faculty of Medicine; Hebrew University of Jerusalem; Jerusalem Israel
| | - Norbert Lehming
- CREATE-NUS-HUJ Program and the Department of Microbiology, Yong Loo Lin School of Medicine; National University of Singapore; Singapore Singapore
| | - Ophry Pines
- Department of Microbiology Molecular Genetics, IMRIC, Faculty of Medicine; Hebrew University of Jerusalem; Jerusalem Israel
- CREATE-NUS-HUJ Program and the Department of Microbiology, Yong Loo Lin School of Medicine; National University of Singapore; Singapore Singapore
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12
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Thomas S, Hao L, Ricke WA, Li L. Biomarker discovery in mass spectrometry-based urinary proteomics. Proteomics Clin Appl 2016; 10:358-70. [PMID: 26703953 DOI: 10.1002/prca.201500102] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 12/05/2015] [Accepted: 12/21/2015] [Indexed: 01/03/2023]
Abstract
Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS-based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS-based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians.
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Affiliation(s)
- Samuel Thomas
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Ling Hao
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - William A Ricke
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Urology, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
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13
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Cho KC, Kang JW, Choi Y, Kim TW, Kim KP. Effects of peptide acetylation and dimethylation on electrospray ionization efficiency. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:105-10. [PMID: 26889926 DOI: 10.1002/jms.3723] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 10/08/2015] [Accepted: 10/20/2015] [Indexed: 05/05/2023]
Abstract
Peptide acetylation and dimethylation have been widely used to derivatize primary amino groups (peptide N-termini and the ε-amino group of lysines) for chemical isotope labeling of quantitative proteomics or for affinity tag labeling for selection and enrichment of labeled peptides. However, peptide acetylation results in signal suppression during electrospray ionization (ESI) due to charge neutralization. In contrast, dimethylated peptides show increased ionization efficiency after derivatization, since dimethylation increases hydrophobicity and maintains a positive charge on the peptide under common LC conditions. In this study, we quantitatively compared the ESI efficiencies of acetylated and dimethylated model peptides and tryptic peptides of BSA. Dimethylated peptides showed higher ionization efficiency than acetylated peptides for both model peptides and tryptic BSA peptides. At the proteome level, peptide dimethylation led to better protein identification than peptide acetylation when tryptic peptides of mouse brain lysate were analyzed with LC-ESI-MS/MS. These results demonstrate that dimethylation of tryptic peptides enhanced ESI efficiency and provided up to two-fold improved protein identification sensitivity in comparison with acetylation.
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Affiliation(s)
- Kyung-Cho Cho
- Department of Applied Chemistry, Kyung Hee University, Yongin-si, 446-701, Korea
| | - Jeong Won Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin-si, 446-701, Korea
| | - Yuri Choi
- Department of Applied Chemistry, Kyung Hee University, Yongin-si, 446-701, Korea
| | - Tae Woo Kim
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin-si, 446-701, Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Kyung Hee University, Yongin-si, 446-701, Korea
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14
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Devabhaktuni A, Elias JE. Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets. J Proteome Res 2016; 15:732-42. [PMID: 26743026 DOI: 10.1021/acs.jproteome.5b00861] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dependent on concise, predefined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference databases. However, such algorithms have been difficult to apply to complex protein mixtures, in part due to a lack of methods for automatically validating de novo sequencing results. Here, we present novel metrics for benchmarking de novo sequencing algorithm performance on large-scale proteomics data sets and present a method for accurately calibrating false discovery rates on de novo results. We also present a novel algorithm (LADS) that leverages experimentally disambiguated fragmentation spectra to boost sequencing accuracy and sensitivity. LADS improves sequencing accuracy on longer peptides relative to that of other algorithms and improves discriminability of correct and incorrect sequences. Using these advancements, we demonstrate accurate de novo identification of peptide sequences not identifiable using database search-based approaches.
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Affiliation(s)
- Arun Devabhaktuni
- Department of Chemical & Systems Biology, Stanford University , Stanford, California 94035, United States
| | - Joshua E Elias
- Department of Chemical & Systems Biology, Stanford University , Stanford, California 94035, United States
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15
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Nuriel T, Whitehouse J, Ma Y, Mercer EJ, Brown N, Gross SS. ANSID: A Solid-Phase Proteomic Approach for Identification and Relative Quantification of Aromatic Nitration Sites. Front Chem 2016; 3:70. [PMID: 26779476 PMCID: PMC4703760 DOI: 10.3389/fchem.2015.00070] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/11/2015] [Indexed: 12/21/2022] Open
Abstract
Nitration of tyrosine and other aromatic amino acid residues in proteins occurs in the setting of inflammatory, neurodegenerative, and cardiovascular diseases—importantly, this modification has been implicated in the pathogenesis of diverse diseases and the physiological process of aging. To understand the biological consequences of aromatic nitration in both health and disease, it is critical to molecularly identify the proteins that undergo nitration, specify their cognate modification sites and quantify their extent of nitration. To date, unbiased identification of nitrated proteins has often involved painstaking 2D-gel electrophoresis followed by Western Blotting with an anti-nitrotyrosine antibody for detection. Apart from being relatively slow and laborious, this method suffers from limited coverage, the potential for false-positive identifications, and failure to reveal specific amino acid modification sites. To overcome these shortcomings, we have developed a solid-phase, chemical-capture approach for unbiased and high-throughput discovery of nitrotyrosine and nitrotryptophan sites in proteins. Utilizing this method, we have successfully identified several endogenously nitrated proteins in rat brain and a total of 244 nitrated peptides from 145 proteins following in vitro exposure of rat brain homogenates to the nitrating agent peroxynitrite (1 mM). As expected, Tyr residues constituted the great majority of peroxynitrite-mediated protein nitration sites; however, we were surprised to discover several brain proteins that contain nitrated Trp residues. By incorporating a stable-isotope labeling step, this new Aromatic Nitration Site IDentification (ANSID) method was also adapted for relative quantification of nitration site abundances in proteins. Application of the ANSID method offers great potential to advance our understanding of the role of protein nitration in disease pathogenesis and normal physiology.
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Affiliation(s)
- Tal Nuriel
- Department of Pharmacology, Weill Cornell Medical CollegeNew York, NY, USA; Department of Pathology and Cell Biology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical CollegeNew York, NY, USA
| | - Julia Whitehouse
- Department of Pharmacology, Weill Cornell Medical College New York, NY, USA
| | - Yuliang Ma
- Department of Pharmacology, Weill Cornell Medical College New York, NY, USA
| | - Emily J Mercer
- Department of Pharmacology, Weill Cornell Medical CollegeNew York, NY, USA; Department of Surgery, Weill Cornell Medical CollegeNew York, NY, USA
| | - Neil Brown
- Department of Pharmacology, Weill Cornell Medical College New York, NY, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College New York, NY, USA
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16
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Zhang S, Chen L, Shan Y, Sui Z, Wu Q, Zhang L, Liang Z, Zhang Y. Pseudo isobaric peptide termini labelling for relative proteome quantification by SWATH MS acquisition. Analyst 2016; 141:4912-8. [DOI: 10.1039/c6an00388e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The SWATH-pseudo-IPTL method is a promising strategy in quantitative proteomics, and has been efficiently applied in biological studies due to its high quantitative accuracy.
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Affiliation(s)
- Shen Zhang
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- National Chromatographic R. and A. Center
- Dalian 116023
| | - Lingfan Chen
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- National Chromatographic R. and A. Center
- Dalian 116023
| | - Yichu Shan
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- National Chromatographic R. and A. Center
- Dalian 116023
| | - Zhigang Sui
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- National Chromatographic R. and A. Center
- Dalian 116023
| | - Qi Wu
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- National Chromatographic R. and A. Center
- Dalian 116023
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- National Chromatographic R. and A. Center
- Dalian 116023
| | - Zhen Liang
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- National Chromatographic R. and A. Center
- Dalian 116023
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- National Chromatographic R. and A. Center
- Dalian 116023
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17
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Greer T, Hao L, Nechyporenko A, Lee S, Vezina CM, Ricke WA, Marker PC, Bjorling DE, Bushman W, Li L. Custom 4-Plex DiLeu Isobaric Labels Enable Relative Quantification of Urinary Proteins in Men with Lower Urinary Tract Symptoms (LUTS). PLoS One 2015; 10:e0135415. [PMID: 26267142 PMCID: PMC4534462 DOI: 10.1371/journal.pone.0135415] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 07/21/2015] [Indexed: 12/19/2022] Open
Abstract
The relative quantification of proteins using liquid chromatography mass spectrometry (LC-MS) has allowed researchers to compile lists of potential disease markers. These complex quantitative workflows often include isobaric labeling of enzymatically-produced peptides to analyze their relative abundances across multiple samples in a single LC-MS run. Recent efforts by our lab have provided scientists with cost-effective alternatives to expensive commercial labels. Although the quantitative performance of these dimethyl leucine (DiLeu) labels has been reported using known ratios of complex protein and peptide standards, their potential in large-scale proteomics studies using a clinically relevant system has never been investigated. Our work rectifies this oversight by implementing 4-plex DiLeu to quantify proteins in the urine of aging human males who suffer from lower urinary tract symptoms (LUTS). Protein abundances in 25 LUTS and 15 control patients were compared, revealing that of the 836 proteins quantified, 50 were found to be differentially expressed (>20% change) and statistically significant (p-value <0.05). Gene ontology (GO) analysis of the differentiated proteins showed that many were involved in inflammatory responses and implicated in fibrosis. While confirmation of individual protein abundance changes would be required to verify protein expression, this study represents the first report using the custom isobaric label, 4-plex DiLeu, to quantify protein abundances in a clinically relevant system.
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Affiliation(s)
- Tyler Greer
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ling Hao
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anatoliy Nechyporenko
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sanghee Lee
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chad M. Vezina
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Will A. Ricke
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Paul C. Marker
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dale E. Bjorling
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Wade Bushman
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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18
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Chen M, Huang H, He H, Ying W, Liu X, Dai Z, Yin J, Mao N, Qian X, Pan L. Quantitative proteomic analysis of mitochondria from human ovarian cancer cells and their paclitaxel-resistant sublines. Cancer Sci 2015; 106:1075-83. [PMID: 26033570 PMCID: PMC4556398 DOI: 10.1111/cas.12710] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/24/2015] [Accepted: 05/26/2015] [Indexed: 01/10/2023] Open
Abstract
Paclitaxel resistance is a major obstacle for the treatment of ovarian cancer. The chemoresistance mechanisms are partly related to the mitochondria. Identification of the relevant proteins in mitochondria will help in clarifying the possible mechanisms and in selecting effective chemotherapy for patients with paclitaxel resistance. In the present study, mitochondria from two paclitaxel-sensitive human ovarian cancer cell lines (SKOV3 and A2780) and their corresponding resistant cell lines (SKOV3-TR and A2780-TR) were isolated. Guanidine-modified acetyl-stable isotope labeling and liquid chromatography-hybrid linear ion trap Fourier-transform ion cyclotron resonance mass spectrometry (LC-FTICR MS) were performed to find the expressed differential proteins. Comparative proteomic analysis revealed eight differentially expressed proteins in the ovarian cancer cells and their paclitaxel-resistant sublines. Among them, mimitin and 14-3-3 ζ/δ were selected for further research. The effects of mimitin and 14-3-3 ζ/δ were explored using specific siRNA interference in ovarian cancer cell lines and immunohistochemistry in human tissue specimens. The downregulation of mimitin and 14-3-3 ζ/δ using specific siRNA in paclitaxel-resistant ovarian cancer cells led to an increase in the resistance index to paclitaxel. Multivariate analyses demonstrated that lower expression levels of the mimitin and 14-3-3 ζ/δ proteins were positively associated with shorter progression-free survival (PFS) and overall survival (OS) in patients with primary ovarian cancer (mimitin: PFS: P = 0.041, OS: P = 0.003; 14-3-3 ζ/δ: PFS: P = 0.031, OS: P = 0.011). Mimitin and 14-3-3 protein ζ/δ are potential markers of paclitaxel resistance and prognostic factors in ovarian cancer.
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Affiliation(s)
- Ming Chen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong Huang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Haojie He
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, China
| | - Xin Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, China.,Central Laboratory, Yantai Yuhuangding Hospital, Yantai, China
| | - Zhiqin Dai
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Gynecological Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - Jie Yin
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Mao
- Department of Cell Biology, Institute of Basic Medical Sciences, Beijing, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, China
| | - Lingya Pan
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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19
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Applying Proteomics to Investigate Extracellular Matrix in Health and Disease. CURRENT TOPICS IN MEMBRANES 2015; 76:171-96. [PMID: 26610914 DOI: 10.1016/bs.ctm.2015.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The molecular composition of basement membranes (BMs) has traditionally been investigated by candidate-based approaches leading to the identification of key structural components as described in previous chapters. Laminins, collagen IV, nidogens, perlecan, and type XV/XVIII collagen are integral to BMs with isoforms showing tissue specificity. More recently the application of mass spectrometry (MS)-based proteomics has led to the discovery of many more structural and regulatory components of BMs and more broadly, extracellular matrix (ECM). These investigations have revealed tissue-specific signatures of between 100 and 150 ECM components, demonstrating the complexity of the extracellular niche. In addition to providing a structural scaffold for cells, ECM is a dynamic extracellular environment capable of regulating the physical properties of tissues. Global investigations of ECM with proteomics in turn enable systems level analyses and when applied to health and disease states these investigations provide insights into pathways regulating matrix dysregulation. This chapter focuses on the methods used to extract ECM and on the analysis of its composition using MS-based proteomics, and it provides examples of how these approaches have been used to investigate health and disease states.
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20
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Frost DC, Greer T, Xiang F, Liang Z, Li L. Development and characterization of novel 8-plex DiLeu isobaric labels for quantitative proteomics and peptidomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1115-24. [PMID: 25981542 PMCID: PMC4837894 DOI: 10.1002/rcm.7201] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/05/2015] [Accepted: 03/22/2015] [Indexed: 05/08/2023]
Abstract
RATIONALE Relative quantification of proteins via their enzymatically digested peptide products determines disease biomarker candidate lists in discovery studies. Isobaric label-based strategies using TMT and iTRAQ allow for up to 10 samples to be multiplexed in one experiment, but their expense limits their use. The demand for cost-effective tagging reagents capable of multiplexing many samples led us to develop an 8-plex version of our isobaric labeling reagent, DiLeu. METHODS The original 4-plex DiLeu reagent was extended to an 8-plex set by coupling isotopic variants of dimethylated leucine to an alanine balance group designed to offset the increasing mass of the label's reporter group. Tryptic peptides from a single protein digest, a protein mixture digest, and Saccharomyces cerevisiae lysate digest were labeled with 8-plex DiLeu and analyzed via nanospray liquid chromatography/tandem mass spectrometry (nanoLC/MS(2) ) on a Q-Exactive Orbitrap mass spectrometer. Characteristics of 8-plex DiLeu-labeled peptides, including quantitative accuracy and fragmentation, were examined. RESULTS An 8-plex set of DiLeu reagents with 1 Da spaced reporters was synthesized at a yield of 36%. The average cost to label eight 100 µg peptide samples was calculated to be approximately $15. Normalized collision energy tests on the Q-Exactive revealed that a higher-energy collisional dissociation value of 27 generated the optimum number of high-quality spectral matches. Relative quantification of DiLeu-labeled peptides yielded normalized median ratios accurate to within 12% of their expected values. CONCLUSIONS Cost-effective 8-plex DiLeu reagents can be synthesized and applied to relative peptide and protein quantification. These labels increase the multiplexing capacity of our previous 4-plex implementation without requiring high-resolution instrumentation to resolve reporter ion signals.
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Affiliation(s)
| | - Tyler Greer
- Department of Chemistry, University of Wisconsin–Madison
| | - Feng Xiang
- School of Pharmacy, University of Wisconsin–Madison
| | - Zhidan Liang
- School of Pharmacy, University of Wisconsin–Madison
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin–Madison
- Department of Chemistry, University of Wisconsin–Madison
- Address reprint requests to: Dr. Lingjun Li, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI 53705, USA. . Phone: (608) 265-8491, Fax: (608) 262-5345
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21
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Zhang S, Wu Q, Shan Y, Sui Z, Zhang L, Zhang Y. A paired ions scoring algorithm based on Morpheus for simultaneous identification and quantification of proteome samples prepared by isobaric peptide termini labeling strategies. Proteomics 2015; 15:1781-8. [PMID: 25643849 DOI: 10.1002/pmic.201400262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 12/10/2014] [Accepted: 01/19/2015] [Indexed: 11/07/2022]
Abstract
The isobaric peptide termini labeling (IPTL) method is a promising strategy in quantitative proteomics for its high accuracy, while the increased complexity of MS2 spectra originated from the paired b, y ions has adverse effect on the identification and the coverage of quantification. Here, a paired ions scoring algorithm (PISA) based on Morpheus, a database searching algorithm specifically designed for high-resolution MS2 spectra, was proposed to address this issue. PISA was first tested on two 1:1 mixed IPTL datasets, and increases in peptide to spectrum matchings, distinct peptides and protein groups compared to Morpheus itself and MASCOT were shown. Furthermore, the quantification is simultaneously performed and 100% quantification coverage is achieved by PISA since each of the identified peptide to spectrum matchings has several pairs of fragment ions which could be used for quantification. Then the PISA was applied to the relative quantification of human hepatocellular carcinoma cell lines with high and low metastatic potentials prepared by an IPTL strategy.
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Affiliation(s)
- Shen Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qi Wu
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Yichu Shan
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China
| | - Zhigang Sui
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Dalian, P. R. China
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22
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Frost DC, Greer T, Li L. High-resolution enabled 12-plex DiLeu isobaric tags for quantitative proteomics. Anal Chem 2014; 87:1646-54. [PMID: 25405479 PMCID: PMC4318621 DOI: 10.1021/ac503276z] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Multiplex
isobaric tags (e.g., tandem mass tags (TMT) and isobaric
tags for relative and absolute quantification (iTRAQ)) are a valuable
tool for high-throughput mass spectrometry based quantitative proteomics.
We have developed our own multiplex isobaric tags, DiLeu, that feature
quantitative performance on par with commercial offerings but can
be readily synthesized in-house as a cost-effective alternative. In
this work, we achieve a 3-fold increase in the multiplexing capacity
of the DiLeu reagent without increasing structural complexity by exploiting
mass defects that arise from selective incorporation of 13C, 15N, and 2H stable isotopes in the reporter
group. The inclusion of eight new reporter isotopologues that differ
in mass from the existing four reporters by intervals of 6 mDa yields
a 12-plex isobaric set that preserves the synthetic simplicity and
quantitative performance of the original implementation. We show that
the new reporter variants can be baseline-resolved in high-resolution
higher-energy C-trap dissociation (HCD) spectra, and we demonstrate
accurate 12-plex quantitation of a DiLeu-labeled Saccharomyces
cerevisiae lysate digest via high-resolution nano
liquid chromatography–tandem mass spectrometry (nanoLC–MS2) analysis on an Orbitrap Elite mass spectrometer.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin , 777 Highland Avenue, Madison, Wisconsin 53705, United States
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23
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Yang W, Kernstock R, Simmons N, Alak A. Guanidinated protein internal standard for immunoaffinity-liquid chromatography/tandem mass spectrometry quantitation of protein therapeutics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1489-1500. [PMID: 24861599 DOI: 10.1002/rcm.6924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 04/14/2014] [Accepted: 04/15/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE A protein internal standard (IS) is essential and superior to a peptide IS to achieve reproducible results in the quantitation of protein therapeutics using immunoaffinity-liquid chromatography/tandem mass spectrometry (LC/MS/MS). Guanidination has been used as a protein post-modification technique for more than half a century. A decade ago, the modification was applied to lysine-ending peptides to enhance their MALDI responses and peptide sequencing coverage. However, rarely has tryptic digestion of guanidinated proteins been investigated, likely due to the early conclusion that trypsin did not hydrolyze peptide bonds involving homoarginine in guanidinated proteins. In this study, the opposite was observed. Guanidinated lysine residues of proteins did not hinder the access of trypsin allowing for proteolytic digestion. Based on this observation, a new concept of internal standard, named Guanidinated Protein Internal Standard (GP-IS), was proposed for LC/MS/MS quantitation of protein therapeutics. METHODS The GP-IS is prepared by treating a portion of the therapeutic protein (analyte) with guanidine to convert arginine residues in the protein into homoarginine residues. After tryptic digestion, the GP-IS produces a series of homoarginine-ending peptides plus another series of arginine-ending peptides. One of the homoarginine-ending peptides, which corresponds to the analyte surrogate (lysine-ending) peptide, was chosen as a peptide internal standard (GP-PIS) for LC/MS/MS quantitation. RESULTS Using this GP-IS approach, a sensitive and robust immunoaffinity-LC/MS/MS assay was developed and fully validated with a linearity range from 10 to 1000 ng/mL using 200 μL of human serum for the quantitation of an Astellas protein drug in clinical development. CONCLUSIONS The proposed strategy allows LC/MS/MS to play an ever-increasing role in bioanalytical support for protein therapeutics development because of its capability of completely tracking all variations from the beginning to the end of sample analysis, easier preparation compared to isotope-labeled protein-IS, and greater flexibility for changing to alternate analyte surrogate peptides.
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Affiliation(s)
- Wenchu Yang
- Bioanalysis-US, Astellas Research Institute of America, Skokie, IL, 60077, USA
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24
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Relative quantitation of glycopeptides based on stable isotope labeling using MALDI-TOF MS. Molecules 2014; 19:9944-61. [PMID: 25010467 PMCID: PMC6271863 DOI: 10.3390/molecules19079944] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/01/2014] [Accepted: 07/07/2014] [Indexed: 12/19/2022] Open
Abstract
We have developed an effective, sensitive method for quantitative glycopeptide profiling using stable isotope labeling and MALDI-TOF mass spectrometry (MS). In this study, we synthesized benzoic acid-d0N-succinimidyl ester (BzOSu) and benzoic acid-d5N-succinimidyl ester (d-BzOSu) as light and heavy isotope reagents for stable isotope quantification for the comparative analysis of glycopeptides. Using this approach provided enhanced ionization efficiency in both positive and negative modes by MALDI-TOF MS. These reagents were quantitatively reacted with glycopeptides from human serum IgG (hIgG) at a wide range of concentrations; the labeling efficiency of the glycopeptides showed high reproducibility and a good calibration curve was obtained. To demonstrate the practical utility of this approach, we characterized the structures of glycopeptides from hIgG and from IgG1 produced by myeloma plasma. The glycopeptides were quantitatively analyzed by mixing Bz-labeled IgG1 glycopeptides with d-Bz-labeled hIgG glycopeptides. Glycan structural identification of the hIgG glycopeptides was demonstrated by combining the highly specific recognition of endo-β-N-acetyl glucosaminidases from Streptococcus pyogenes (endoS) or from Streptococcus pneumoniae (endo-D) with MALDI-TOF MS analysis. The obtained data revealed the glycan profile and the ratio of glycan structural isomers containing a galactosylated extension on IgG1, IgG2 and IgG3 glycopetides.
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25
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Mortera SL, Dioni I, Greco V, Neri C, Rovero P, Urbani A. pH-regulated formation of side products in the reductive amination approach for differential labeling of peptides in relative quantitative experiments. Electrophoresis 2014; 35:1259-67. [DOI: 10.1002/elps.201300484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stefano Levi Mortera
- Department of System Medicine; University of Rome Tor Vergata; Rome Italy
- Proteomic and Metabonomic Laboratory; Santa Lucia Foundation; Rome Italy
| | - Ilaria Dioni
- Section of Pharmaceutical Sciences and Nutraceutics; Department NeuroFarBa; Laboratory of Peptide and Protein Chemistry and Biology; University of Florence; Florence Italy
| | - Viviana Greco
- Proteomic and Metabonomic Laboratory; Santa Lucia Foundation; Rome Italy
| | - Cristina Neri
- Proteomic and Metabonomic Laboratory; Santa Lucia Foundation; Rome Italy
| | - Paolo Rovero
- Section of Pharmaceutical Sciences and Nutraceutics; Department NeuroFarBa; Laboratory of Peptide and Protein Chemistry and Biology; University of Florence; Florence Italy
| | - Andrea Urbani
- Department of System Medicine; University of Rome Tor Vergata; Rome Italy
- Proteomic and Metabonomic Laboratory; Santa Lucia Foundation; Rome Italy
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26
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Pan Y, Ye M, Zheng H, Cheng K, Sun Z, Liu F, Liu J, Wang K, Qin H, Zou H. Trypsin-Catalyzed N-Terminal Labeling of Peptides with Stable Isotope-Coded Affinity Tags for Proteome Analysis. Anal Chem 2014; 86:1170-7. [DOI: 10.1021/ac403060d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanbo Pan
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Zheng
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cheng
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Sun
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangjie Liu
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liu
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keyun Wang
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hanfa Zou
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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27
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Tang Y, Mackey J, Lai R, Ghosh S, Santos C, Graham K, Damaraju S, Pasdar M, Li L. Quantitative proteomic analysis of HER2 normal and overexpressing MCF-7 breast cancer cells revealed proteomic changes accompanied with HER2 gene amplification. J Proteomics 2013; 91:200-9. [DOI: 10.1016/j.jprot.2013.06.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 06/29/2013] [Indexed: 12/18/2022]
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28
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Fu F, Cheng VWT, Wu Y, Tang Y, Weiner JH, Li L. Comparative proteomic and metabolomic analysis of Staphylococcus warneri SG1 cultured in the presence and absence of butanol. J Proteome Res 2013; 12:4478-89. [PMID: 23961999 DOI: 10.1021/pr400533m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The complete genome of the solvent tolerant Staphylococcus warneri SG1 was recently published. This Gram-positive bacterium is tolerant to a large spectrum of organic solvents including short-chain alcohols, alkanes, esters and cyclic aromatic compounds. In this study, we applied a two-dimensional liquid chromatography (2D-LC) mass spectrometry (MS) shotgun approach, in combination with quantitative 2-MEGA (dimethylation after guanidination) isotopic labeling, to compare the proteomes of SG1 grown under butanol-free and butanol-challenged conditions. In total, 1585 unique proteins (representing 65% of the predicted open reading frames) were identified, covering all major metabolic pathways. Of the 967 quantifiable proteins by 2-MEGA labeling, 260 were differentially expressed by at least 1.5-fold. These proteins are involved in energy metabolism, oxidative stress response, lipid and cell envelope biogenesis, or have chaperone functions. We also applied differential isotope labeling LC-MS to probe metabolite changes in key metabolic pathways upon butanol stress. This is the first comprehensive proteomic and metabolomic study of S. warneri SG1 and presents an important step toward understanding its physiology and mechanism of solvent tolerance.
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Affiliation(s)
- Feifei Fu
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta T6G2G2, Canada
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29
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Lo A, Weiner JH, Li L. Analytical performance of reciprocal isotope labeling of proteome digests for quantitative proteomics and its application for comparative studies of aerobic and anaerobic Escherichia coli proteomes. Anal Chim Acta 2013; 795:25-35. [DOI: 10.1016/j.aca.2013.07.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/14/2013] [Accepted: 07/29/2013] [Indexed: 12/18/2022]
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30
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Automation of dimethylation after guanidination labeling chemistry and its compatibility with common buffers and surfactants for mass spectrometry-based shotgun quantitative proteome analysis. Anal Chim Acta 2013; 788:81-8. [DOI: 10.1016/j.aca.2013.05.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/14/2013] [Accepted: 05/17/2013] [Indexed: 12/29/2022]
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31
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Kweon HK, Andrews PC. Quantitative analysis of global phosphorylation changes with high-resolution tandem mass spectrometry and stable isotopic labeling. Methods 2013; 61:251-9. [PMID: 23611819 PMCID: PMC3700606 DOI: 10.1016/j.ymeth.2013.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 03/05/2013] [Accepted: 04/13/2013] [Indexed: 11/23/2022] Open
Abstract
Quantitative measurement of specific protein phosphorylation sites is a primary interest of biologists, as site-specific phosphorylation information provides insights into cell signaling networks and cellular dynamics at a system level. Over the last decade, selective phosphopeptide enrichment methods including IMAC and metal oxides (TiO₂ and ZrO₂) have been developed and greatly facilitate large scale phosphoproteome analysis of various cells, tissues and living organisms, in combination with modern mass spectrometers featuring high mass accuracy and high mass resolution. Various quantification strategies have been applied to detecting relative changes in expression of proteins, peptides, and specific modifications between samples. The combination of mass spectrometry-based phosphoproteome analysis with quantification strategies provides a straightforward and unbiased method to identify and quantify site-specific phosphorylation. We describe common strategies for mass spectrometric analysis of stable isotope labeled samples, as well as two widely applied phosphopeptide enrichment methods based on IMAC(NTA-Fe³⁺) and metal oxide (ZrO₂). Instrumental configurations for on-line LC-tandem mass spectrometric analysis and parameters of conventional bioinformatic analysis of large data sets are also considered for confident identification, localization, and reliable quantification of site-specific phosphorylation.
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Affiliation(s)
- Hye Kyong Kweon
- Department of Biological Chemistry, University of Michigan, USA.
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32
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Abstract
Mass spectrometry (MS) analysis of peptides and proteins has evolved dramatically over the last 20 years. Improvement of MS instrumentation, computational data analysis, and the availability of complete sequence databases for many species have made large-scale proteomics analyses possible. The measurement of global protein abundance by quantitative mass spectrometry has the potential to increase both speed and impact of biological and clinical research. However, to be able to detect and identify potential biomarkers, reproducible and accurate quantification is essential. The following chapter describes how to perform quantitative protein profiling using stable isotope labeling methods. Throughout, there is a focus on guidance in selection of an appropriate labeling strategy. With that in mind, we have included a section on acquisition and understanding of the liquid chromatography-mass spectrometry (LC-MS) data format. Further, we describe the different stable isotope labeling methods and their pros and cons. We start by giving an overview of the overall quantitative proteomics workflow in which extracting relevant biological information from the acquired data is the ultimate goal.
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Affiliation(s)
- Johan Lengqvist
- Biopharmaceutical Research Unit, Department of Protein Science, Novo Nordisk A/S, Måløv, Denmark
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33
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Nihashi Y, Miyashita M, Awane H, Miyagawa H. Differential 14N/15N-Labeling of Peptides Using N-Terminal Charge Derivatization with a High-Proton Affinity for Straightforward de novo Peptide Sequencing. Mass Spectrom (Tokyo) 2013; 2:A0024. [DOI: 10.5702/massspectrometry.a0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 10/29/2013] [Indexed: 11/23/2022] Open
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34
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Matthiesen R, Carvalho AS. Methods and algorithms for quantitative proteomics by mass spectrometry. Methods Mol Biol 2013; 1007:183-217. [PMID: 23666727 DOI: 10.1007/978-1-62703-392-3_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein quantitation by mass spectrometry (MS) is attractive since it is possible to obtain both identification and quantitative values of proteins and their posttranslational modifications in a single experiment. In contrast, protein arrays only provide quantitative values of targeted proteins and their modifications. There are an overwhelming number of quantitative MS methods for protein and peptide quantitation. The aim here is to provide an overview of the most common MS methods and algorithms used in quantitative proteomics and discuss the computational algorithms needed to reliably quantitate proteins, peptides, and their posttranslational modifications. One of the main challenges in data analysis of many experimental projects is to pipe together a number of software solutions that are either commercial or freely available. The aim of this chapter is to provide a good set of algorithms, ideas, and resources that can easily be implemented in scripting language like R, Python, or Perl. By understanding the algorithmic ideas presented here, data from any instrument or modified experimental protocol can be analyzed and is therefore in the authors' opinion more valuable than a black box concept.
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Affiliation(s)
- Rune Matthiesen
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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35
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A highly sensitive isotope-coded derivatization method and its application for the mass spectrometric analysis of analytes containing the carboxyl group. Anal Chim Acta 2013; 758:114-21. [DOI: 10.1016/j.aca.2012.11.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 11/01/2012] [Accepted: 11/06/2012] [Indexed: 11/20/2022]
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36
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Rauniyar N, Gao B, McClatchy DB, Yates JR. Comparison of protein expression ratios observed by sixplex and duplex TMT labeling method. J Proteome Res 2012; 12:1031-9. [PMID: 23214967 DOI: 10.1021/pr3008896] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Stable isotope labeling via isobaric derivatization of peptides is a universally applicable approach that enables concurrent identification and quantification of proteins in different samples using tandem mass spectrometry. In this study, we evaluated the performance of amine-reactive isobaric tandem mass tag (TMT), available as duplex and sixplex sets, with regard to their ability to elucidate protein expression changes. Using rat brain tissue from two different developmental time points, postnatal day 1 (p1) and 45 (p45), as a model system, we compared the protein expression ratios (p45/p1) observed using duplex TMT tags in triplicate measurements versus sixplex tag in a single LC-MS/MS analysis. A correlation of 0.79 in relative protein abundance was observed in the proteins quantified by these two sets of reagents. However, more proteins passed the criteria for significant fold change (-1.0 ≤ log(2) ratio (p45/p1) ≥ +1.0 and p < 0.05) in the sixplex analysis. Nevertheless, in both methods most proteins showing significant fold change were identified by multiple spectra, increasing their quantification precision. Additionally, the fold change in p45 rats against p1, observed in TMT experiments, was corroborated by a metabolic labeling strategy where relative quantification of differentially expressed proteins was obtained using (15)N-labeled p45 rats as an internal standard.
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Affiliation(s)
- Navin Rauniyar
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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37
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Leng J, Zhu D, Wu D, Zhu T, Zhao N, Guo Y. Analysis of the differentially expressed low molecular weight peptides in human serum via an N-terminal isotope labeling technique combining nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2555-2562. [PMID: 23008073 DOI: 10.1002/rcm.6369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Peptidomics analysis of human serum is challenging due to the low abundance of serum peptides and interference from the complex matrix. This study analyzed the differentially expressed (DE) low molecular weight peptides in human serum integrating a DMPITC-based N-terminal isotope labeling technique with nano-liquid chromatography and matrix-assisted laser desorption/ionization mass spectrometry (nano-LC/MALDI-MS). METHODS The workflow introduced a [d(6)]-4,6-dimethoxypyrimidine-2-isothiocyanate (DMPITC)-labeled mixture of aliquots from test samples as the internal standard. The spiked [d(0)]-DMPITC-labeled samples were separated by nano-LC then spotted on the MALDI target. Both quantitative and qualitative studies for serum peptides were achieved based on the isotope-labeled peaks. RESULTS The DMPITC labeling technique combined with nano-LC/MALDI-MS not only minimized the errors in peptide quantitation, but also allowed convenient recognition of the labeled peptides due to the 6 Da mass difference. The data showed that the entire research procedure as well as the subsequent data analysis method were effective, reproducible, and sensitive for the analysis of DE serum peptides. CONCLUSIONS This study successfully established a research model for DE serum peptides using DMPITC-based N-terminal isotope labeling and nano-LC/MALDI-MS. Application of the DMPITC-based N-terminal labeling technique is expected to provide a promising tool for the investigation of peptides in vivo, especially for the analysis of DE peptides under different biological conditions.
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Affiliation(s)
- Jiapeng Leng
- Shanghai Mass Spectrometry Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
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38
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Moskaleva NE, Zgoda VG. [Current methods of cytochrome p450 analysis]. BIOMEDITSINSKAIA KHIMIIA 2012; 58:617-634. [PMID: 23350195 DOI: 10.18097/pbmc20125806617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Current review describes recent approaches of cytochrome P450 concentration and activity evaluation. Special attention paid to modem methods of proteomic analysis such as electrophoresis and chromato-mass-spectrometry. Methods of targeted proteomic applicable for quantitative and qualitative study of P450s in biological samples as well as methods for the enzyme activity measurements are reviewed. Finally, data on correlation between certain P450 isoform content and its specific enzymatic activities were described and discussed in the review.
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39
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Yang SJ, Nie AY, Zhang L, Yan GQ, Yao J, Xie LQ, Lu HJ, Yang PY. A novel quantitative proteomics workflow by isobaric terminal labeling. J Proteomics 2012; 75:5797-806. [DOI: 10.1016/j.jprot.2012.07.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/01/2012] [Accepted: 07/04/2012] [Indexed: 12/28/2022]
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40
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Huang SY, Hsieh YT, Chen CH, Chen CC, Sung WC, Chou MY, Chen SF. Automatic Disulfide Bond Assignment Using a1Ion Screening by Mass Spectrometry for Structural Characterization of Protein Pharmaceuticals. Anal Chem 2012; 84:4900-6. [DOI: 10.1021/ac3005007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Kovanich D, Cappadona S, Raijmakers R, Mohammed S, Scholten A, Heck AJR. Applications of stable isotope dimethyl labeling in quantitative proteomics. Anal Bioanal Chem 2012; 404:991-1009. [DOI: 10.1007/s00216-012-6070-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 04/13/2012] [Accepted: 04/23/2012] [Indexed: 01/03/2023]
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42
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Lin CY, Ma YC, Pai PJ, Her GR. A comparative study of glycoprotein concentration, glycoform profile and glycosylation site occupancy using isotope labeling and electrospray linear ion trap mass spectrometry. Anal Chim Acta 2012; 728:49-56. [DOI: 10.1016/j.aca.2012.03.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/26/2012] [Accepted: 03/31/2012] [Indexed: 12/19/2022]
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43
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Zimnicka M, Moss CL, Chung TW, Hui R, Tureček F. Tunable charge tags for electron-based methods of peptide sequencing: design and applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:608-620. [PMID: 21952752 DOI: 10.1007/s13361-011-0184-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 05/24/2011] [Accepted: 05/24/2011] [Indexed: 05/31/2023]
Abstract
Charge tags using basic auxiliary functional groups 6-aminoquinolinylcarboxamido, 4-aminopyrimidyl-1-methylcarboxamido, 2-aminobenzoimidazolyl-1-methylcarboxamido, and the fixed-charge 4-(dimethylamino)pyridyl-1-carboxamido moiety are evaluated as to their properties in electron transfer dissociation mass spectra of arginine C-terminated peptides. The neutral tags have proton affinities that are competitive with those of amino acid residues in peptides. Charge reduction by electron transfer from fluoranthene anion-radicals results in peptide backbone dissociations that improve sequence coverage by providing extensive series of N-terminal c-type fragments without impeding the formation of C-terminal z fragments. Comparison of ETD mass spectra of free and tagged peptides allows one to resolve ambiguities in fragment ion assignment through mass shifts of c ions. Simple chemical procedures are reported for N-terminal tagging of Arg-containing tryptic peptides.
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Affiliation(s)
- Magdalena Zimnicka
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA 98195-1700, USA
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44
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She YM, Rosu-Myles M, Walrond L, Cyr TD. Quantification of protein isoforms in mesenchymal stem cells by reductive dimethylation of lysines in intact proteins. Proteomics 2012; 12:369-79. [PMID: 22144135 PMCID: PMC3440571 DOI: 10.1002/pmic.201100308] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 10/11/2011] [Accepted: 11/02/2011] [Indexed: 11/05/2022]
Abstract
Mass spectrometry (MS)-based quantification of highly homologous proteins in complex samples has proven difficult due to subtle sequence variations and the wide dynamic range of protein isoforms present. Herein, we report the use of reductive dimethylation on intact proteins to quantitatively compare protein isoform expression in the nucleus and cytoplasm of mesenchymal stem cells (MSC) and normal stroma. By coupling fixed-charge MS/MS scanning, high-resolution UPLC FT-MS data-dependent acquisition and MASCOT-based data mining, hydrogen/deuterium-labeled dimethyl-lysine peptides were simultaneously captured allowing the accurate comparison of 123 protein isoforms in parallel LC MS/MS runs. Thirty-four isoforms were identified that had expression levels specific to MSC. Where possible, proteomic analyses were verified by Western blotting and were demonstrated to be divergent from the level of gene transcription detected for certain proteins. Our analysis provides a protein isoform signature specific to MSC and demonstrates the suitability of dimethyl-lysine labeling on intact proteins for quantifying highly homologous proteins on a proteome-wide scale.
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Affiliation(s)
- Yi-Min She
- Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, Canada
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45
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Guo J, Prokai-Tatrai K, Prokai L. Relative quantitation of protein nitration by liquid chromatography-mass spectrometry using isotope-coded dimethyl labeling and chemoprecipitation. J Chromatogr A 2012; 1232:266-75. [PMID: 22285050 DOI: 10.1016/j.chroma.2011.12.100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 12/15/2011] [Accepted: 12/30/2011] [Indexed: 12/19/2022]
Abstract
Protein nitration has been recognized as an important biomarker for nitroxidative stress associated with various diseases. While identification of protein targets for nitration is important, its quantitative profiling also is necessary to understand the biological impact of this low-abundance posttranslational modification. We have previously reported an efficient and straightforward enrichment method for nitropeptides to reduce sample complexity and permit unambiguous site-specific identifications by LC-MS analyses. This approach relies on two chemical derivatization steps: specifically reductive methylation of aliphatic amines and, then, conversion of nitrotyrosines to the corresponding aminotyrosines before their selective capture by a solid-phase reagent we introduced previously. Hence, the method inherently offers the opportunity for relative quantitation of nitropeptides by using isotopic variants of formaldehyde for reductive methylation. This simple method was tested via LC-MS analyses of differently N-methylated nitropeptides and nitroubiquitin as a model nitroprotein enriched from human serum albumin digest and from human plasma, respectively.
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Affiliation(s)
- Jia Guo
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
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46
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Rauniyar N, Prokai L. Isotope-coded dimethyl tagging for differential quantification of posttranslational protein carbonylation by 4-hydroxy-2-nonenal, an end-product of lipid peroxidation. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:976-85. [PMID: 22012663 PMCID: PMC3197809 DOI: 10.1002/jms.1978] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Peroxidation of cellular membrane lipids, rich in polyunsaturated fatty acids, generates electrophilic, α, β-unsaturated aldehydes such as 4-hydroxy-2-nonenal (HNE). HNE is a highly reactive and cytotoxic molecule that can react with the nucleophilic sites in proteins causing posttranslational modification. The identification of protein targets is an important first step; however, quantitative profiling of site-specific modifications is necessary to understand the biological impact of HNE-induced carbonylation. We report a method that uses light (H(12)CHO) and heavy (D(13)CDO) isotopic variant of formaldehyde to differentially label primary amines (N-termini and ε-amino group of lysines) in peptides through reductive methylation and, combined with selective enrichment of modified peptides, permits comparison of the extent of carbonylation in two samples after mixing for simultaneous liquid chromatography-mass spectrometry. Specifically, dimethyl-labeled peptide carbonyls were fractionated from unmodified peptides using solid-phase hydrazide chemistry to immobilize them to porous glass beads and, after removing the unmodified peptides by thoroughly washing the beads, subsequently recover them by acid-catalyzed hydrolysis. The method was developed using HNE-modified synthetic peptides and also showing enrichment from a complex matrix of digested human plasma proteins. Applicability was confirmed using apomyoglobin as an analyte, implicating thereby its potential value to proteome-wide identification and relative quantification of posttranslational protein carbonylation with residue-specific information. Because HNE attachment may not necessarily cause change in protein abundance, this modification-focused quantification should facilitate the characterization of accompanied changes in protein function and, also, provide important insights into molecular signaling mechanisms and a better understanding of cellular processes associated with oxidative stress.
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Affiliation(s)
| | - Laszlo Prokai
- Correspondence to: Laszlo Prokai, Department of Molecular Biology & Immunology, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76107
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47
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Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates. Nat Protoc 2011; 6:1578-611. [PMID: 21959240 DOI: 10.1038/nprot.2011.382] [Citation(s) in RCA: 236] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Analysis of the sequence and nature of protein N termini has many applications. Defining the termini of proteins for proteome annotation in the Human Proteome Project is of increasing importance. Terminomics analysis of protease cleavage sites in degradomics for substrate discovery is a key new application. Here we describe the step-by-step procedures for performing terminal amine isotopic labeling of substrates (TAILS), a 2- to 3-d (depending on method of labeling) high-throughput method to identify and distinguish protease-generated neo-N termini from mature protein N termini with all natural modifications with high confidence. TAILS uses negative selection to enrich for all N-terminal peptides and uses primary amine labeling-based quantification as the discriminating factor. Labeling is versatile and suited to many applications, including biochemical and cell culture analyses in vitro; in vivo analyses using tissue samples from animal and human sources can also be readily performed. At the protein level, N-terminal and lysine amines are blocked by dimethylation (formaldehyde/sodium cyanoborohydride) and isotopically labeled by incorporating heavy and light dimethylation reagents or stable isotope labeling with amino acids in cell culture labels. Alternatively, easy multiplex sample analysis can be achieved using amine blocking and labeling with isobaric tags for relative and absolute quantification, also known as iTRAQ. After tryptic digestion, N-terminal peptide separation is achieved using a high-molecular-weight dendritic polyglycerol aldehyde polymer that binds internal tryptic and C-terminal peptides that now have N-terminal alpha amines. The unbound naturally blocked (acetylation, cyclization, methylation and so on) or labeled mature N-terminal and neo-N-terminal peptides are recovered by ultrafiltration and analyzed by tandem mass spectrometry (MS/MS). Hierarchical substrate winnowing discriminates substrates from the background proteolysis products and non-cleaved proteins by peptide isotope quantification and bioinformatics search criteria.
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48
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Lu J, Boeren S, de Vries SC, van Valenberg HJF, Vervoort J, Hettinga K. Filter-aided sample preparation with dimethyl labeling to identify and quantify milk fat globule membrane proteins. J Proteomics 2011; 75:34-43. [PMID: 21907314 DOI: 10.1016/j.jprot.2011.07.031] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 07/19/2011] [Accepted: 07/29/2011] [Indexed: 10/17/2022]
Abstract
Bovine milk is a major nutrient source in many countries and it is produced at an industrial scale. Milk is a complex mixture of proteins, fats, carbohydrates, vitamins and minerals. The composition of the bovine milk samples can vary depending on the genetic makeup of the bovine species as well as environmental factors. It is therefore important to study the qualitative and quantitative differences of bovine milk samples. Proteins in milk can be present in casein micelles, in the serum (the water soluble fraction) or in fat globules. These fat globules have a double membrane layer with proteins being bound to or being incapsulated in the membrane layer. The identification and molecular composition of the milk proteins have gained increased interest in recent years. Proteomic techniques make it now possible to identify up to many thousands of proteins in one sample, however quantification of proteins is as yet not straightforward. We analyzed the proteins of the milk fat globule membrane using dimethyl labeling methods combined with a filter-aided sample preparation protocol. Using these methods, it is now possible to quantitatively study the detailed protein composition of many milk samples in a short period of time.
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Affiliation(s)
- Jing Lu
- Dairy Science and Technology, Product Design and Quality Management Group, Wageningen University and Research Center, Bomenweg 2, 6700 EV, Wageningen, Netherlands
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49
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Leng J, Wang H, Zhang L, Zhang J, Wang H, Cai T, Yao J, Guo Y. Integration of high accuracy N-terminus identification in peptide sequencing and comparative protein analysis via isothiocyanate-based isotope labeling reagent with ESI ion-trap TOF MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1204-1213. [PMID: 21953103 DOI: 10.1007/s13361-011-0129-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/23/2011] [Accepted: 03/13/2011] [Indexed: 05/31/2023]
Abstract
A multifunctional isothiocyanate-based isotope labeling reagent, [d (0)]-/[d (6)]-4,6-dimethoxy pyrimidine-2-isothiocyanate (DMPITC), has been developed for accurate N-terminus identification in peptide sequencing and comparative protein analysis by ESI Ion-trap TOF mass spectrometry. In contrast with the conventional labeling reagent phenyl isothiocyanate (PITC), DMPITC showed more desirable properties such as rapid labeling, sensitivity enhancement, and facilitating peptide sequencing. More significantly, DMPITC-based labeling strategy possessed the capacity of higher reliable N-terminus identification owning to the high-yield b(1) ion combined with the isotope validation of 6 Da. Meanwhile, it also showed potential in differentiating isomeric residues of leucine and isoleucine at N-terminus on the basis of the relative abundance ratios between the fragment ions of their respective b(1) ions. The strategy not only allows accurate interpretation for peptide but also ensures rapid and sensitive comparative analysis for protein by direct MS analysis. Using trypsin-digested bovine serum albumin (BSA), both peptide N-terminus identification and quantitative analysis were accomplished with high accuracy, efficiency, and reproducibility. The application of DMPITC-based labeling strategy is expected to serve as a promising tool for proteome research.
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Affiliation(s)
- Jiapeng Leng
- Shanghai Mass Spectrometry Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd., Shanghai, 200032, China
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Li S, Liu X, Wei L, Wang H, Zhang J, Wei H, Qian X, Jiang Y, He F. Plasma biomarker screening for liver fibrosis with the N-terminal isotope tagging strategy. SCIENCE CHINA-LIFE SCIENCES 2011; 54:393-402. [PMID: 21574042 PMCID: PMC7088802 DOI: 10.1007/s11427-011-4165-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 02/22/2011] [Indexed: 02/08/2023]
Abstract
A non-invasive diagnostic approach is crucial for the evaluation of severity of liver disease, treatment decisions, and assessing drug efficacy. This study evaluated plasma proteomic profiling via an N-terminal isotope tagging strategy coupled with liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry measurement to detect liver fibrosis staging. Pooled plasma from different liver fibrosis stages, which were assessed in advance by the current gold-standard of liver biopsy, was quantitatively analyzed. A total of 72 plasma proteins were found to be dysregulated during the fibrogenesis process, and this finding constituted a valuable candidate plasma biomarker bank for follow-up analysis. Validation results of fibronectin by Western blotting reconfirmed the mass-based data. Ingenuity Pathways Analysis showed four types of metabolic networks for the functional effect of liver fibrosis disease in chronic hepatitis B patients. Consequently, quantitative proteomics via the N-terminal acetyl isotope labeling technique provides an effective and useful tool for screening plasma candidate biomarkers for liver fibrosis. We quantitatively monitored the fibrogenesis process in CHB patients. We discovered many new valuable candidate biomarkers for the diagnosis of liver fibrosis and also partly identified the mechanism involved in liver fibrosis disease. These results provide a clearer understanding of liver fibrosis pathophysiology and will also hopefully lead to improvement of clinical diagnosis and treatment.
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Affiliation(s)
- ShuLong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
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