1
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. Mass Spectrom Rev 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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2
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Tian X, Permentier HP, Bischoff R. Chemical isotope labeling for quantitative proteomics. Mass Spectrom Rev 2023; 42:546-576. [PMID: 34091937 PMCID: PMC10078755 DOI: 10.1002/mas.21709] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry-based proteome quantification approaches. An increasingly attractive strategy is multiplex isotope labeling, which significantly improves the accuracy, precision and throughput of quantitative proteomics in the data-dependent acquisition mode. Isotope labeling-based approaches can be classified into MS1-based and MS2-based quantification. In this review, we give an overview of approaches based on chemical isotope labeling and discuss their principles, benefits, and limitations with the goal to give insights into fundamental questions and provide a useful reference for choosing a method for quantitative proteomics. As a perspective, we discuss the current possibilities and limitations of multiplex, isotope labeling approaches for the data-independent acquisition mode, which is increasing in popularity.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Hjalmar P. Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
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3
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Sivanich MK, Gu T, Tabang DN, Li L. Recent advances in isobaric labeling and applications in quantitative proteomics. Proteomics 2022; 22:e2100256. [PMID: 35687565 PMCID: PMC9787039 DOI: 10.1002/pmic.202100256] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/21/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022]
Abstract
Mass spectrometry (MS) has emerged at the forefront of quantitative proteomic techniques. Liquid chromatography-mass spectrometry (LC-MS) can be used to determine abundances of proteins and peptides in complex biological samples. Several methods have been developed and adapted for accurate quantification based on chemical isotopic labeling. Among various chemical isotopic labeling techniques, isobaric tagging approaches rely on the analysis of peptides from MS2-based quantification rather than MS1-based quantification. In this review, we will provide an overview of several isobaric tags along with some recent developments including complementary ion tags, improvements in sensitive quantitation of analytes with lower abundance, strategies to increase multiplexing capabilities, and targeted analysis strategies. We will also discuss limitations of isobaric tags and approaches to alleviate these restrictions through bioinformatic tools and data acquisition methods. This review will highlight several applications of isobaric tags, including biomarker discovery and validation, thermal proteome profiling, cross-linking for structural investigations, single-cell analysis, top-down proteomics, along with applications to different molecules including neuropeptides, glycans, metabolites, and lipids, while providing considerations and evaluations to each application.
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Affiliation(s)
| | - Ting‐Jia Gu
- School of PharmacyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | | | - Lingjun Li
- Department of ChemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA,School of PharmacyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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4
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Johannsen C, Koehler CJ, Thiede B. Comparison of LFQ and IPTL for Protein Identification and Relative Quantification. Molecules 2021; 26:5330. [PMID: 34500763 DOI: 10.3390/molecules26175330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Mass spectrometry-based quantitative proteome profiling is most commonly performed by label-free quantification (LFQ), stable isotopic labeling with amino acids in cell culture (SILAC), and reporter ion-based isobaric labeling methods (TMT and iTRAQ). Isobaric peptide termini labeling (IPTL) was described as an alternative to these methods and is based on crosswise labeling of both peptide termini and MS2 quantification. High quantification accuracy was assumed for IPTL because multiple quantification points are obtained per identified MS2 spectrum. A direct comparison of IPTL with other quantification methods has not been performed yet because IPTL commonly requires digestion with endoproteinase Lys-C. (2) Methods: To enable tryptic digestion of IPTL samples, a novel labeling for IPTL was developed that combines metabolic labeling (Arg-0/Lys-0 and Arg-d4/Lys-d4, respectively) with crosswise N-terminal dimethylation (d4 and d0, respectively). (3) Results: The comparison of IPTL with LFQ revealed significantly more protein identifications for LFQ above homology ion scores but not above identity ion scores. (4) Conclusions: The quantification accuracy was superior for LFQ despite the many quantification points obtained with IPTL.
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5
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Abstract
In recent decades, mass spectrometry has moved more than ever before into the front line of protein-centered research. After being established at the qualitative level, the more challenging question of quantification of proteins and peptides using mass spectrometry has become a focus for further development. In this chapter, we discuss and review actual strategies and problems of the methods for the quantitative analysis of peptides, proteins, and finally proteomes by mass spectrometry. The common themes, the differences, and the potential pitfalls of the main approaches are presented in order to provide a survey of the emerging field of quantitative, mass spectrometry-based proteomics.
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Affiliation(s)
- Svitlana Rozanova
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Miroslav Nikolov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.,Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany.,Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany. .,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany.
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6
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Tian X, de Vries MP, Permentier HP, Bischoff R. A Versatile Isobaric Tag Enables Proteome Quantification in Data-Dependent and Data-Independent Acquisition Modes. Anal Chem 2020; 92:16149-16157. [PMID: 33256395 PMCID: PMC7745205 DOI: 10.1021/acs.analchem.0c03858] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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Quantifying proteins based on peptide-coupled
reporter ions is
a multiplexed quantitative strategy in proteomics that alleviates
the problem of ratio distortion caused by peptide cofragmentation,
as commonly observed in other reporter-ion-based approaches, such
as TMT and iTRAQ. Data-independent acquisition (DIA) is an attractive
alternative to data-dependent acquisition (DDA) due to its better
reproducibility. While multiplexed labeling is widely used in DDA,
it is rarely used in DIA, presumably because current approaches lead
to more complex MS2 spectra, severe ratio distortion, or to a reduction
in quantification accuracy and precision. Herein, we present a versatile
acetyl-alanine-glycine (Ac-AG) tag that conceals quantitative information
in isobarically labeled peptides and reveals it upon tandem MS in
the form of peptide-coupled reporter ions. Since the peptide-coupled
reporter ion is precursor-specific while fragment ions of the peptide
backbone originating from different labeling channels are identical,
the Ac-AG tag is compatible with both DDA and DIA. By isolating the
monoisotopic peak of the precursor ion in DDA, intensities of the
peptide-coupled reporter ions represent the relative ratios between
constituent samples, whereas in DIA, the ratio can be inferred after
deconvoluting the peptide-coupled reporter ion isotopes. The proteome
quantification capability of the Ac-AG tag was demonstrated by triplex
labeling of a yeast proteome spiked with bovine serum albumin (BSA)
over a 10-fold dynamic range. Within this complex proteomics background,
BSA spiked at 1:5:10 ratios was detected at ratios of 1.00:4.87:10.13
in DDA and 1.16:5.20:9.64 in DIA.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 16, 9713 AV Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Hjalmar P Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 16, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 16, 9713 AV Groningen, The Netherlands
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7
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Tian X, de Vries MP, Permentier HP, Bischoff R. A Collision-Induced Dissociation Cleavable Isobaric Tag for Peptide Fragment Ion-Based Quantification in Proteomics. J Proteome Res 2020; 19:3817-3824. [PMID: 32786690 PMCID: PMC7476077 DOI: 10.1021/acs.jproteome.0c00371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quantifying peptides based on unique peptide fragment ions avoids the issue of ratio distortion that is commonly observed for reporter ion-based quantification approaches. Herein, we present a collision-induced dissociation-cleavable, isobaric acetyl-isoleucine-proline-glycine (Ac-IPG) tag, which conserves the merits of quantifying peptides based on unique fragments while reducing the complexity of the b-ion series compared to conventional fragment ion-based quantification methods thus facilitating data processing. Multiplex labeling is based on selective N-terminal dimethylation followed by derivatization of the ε-amino group of the C-terminal Lys residue of LysC peptides with isobaric Ac-IPG tags having complementary isotope distributions on Pro-Gly and Ac-Ile. Upon fragmentation between Ile and Pro, the resulting y ions, with the neutral loss of Ac-Ile, can be distinguished between the different labeling channels based on different numbers of isotope labels on the Pro-Gly part and thus contain the information for relative quantification, while b ions of different labeling channels have the same m/z values. The proteome quantification capability of this method was demonstrated by triplex labeling of a yeast proteome spiked with bovine serum albumin (BSA) over a 10-fold dynamic range. With the yeast proteins as the background, BSA was detected at ratios of 1.14:5.06:9.78 when spiked at 1:5:10 ratios. The raw mass data is available on the ProteomeXchange with the identifier PXD 018790.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Marcel P de Vries
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen 9713 GZ, The Netherlands
| | - Hjalmar P Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
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8
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Ma J, Zheng S, Wang H, Li C, Ran Q. Site-selective, reversible, pH-induced N-terminal maleylation and its application for proteomics research. Rapid Commun Mass Spectrom 2020; 34:e8800. [PMID: 32246864 DOI: 10.1002/rcm.8800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/26/2020] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Compared with traditional labelling reagents used in proteomics, maleic anhydride is milder and can be easily removed under certain conditions, thus simplifying chemical derivatization. METHODS The proposed strategy combined a site-specific chemical labelling reaction with mass spectrometry. Site-selective, reversible N-terminal maleylation was controlled by pH. RESULTS Selective maleyl N-terminal labelling was achieved with high efficiency under the optimized reaction conditions. The demaleylation conditions were also optimized. The sequence coverage of histone H4 increased from 77% to 95% after the maleyl labels were removed, and the number of maleylated peptides was five times that of the unlabelled peptides. We further verified the reversible and selective N-terminal labelling properties of maleic anhydride through propionylation labelling at the peptide/protein level. CONCLUSIONS A new method for site-selective maleylation of the N-terminal amino groups of a peptide was explored. Through the optimization experiment, good efficiency was achieved for this labelling reaction. The reversibility of maleylation labelling was also explored and applied for the identification of post-translational modifications of histones. Thus, site-selective, reversible, pH-induced N-terminal labelling using maleic anhydride has greater potential for application in proteomics than any other labelling methods.
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Affiliation(s)
- Jianfeng Ma
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, China
- State Key Laboratory of High Performance Civil Engineering Materials, Jiangsu Sobute New Materials Co. Ltd., Nanjing, China
| | - Shuzhen Zheng
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Haidong Wang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Chongjie Li
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Qianping Ran
- State Key Laboratory of High Performance Civil Engineering Materials, Jiangsu Sobute New Materials Co. Ltd., Nanjing, China
- School of Material Science and Engineering, Southeast University, Nanjing, China
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9
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Tian X, de Vries MP, Visscher SWJ, Permentier HP, Bischoff R. Selective Maleylation-Directed Isobaric Peptide Termini Labeling for Accurate Proteome Quantification. Anal Chem 2020; 92:7836-7844. [PMID: 32319746 PMCID: PMC7271076 DOI: 10.1021/acs.analchem.0c01059] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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Isobaric peptide
termini labeling (IPTL) is an attractive protein
quantification method because it provides more accurate and reliable
quantification information than traditional isobaric labeling methods
(e.g., TMT and iTRAQ) by making use of the entire fragment-ion series
instead of only a single reporter ion. The multiplexing capacity of
published IPTL implementations is, however, limited to three. Here,
we present a selective maleylation-directed isobaric peptide termini
labeling (SMD-IPTL) approach for quantitative proteomics of LysC protein
digestion. SMD-IPTL extends the multiplexing capacity to 4-plex with
the potential for higher levels of multiplexing using commercially
available 13C/15N labeled amino acids. SMD-IPTL
is achieved in a one-pot reaction in three consecutive steps: (1)
selective maleylation at the N-terminus; (2) labeling at the ε-NH2 group of the C-terminal Lys with isotopically labeled acetyl-alanine;
(3) thiol Michael addition of an isotopically labeled acetyl-cysteine
at the maleylated N-terminus. The isobarically labeled peptides are
fragmented into sets of b- and y-ion clusters upon LC-MS/MS, which
convey not only sequence information but also quantitative information
for every labeling channel and avoid the issue of ratio distortion
observed with reporter-ion-based approaches. We demonstrate the SMD-IPTL
approach with a 4-plex labeled sample of bovine serum albumin (BSA)
and yeast lysates mixed at different ratios. With the use of SMD-IPTL
for labeling and a narrow precursor isolation window of 0.8 Th with
an offset of −0.2 Th, accurate ratios were measured across
a 10-fold mixing range of BSA in a background of yeast proteome. With
the yeast proteins mixed at ratios of 1:5:1:5, BSA was detected at
ratios of 0.94:2.46:4.70:9.92 when spiked at 1:2:5:10 ratios with
an average standard deviation of peptide ratios of 0.34.
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Affiliation(s)
| | - Marcel P de Vries
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
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10
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Liu J, Shan Y, Zhou Y, Liang Z, Zhang L, Zhang Y. Advances and applications of stable isotope labeling-based methods for proteome relative quantitation. Trends Analyt Chem 2020; 124:115815. [DOI: 10.1016/j.trac.2020.115815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Abstract
Mass spectrometry-based quantitative proteomics is a powerful tool for gaining insights into function and dynamics of biological systems. However, peptides with different sequences have different ionization efficiencies, and their intensities in a mass spectrum are not correlated with their abundances. Therefore, various label-free or stable isotope label-based quantitation methods have emerged to assist mass spectrometry to perform comparative proteomic experiments, thus enabling nonbiased identification of thousands of proteins differentially expressed in healthy versus diseased cells. Here, we discuss the most widely used label-free and metabolic-, enzymatic-, and chemical labeling-based proteomic strategies for relative and absolute quantitation. We summarize the specific strengths and weaknesses of each technique in terms of quantification accuracy, proteome coverage, multiplexing capability, and robustness. Applications of each strategy for solving specific biological complexities are also presented.
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Affiliation(s)
- J Astor Ankney
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Adil Muneer
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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12
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Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
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13
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
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14
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew Chem Int Ed Engl 2018; 57:1758-1784. [PMID: 28815899 DOI: 10.1002/anie.201704146] [Citation(s) in RCA: 391] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (3 H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
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15
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Abstract
We present an analytical strategy, dimethylation-deuteration and oxygen-exchange IPTL (diDO-IPTL), for high-precision, broad-coverage quantitative proteomics. The diDO-IPTL approach combines two advances in isobaric peptide terminal labeling (IPTL) methodology: first, a one-pot chemical labeling strategy for attaching isotopic tags to both the N- and C-termini of tryptic peptides, and second, a search engine (based on the Morpheus algorithm) optimized for identification and quantification of twinned peaks from peptide fragment ions in MS2 spectra. The diDO-IPTL labeling chemistry uses only high-purity, relatively inexpensive isotopic reagents (18O water and deuterated formaldehyde) and requires no postlabeling cleanup or isotopic impurity corrections. This strategy produces proteome-scale relative quantification results with high accuracy and precision, suitable for the detection of small protein abundance variations between complex biological samples. In a two-proteome mixture experiment, diDO-IPTL quantification discriminates 1.5-fold changes in abundance of over 1000 proteins with 88% accuracy. The diDO-IPTL methodology is a high-precision, economical approach to quantitative proteomics that is applicable to a wide variety of sample types.
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Affiliation(s)
- Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago , 5734 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago , 5734 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Adriana Rizzo
- Department of the Geophysical Sciences, University of Chicago , 5734 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Daniel Muratore
- Department of the Geophysical Sciences, University of Chicago , 5734 South Ellis Avenue, Chicago, Illinois 60637, United States
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16
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Tian S, Zheng S, Han Y, Guo Z, Zhai G, Bai X, He X, Fan E, Zhang Y, Zhang K. Maleic Anhydride Labeling-Based Approach for Quantitative Proteomics and Successive Derivatization of Peptides. Anal Chem 2017; 89:8259-8265. [DOI: 10.1021/acs.analchem.7b01120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shanshan Tian
- 2011 Collaborative
Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key
Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease, Ministry of Education, Department of Biochemistry
and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Shuzhen Zheng
- Department
of Chemistry, Nankai University, Tianjin 300071, China
| | - Yanpu Han
- Department
of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhenchang Guo
- 2011 Collaborative
Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key
Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease, Ministry of Education, Department of Biochemistry
and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Guijin Zhai
- 2011 Collaborative
Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key
Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease, Ministry of Education, Department of Biochemistry
and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Xue Bai
- 2011 Collaborative
Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key
Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease, Ministry of Education, Department of Biochemistry
and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Xiwen He
- Department
of Chemistry, Nankai University, Tianjin 300071, China
| | - Enguo Fan
- Institut
für Biochemie und Molekularbiologie, Universität Freiburg, Stefan-Meier-Strasse 17, Freiburg 79104, Germany
- Department
of Microbiology and Parasitology, Institute of Basic
Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Yukui Zhang
- Department
of Chemistry, Nankai University, Tianjin 300071, China
- National
Chromatographic Research and Analysis Center, Dalian Institute of
Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Kai Zhang
- 2011 Collaborative
Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key
Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease, Ministry of Education, Department of Biochemistry
and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
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17
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Zhang S, Shan Y, Zhang S, Sui Z, Zhang L, Liang Z, Zhang Y. NIPTL-Novo: Non-isobaric peptide termini labeling assisted peptide de novo sequencing. J Proteomics 2017; 154:40-48. [DOI: 10.1016/j.jprot.2016.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 12/28/2022]
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18
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Psatha K, Kollipara L, Voutyraki C, Divanach P, Sickmann A, Rassidakis GZ, Drakos E, Aivaliotis M. Deciphering lymphoma pathogenesis via state-of-the-art mass spectrometry-based quantitative proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1047:2-14. [PMID: 27979587 DOI: 10.1016/j.jchromb.2016.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/18/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022]
Abstract
Mass spectrometry-based quantitative proteomics specifically applied to comprehend the pathogenesis of lymphoma has incremental value in deciphering the heterogeneity in complex deregulated molecular mechanisms/pathways of the lymphoma entities, implementing the current diagnostic and therapeutic strategies. Essential global, targeted and functional differential proteomics analyses although still evolving, have been successfully implemented to shed light on lymphoma pathogenesis to discover and explore the role of potential lymphoma biomarkers and drug targets. This review aims to outline and appraise the present status of MS-based quantitative proteomic approaches in lymphoma research, introducing the current state-of-the-art MS-based proteomic technologies, the opportunities they offer in biological discovery in human lymphomas and the related limitation issues arising from sample preparation to data evaluation. It is a synopsis containing information obtained from recent research articles, reviews and public proteomics repositories (PRIDE). We hope that this review article will aid, assimilate and assess all the information aiming to accelerate the development and validation of diagnostic, prognostic or therapeutic targets for an improved and empowered clinical proteomics application in lymphomas in the nearby future.
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Affiliation(s)
- Konstantina Psatha
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece; School of Medicine, National and Kapodistrian University of Athens, Athens, Greece; Department of Pathology, School of Medicine, University of Crete, Heraklion, Greece
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | | | - Peter Divanach
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom; Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, Bochum, Germany
| | - George Z Rassidakis
- School of Medicine, National and Kapodistrian University of Athens, Athens, Greece; Department of Pathology and Cytology, Karolinska University Hospital and Karolinska Institute, Radiumhemmet, Stockholm, SE-17176, Sweden
| | - Elias Drakos
- Department of Pathology, School of Medicine, University of Crete, Heraklion, Greece
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19
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Chen L, Shan Y, Weng Y, Yuan H, Zhang S, Fan R, Sui Z, Zhang X, Zhang L, Zhang Y. Depletion of internal peptides by site-selective blocking, phosphate labeling, and TiO2 adsorption for in-depth analysis of C-terminome. Anal Bioanal Chem 2016; 408:3867-74. [DOI: 10.1007/s00216-016-9476-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 01/18/2023]
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Biswas S, Song W, Borges C, Lindsay S, Zhang P. Click Addition of a DNA Thread to the N-Termini of Peptides for Their Translocation through Solid-State Nanopores. ACS Nano 2015; 9:9652-64. [PMID: 26364915 PMCID: PMC5648329 DOI: 10.1021/acsnano.5b04984] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Foremost among the challenges facing single molecule sequencing of proteins by nanopores is the lack of a universal method for driving proteins or peptides into nanopores. In contrast to nucleic acids, the backbones of which are uniformly negatively charged nucleotides, proteins carry positive, negative and neutral side chains that are randomly distributed. Recombinant proteins carrying a negatively charged oligonucleotide or polypeptide at the C-termini can be translocated through a α-hemolysin (α-HL) nanopore, but the required genetic engineering limits the generality of these approaches. In this present study, we have developed a chemical approach for addition of a charged oligomer to peptides so that they can be translocated through nanopores. As an example, an oligonucleotide PolyT20 was tethered to peptides through first selectively functionalizing their N-termini with azide followed by a click reaction. The data show that the peptide-PolyT20 conjugates translocated through nanopores, whereas the unmodified peptides did not. Surprisingly, the conjugates with their peptides tethered at the 5'-end of PolyT20 passed the nanopores more rapidly than the PolyT20 alone. The PolyT20 also yielded a wider distribution of blockade currents. The same broad distribution was found for a conjugate with its peptide tethered at the 3'-end of PolyT20, suggesting that the larger blockades (and longer translocation times) are associated with events in which the 5'-end of the PolyT20 enters the pore first.
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Affiliation(s)
- Sudipta Biswas
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Weisi Song
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Chad Borges
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Corresponding Author: The author(s) to whom correspondence should be addressed: ;
| | - Peiming Zhang
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
- Corresponding Author: The author(s) to whom correspondence should be addressed: ;
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22
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Xie LQ, Zhang L, Nie AY, Yan GQ, Yao J, Zhang Y, Yang PY, Lu HJ. ITMSQ: A software tool for N- and C-terminal fragment ion pairs based isobaric tandem mass spectrometry quantification. Proteomics 2015; 15:3755-64. [PMID: 26349451 DOI: 10.1002/pmic.201400513] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 08/04/2015] [Accepted: 09/04/2015] [Indexed: 11/10/2022]
Abstract
Tandem MS (MS2) quantification using the series of N- and C-terminal fragment ion pairs generated from isobaric-labelled peptides was recently considered an accurate strategy in quantitative proteomics. However, the presence of multiplexed terminal fragment ion in MS2 spectra may reduce the efficiency of peptide identification, resulting in lower identification scores or even incorrect assignments. To address this issue, we developed a quantitative software tool, denoted isobaric tandem MS quantification (ITMSQ), to improve N- and C-terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. We performed an analysis of in vivo terminal amino acid labelling labelled HeLa samples and found that the numbers of quantified proteins and peptides increased by 13.64 and 27.52% after spectrum splitting, respectively. In conclusion, ITMSQ provides an accurate and reliable quantitative solution for N- and C-terminal fragment ion pairs based isobaric MS2 quantitative methods.
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Affiliation(s)
- Li-Qi Xie
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Ai-Ying Nie
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Guo-Quan Yan
- Department of Chemistry, Fudan University, Shanghai, P. R. China
| | - Jun Yao
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Yang Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Peng-Yuan Yang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China.,Department of Chemistry, Fudan University, Shanghai, P. R. China
| | - Hao-Jie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China.,Department of Chemistry, Fudan University, Shanghai, P. R. China
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23
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Chahrour O, Cobice D, Malone J. Stable isotope labelling methods in mass spectrometry-based quantitative proteomics. J Pharm Biomed Anal 2015; 113:2-20. [PMID: 25956803 DOI: 10.1016/j.jpba.2015.04.013] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 02/04/2023]
Abstract
Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.
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Affiliation(s)
| | - Diego Cobice
- Spectroscopy Group, Analytical Services, Almac, UK
| | - John Malone
- Spectroscopy Group, Analytical Services, Almac, UK
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24
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Weng Y, Sui Z, Jiang H, Shan Y, Chen L, Zhang S, Zhang L, Zhang Y. Releasing N-glycan from peptide N-terminus by N-terminal succinylation assisted enzymatic deglycosylation. Sci Rep 2015; 5:9770. [PMID: 25902405 PMCID: PMC4405948 DOI: 10.1038/srep09770] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/18/2015] [Indexed: 01/13/2023] Open
Abstract
Due to the important roles of N-glycoproteins in various biological processes, the global N-glycoproteome analysis has been paid much attention. However, by current strategies for N-glycoproteome profiling, peptides with glycosylated Asn at N-terminus (PGANs), generated by protease digestion, could hardly be identified, due to the poor deglycosylation capacity by enzymes. However, theoretically, PGANs occupy 10% of N-glycopeptides in the typical tryptic digests. Therefore, in this study, we developed a novel strategy to identify PGANs by releasing N-glycans through the N-terminal site-selective succinylation assisted enzymatic deglycosylation. The obtained PGANs information is beneficial to not only achieve the deep coverage analysis of glycoproteomes, but also discover the new biological functions of such modification.
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Affiliation(s)
- Yejing Weng
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Jiang
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichu Shan
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lingfan Chen
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shen Zhang
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Shen JX, Liu G, Zhao Y. Strategies for improving sensitivity and selectivity for the quantitation of biotherapeutics in biological matrix using LC-MS/MS. Expert Rev Proteomics 2015; 12:125-31. [DOI: 10.1586/14789450.2015.1024225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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27
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Zhang S, Wu Q, Shan Y, Zhou Y, Zhang L, Zhang Y. Partially isobaric peptide termini labeling assisted proteome quantitation based on MS and MS/MS signals. J Proteomics 2015; 114:152-60. [DOI: 10.1016/j.jprot.2014.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/16/2014] [Accepted: 11/20/2014] [Indexed: 12/24/2022]
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28
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Zhou Y, Shan Y, Zhang L, Zhang Y. Recent advances in stable isotope labeling based techniques for proteome relative quantification. J Chromatogr A 2014; 1365:1-11. [PMID: 25246102 DOI: 10.1016/j.chroma.2014.08.098] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 08/24/2014] [Accepted: 08/27/2014] [Indexed: 12/27/2022]
Abstract
The large scale relative quantification of all proteins expressed in biological samples under different states is of great importance for discovering proteins with important biological functions, as well as screening disease related biomarkers and drug targets. Therefore, the accurate quantification of proteins at proteome level has become one of the key issues in protein science. Herein, the recent advances in stable isotope labeling based techniques for proteome relative quantification were reviewed, from the aspects of metabolic labeling, chemical labeling and enzyme-catalyzed labeling. Furthermore, the future research direction in this field was prospected.
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Abstract
Clinical proteomics research aims at i) discovery of protein biomarkers for screening, diagnosis and prognosis of disease, ii) discovery of protein therapeutic targets for improvement of disease prevention, treatment and follow-up, and iii) development of mass spectrometry (MS)-based assays that could be implemented in clinical chemistry, microbiology or hematology laboratories. MS has been increasingly applied in clinical proteomics studies for the identification and quantification of proteins. Bioinformatics plays a key role in the exploitation of MS data in several aspects such as the generation and curation of protein sequence databases, the development of appropriate software for MS data treatment and integration with other omics data and the establishment of adequate standard files for data sharing. In this article, we discuss the main MS approaches and bioinformatics solutions that are currently applied to accomplish the objectives of clinical proteomic research.
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30
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Xie LQ, Nie AY, Yang SJ, Zhao C, Zhang L, Yang PY, Lu HJ. Global in vivo terminal amino acid labeling for exploring differential expressed proteins induced by dialyzed serum cultivation. Analyst 2014; 139:4497-504. [PMID: 25028700 DOI: 10.1039/c4an00728j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An accurate and high throughput isobaric MS2 quantification strategy based on metabolic labeling and trypsin digestion.
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Affiliation(s)
- Li-Qi Xie
- Shanghai Cancer Center and Department of Chemistry
- Fudan University
- Shanghai 200032, P. R. China
- Key Laboratory of Medical Molecular Virology and Institutes of Biomedical Sciences
- Shanghai Medical College
| | - Ai-Ying Nie
- Shanghai Cancer Center and Department of Chemistry
- Fudan University
- Shanghai 200032, P. R. China
| | - Shu-Jun Yang
- Shanghai Cancer Center and Department of Chemistry
- Fudan University
- Shanghai 200032, P. R. China
| | - Chao Zhao
- Key Laboratory of Medical Molecular Virology and Institutes of Biomedical Sciences
- Shanghai Medical College
- Fudan University
- Shanghai 200032, P. R. China
| | - Lei Zhang
- Shanghai Cancer Center and Department of Chemistry
- Fudan University
- Shanghai 200032, P. R. China
| | - Peng-Yuan Yang
- Shanghai Cancer Center and Department of Chemistry
- Fudan University
- Shanghai 200032, P. R. China
| | - Hao-Jie Lu
- Shanghai Cancer Center and Department of Chemistry
- Fudan University
- Shanghai 200032, P. R. China
- Key Laboratory of Medical Molecular Virology and Institutes of Biomedical Sciences
- Shanghai Medical College
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Abstract
Discovering differentially expressed proteins in various biological samples requires proteome quantification methods with accuracy, precision, and wide dynamic range. This study describes a mass defect-based pseudo-isobaric dimethyl labeling (pIDL) method based on the subtle mass defect differences between (12)C/(13)C and (1)H/(2)H. Lys-C protein digests were labeled with CD2O/(13)CD2O and reduced with NaCNBD3/NaCNBH3 as heavy and light isotopologues, respectively. The fragment ion pairs with mass differences of 5.84 mDa were resolved by high-resolution tandem mass spectrometry (MS/MS) and used for quantification. The pIDL method described here resulted in highly accurate and precise quantification results with approximately 100-fold dynamic range. Furthermore, the pIDL method was extended to 4-plex proteome quantification and applied to the quantitative analysis of proteomes from Hca-P and Hca-F, two mouse hepatocarcinoma ascites syngeneic cell lines with low and high lymph node metastasis rates.
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Affiliation(s)
- Yuan Zhou
- National Chromatographic Research and Analysis Center, Key Lab of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, China
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32
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Megger DA, Bracht T, Meyer HE, Sitek B. Label-free quantification in clinical proteomics. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2013; 1834:1581-90. [DOI: 10.1016/j.bbapap.2013.04.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 03/26/2013] [Accepted: 04/01/2013] [Indexed: 12/31/2022]
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33
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Lim C, Chan S. Single laboratory method validation comparing MS3 with FI/MS fingerprinting, and quantitation strategies for the accurate determination of ochratoxins in beer. WORLD MYCOTOXIN J 2013. [DOI: 10.3920/wmj2012.1522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The current mycotoxin safety concerns demand the availability of reliable and selective control systems to measure the content of mycotoxins present in daily food. To address this, we report a prospective analytical tool involving the application of a flow injection mass spectrometry (FI/MS) tandem artificial neural network (ANN) strategy to predict the amount of ochratoxin A and B (OTA and OTB) in beer. Triple stage mass spectrometry (MS3) aided by chromatographic separation was applied as a reference method for comparison. 0.1% formic acid and methanol were used to convert ochratoxins into their respective ions under negative MS polarity. For experiments involving MS3, ochratoxins were separated by reversed-phase liquid chromatography in a 6 min run, ionised using electrospray ionisation, and detected by tandem mass spectrometry. Analyte-specific mass-to-charge ratios were used to perform quantitation in MS3 mode. For experiments involving FI/MS, no chromatographic separation was performed. Approximately 2% of the mass spectra was used for model construction. ANN models representing each ochratoxin were individually trained and validated using three sets of matrix-matched and matrix-free calibration curves at nine concentration levels of 2.5, 10, 25, 50, 100, 200, 300, 400 and 500 μg/l. Quintuplicate analyses were made in FI/ MS mode providing a total of 270 spectra for both OTA and OTB. Single measurement was made for each sample in MS3 mode. A root-mean-square error value of <1% was reported for both ochratoxin models in beer. Limits of quantitation were determined to be 0.2 μg/kg for both MS3 and FI/MS mode. Recovery assessment was performed over two days using beer blanks (n=6) spiked at three concentration levels of 5, 100 and 200 μg/kg. Extraction using acetonitrile provided excellent recovery ranges of 88 to 102% for both MS techniques. Relative standard deviations of 10% or better were achieved for interday spike recovery experiments. The successful utilisation of FI/MS without performing chromatographic separation implies the availability of a new analytical tool relevant to the field of mycotoxin analysis, possibly offering analyte specificity exceeding the capability of MS3 through chemometry.
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Affiliation(s)
- C.W. Lim
- Food Safety Laboratory, Applied Sciences Group, Health Sciences Authority, 11 Outram Road, Singapore 169078, Singapore
| | - S.H. Chan
- Food Safety Laboratory, Applied Sciences Group, Health Sciences Authority, 11 Outram Road, Singapore 169078, Singapore
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Liu M, Zhang Z, Zang T, Spahr C, Cheetham J, Ren D, Sunny Zhou Z. Discovery of undefined protein cross-linking chemistry: a comprehensive methodology utilizing 18O-labeling and mass spectrometry. Anal Chem 2013; 85:5900-8. [PMID: 23634697 PMCID: PMC3691076 DOI: 10.1021/ac400666p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Characterization of protein cross-linking, particularly without prior knowledge of the chemical nature and site of cross-linking, poses a significant challenge, because of their intrinsic structural complexity and the lack of a comprehensive analytical approach. Toward this end, we have developed a generally applicable workflow-XChem-Finder-that involves four stages: (1) detection of cross-linked peptides via (18)O-labeling at C-termini; (2) determination of the putative partial sequences of each cross-linked peptide pair using a fragment ion mass database search against known protein sequences coupled with a de novo sequence tag search; (3) extension to full sequences based on protease specificity, the unique combination of mass, and other constraints; and (4) deduction of cross-linking chemistry and site. The mass difference between the sum of two putative full-length peptides and the cross-linked peptide provides the formulas (elemental composition analysis) for the functional groups involved in each cross-linking. Combined with sequence restraint from MS/MS data, plausible cross-linking chemistry and site were inferred, and ultimately confirmed, by matching with all data. Applying our approach to a stressed IgG2 antibody, 10 cross-linked peptides were discovered and found to be connected via thioethers originating from disulfides at locations that had not been previously recognized. Furthermore, once the cross-link chemistry was revealed, a targeted cross-link search yielded 4 additional cross-linked peptides that all contain the C-terminus of the light chain.
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Affiliation(s)
- Min Liu
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Zhongqi Zhang
- Process and Product Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Tianzhu Zang
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Chris Spahr
- Biologic Optimization, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Janet Cheetham
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Da Ren
- Process and Product Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Zhaohui Sunny Zhou
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
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Arczewska KD, Tomazella GG, Lindvall JM, Kassahun H, Maglioni S, Torgovnick A, Henriksson J, Matilainen O, Marquis BJ, Nelson BC, Jaruga P, Babaie E, Holmberg CI, Bürglin TR, Ventura N, Thiede B, Nilsen H. Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1. Nucleic Acids Res 2013; 41:5368-81. [PMID: 23580547 PMCID: PMC3664812 DOI: 10.1093/nar/gkt225] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Transcription-blocking oxidative DNA damage is believed to contribute to aging and to underlie activation of oxidative stress responses and down-regulation of insulin-like signaling (ILS) in Nucleotide Excision Repair (NER) deficient mice. Here, we present the first quantitative proteomic description of the Caenorhabditis elegans NER-defective xpa-1 mutant and compare the proteome and transcriptome signatures. Both methods indicated activation of oxidative stress responses, which was substantiated biochemically by a bioenergetic shift involving increased steady-state reactive oxygen species (ROS) and Adenosine triphosphate (ATP) levels. We identify the lesion-detection enzymes of Base Excision Repair (NTH-1) and global genome NER (XPC-1 and DDB-1) as upstream requirements for transcriptomic reprogramming as RNA-interference mediated depletion of these enzymes prevented up-regulation of genes over-expressed in the xpa-1 mutant. The transcription factors SKN-1 and SLR-2, but not DAF-16, were identified as effectors of reprogramming. As shown in human XPA cells, the levels of transcription-blocking 8,5'-cyclo-2'-deoxyadenosine lesions were reduced in the xpa-1 mutant compared to the wild type. Hence, accumulation of cyclopurines is unlikely to be sufficient for reprogramming. Instead, our data support a model where the lesion-detection enzymes NTH-1, XPC-1 and DDB-1 play active roles to generate a genomic stress signal sufficiently strong to result in transcriptomic reprogramming in the xpa-1 mutant.
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Affiliation(s)
- Katarzyna D Arczewska
- The Biotechnology Centre, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
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Affiliation(s)
- Christian J. Koehler
- The Biotechnology
Centre of
Oslo, University of Oslo, P.O. Box 1125
Blindern, 0317 Oslo, Norway
| | - Magnus Ø. Arntzen
- The Biotechnology
Centre of
Oslo, University of Oslo, P.O. Box 1125
Blindern, 0317 Oslo, Norway
| | - Gustavo Antonio de Souza
- Department
of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, 0424 Oslo, Norway
| | - Bernd Thiede
- The Biotechnology
Centre of
Oslo, University of Oslo, P.O. Box 1125
Blindern, 0317 Oslo, Norway
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Gao X, Wu H, Lee KC, Liu H, Zhao Y, Cai Z, Jiang Y. Stable Isotope N-Phosphorylation Labeling for Peptide de Novo Sequencing and Protein Quantification Based on Organic Phosphorus Chemistry. Anal Chem 2012; 84:10236-44. [DOI: 10.1021/ac301939v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xiang Gao
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Hanzhi Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
| | - Kim-Chung Lee
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
| | - Hongxia Liu
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Yufen Zhao
- Department of Chemistry and The
Key Laboratory for Chemical Biology of Fujian Province, College of
Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People’s Republic of China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Yuyang Jiang
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
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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] [What about the content of this article? (0)] [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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Han B, Hare M, Wickramasekara S, Fang Y, Maier CS. A comparative 'bottom up' proteomics strategy for the site-specific identification and quantification of protein modifications by electrophilic lipids. J Proteomics 2012; 75:5724-33. [PMID: 22842153 DOI: 10.1016/j.jprot.2012.07.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 06/28/2012] [Accepted: 07/16/2012] [Indexed: 01/06/2023]
Abstract
We report a mass spectrometry-based comparative "bottom up" proteomics approach that combines d(0)/d(4)-succinic anhydride labeling with commercially available hydrazine (Hz)-functionalized beads (Affi-gel Hz beads) for detection, identification and relative quantification of site-specific oxylipid modifications in biological matrices. We evaluated and applied this robust and simple method for the quantitative analysis of oxylipid protein conjugates in cardiac mitochondrial proteome samples isolated from 3- and 24-month-old rat hearts. The use of d(0)/d(4)-succinic anhydride labeling, Hz-bead based affinity enrichment, nanoLC fractionation and MALDI-ToF/ToF tandem mass spectrometry yielded relative quantification of oxylipid conjugates with residue-specific modification information. Conjugation of acrolein (ACR), 4-hydroxy-2-hexenal (HHE), 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-noneal (ONE) to cysteine, histidine and lysine residues were identified. HHE conjugates were the predominant subset of Michael-type adducts detected in this study. The HHE conjugates showed higher levels in mitochondrial preparations from young heart congruent with previous findings by others that the n-3/n-6 PUFA ratio is higher in young heart mitochondrial membranes. Although this study focuses on protein adducts of reactive oxylipids, the method might be equally applicable to protein carbonyl modifications caused by metal catalyzed oxidation reactions.
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Affiliation(s)
- Bingnan Han
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
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Tomazella GG, Kassahun H, Nilsen H, Thiede B. Quantitative proteome analysis reveals RNA processing factors as modulators of ionizing radiation-induced apoptosis in the C. elegans germline. J Proteome Res 2012; 11:4277-88. [PMID: 22757771 DOI: 10.1021/pr300386z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The nematode Caenorhabditis elegans is an organism most recognized for forward and reverse genetic and functional genomic approaches. Proteomic analyses of DNA damage-induced apoptosis have not been shown because of a limited number of cells undergoing apoptosis. We applied mass spectrometry-based quantitative proteomics to evaluate protein changes induced by ionizing radiation (IR) in isolated C. elegans germlines. For this purpose, we used isobaric peptide termini labeling (IPTL) combined with the data analysis tool IsobariQ, which utilizes MS/MS spectra for relative quantification of peak pairs formed during fragmentation. Using stringent statistical critera, we identified 48 proteins to be significantly up- or down-regulated, most of which are part of a highly interconnected protein-protein interaction network dominated by proteins involved in translational control. RNA-mediated depletion of a selection of the IR-regulated proteins revealed that the conserved CAR-1/CGH-1/CEY-3 germline RNP complex acts as a novel negative regulator of DNA-damage induced apoptosis. Finally, a central role of nucleolar proteins in orchestrating these responses was confirmed as the H/ACA snRNP protein GAR-1 was required for IR-induced apoptosis in the C. elegans germline.
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Koehler CJ, Arntzen MØ, Treumann A, Thiede B. Comparison of data analysis parameters and MS/MS fragmentation techniques for quantitative proteome analysis using isobaric peptide termini labeling (IPTL). Anal Bioanal Chem 2012; 404:1103-14. [DOI: 10.1007/s00216-012-5949-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/13/2012] [Accepted: 03/13/2012] [Indexed: 10/28/2022]
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Evans C, Noirel J, Ow SY, Salim M, Pereira-Medrano AG, Couto N, Pandhal J, Smith D, Pham TK, Karunakaran E, Zou X, Biggs CA, Wright PC. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem 2012; 404:1011-27. [PMID: 22451173 DOI: 10.1007/s00216-012-5918-6] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 01/09/2023]
Abstract
The iTRAQ (isobaric tags for relative and absolute quantification) technique is widely employed in proteomic workflows requiring relative quantification. Here, we review the iTRAQ literature; in particular, we focus on iTRAQ usage in relation to other commonly used quantitative techniques e.g. stable isotope labelling in culture (SILAC), label-free methods and selected reaction monitoring (SRM). As a result, we identify several issues arising with respect to iTRAQ. Perhaps frustratingly, iTRAQ's attractiveness has been undermined by a number of technical and analytical limitations: it may not be truly quantitative, as the changes in abundance reported will generally be underestimated. We discuss weaknesses and strengths of iTRAQ as a methodology for relative quantification in the light of this and other technical issues. We focus on technical developments targeted at iTRAQ accuracy and precision, use of 4-plex over 8-plex reagents and application of iTRAQ to post-translational modification (PTM) workflows. We also discuss iTRAQ in relation to label-free approaches, to which iTRAQ is losing ground.
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Affiliation(s)
- Caroline Evans
- The ChELSI Institute, Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
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Qin H, Wang F, Zhang Y, Hu Z, Song C, Wu R, Ye M, Zou H. Isobaric cross-sequence labeling of peptides by using site-selective N-terminus dimethylation. Chem Commun (Camb) 2012; 48:6265-7. [DOI: 10.1039/c2cc31705b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Abstract
Isobaric peptide termini labeling (IPTL) is a recently introduced approach to the chemical labeling of peptides with isotopic reagents. Peptides derived from two different samples are labeled at the N terminus and at the C terminus with isotopically labeled reagents that have identical mass differences. To obtain isobaric peptides, labeling is carried out such that the introduced mass increase at one terminus will exactly match the mass decrease at the other terminus (and the other way around). This results in product ion spectra that display the quantitative difference of the peptide signal derived from the two samples for every b-ion and y-ion in the spectrum. The original IPTL approach required the selective modification of lysines followed by C-18 micropurification of modified peptides and reaction of the N termini. Here, we describe a new approach for IPTL that is based on the selective modification of the peptide N termini with succinic anhydride and subsequent reductive amination of C-terminal lysines with formaldehyde and cyanoborohydride. Both reactions can be carried out in one pot within 10 min and without C-18 micropurification. In addition, we present the software package IsobariQ for straightforward data analysis.
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