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Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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2
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Tian X, Permentier HP, Bischoff R. Chemical isotope labeling for quantitative proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:546-576. [PMID: 34091937 PMCID: PMC10078755 DOI: 10.1002/mas.21709] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [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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Han S, Yan Z, Huang X, Cai S, Zhao M, Zheng Y, Liu X, Xu H, Xie Y, Hou R, Duan JA, Liu R. Response boosting-based approach for absolute quantification of gelatin peptides using LC-MS/MS. Food Chem 2022; 390:133111. [DOI: 10.1016/j.foodchem.2022.133111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/04/2022] [Accepted: 04/26/2022] [Indexed: 11/04/2022]
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4
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Zhang S, Di Y, Yao J, Wang Y, Shu H, Yan G, Zhang L, Lu H. Mass defect-based carbonyl activated tags (mdCATs) for multiplex data-independent acquisition proteome quantification. Chem Commun (Camb) 2021; 57:737-740. [DOI: 10.1039/d0cc06493a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A novel eight-plex mass-defect-based carbonyl activated tag (mdCAT) has been designed for DIA quantification for the first time.
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Affiliation(s)
- Siwen Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Yi Di
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Jun Yao
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Yingjie Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Chinese Academy of Sciences
| | - Hong Shu
- Department of Clinical Laboratory
- Cancer Hospital of Guangxi Medical University
- Nanning
- China
| | - Guoquan Yan
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research
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5
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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: 34] [Impact Index Per Article: 8.5] [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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6
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Chiang S, Zhang W, Farnsworth C, Zhu Y, Lee K, Ouyang Z. Targeted Quantification of Peptides Using Miniature Mass Spectrometry. J Proteome Res 2020; 19:2043-2052. [PMID: 32202427 DOI: 10.1021/acs.jproteome.9b00875] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proteomics by mass spectrometry (MS) allows for the identification of amino acid/peptide sequences in complex mixtures. Peptide analysis and quantitation enables screening of protein biomarkers and targeted protein biomarker analysis for clinical applications. Whereas miniature mass spectrometers have primarily demonstrated point-of-care analyses with simple procedures aiming at drugs and lipids, it would be interesting to explore their potential in analyzing proteins and peptides. In this work, we adapted a miniature MS instrument for peptide analysis. A mass range as wide as 100-2000 m/z was achieved for obtaining peptide spectra using this instrument with dual linear ion traps. MS2 and MS3 can be performed to analyze a wide range of peptides. The parameters of pressure, electric potentials, and solution conditions were optimized to analyze peptides with molecular weights between 900 and 1800 Da. The amino acid sequences were identified using both beam-type and in-trap collision-induced dissociation, and the results were comparable to those obtained by a commercial quadrupole time-of-flight mass spectrometer. With product ion monitoring scan mode, peptide quantitation was performed with a limit of detection of 20 nM achieved for the Met peptide. The method developed has also been applied to the analysis of the trypsin-digested cell lysate of SKBR3 cells with a low expression level of the Met gene.
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Affiliation(s)
- Spencer Chiang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Wenpeng Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Yiying Zhu
- Cell Signaling Technology, Danvers, Massachusetts 01923, United States
| | - Kimberly Lee
- Cell Signaling Technology, Danvers, Massachusetts 01923, United States
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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7
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Advances and applications of stable isotope labeling-based methods for proteome relative quantitation. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Chemical labeling – Assisted mass spectrometry analysis for sensitive detection of cytidine dual modifications in RNA of mammals. Anal Chim Acta 2020; 1098:56-65. [DOI: 10.1016/j.aca.2019.11.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/13/2019] [Accepted: 11/10/2019] [Indexed: 12/15/2022]
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9
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Fouquet TNJ. The Kendrick analysis for polymer mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:933-947. [PMID: 31758605 DOI: 10.1002/jms.4480] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 05/16/2023]
Abstract
The mass spectrum of a polymer often displays repetitive patterns with peak series spaced by the repeating unit(s) of the polymeric backbones, sometimes complexified with different adducts, chain terminations, or charge states. Exploring the complex mass spectral data or filtering the unwanted signal is tedious whether performed manually or automatically. In contrast, the now 60-year-old Kendrick (mass defect) analysis, when adapted to polymer ions, produces visual two-dimensional maps with intuitive alignments of the repetitive patterns and favourable deconvolution of features overlaid in the one-dimensional mass spectrum. This special feature article reports on an up-to-date and theoretically sound use of Kendrick plots as a data processing tool. The approach requires no prior knowledge of the sample but offers promising dynamic capabilities for visualizing, filtering, and sometimes assigning congested mass spectra. Examples of applications of the approach to polymers are discussed throughout the text, but the same tools can be readily extended to other applications, including the analysis of polymers present as pollutants/contaminants, and to other analytes incorporating a repetitive moiety, for example, oils or lipids. In each of these instances, data processing can benefit from the application of an updated and interactive Kendrick analysis.
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Affiliation(s)
- Thierry N J Fouquet
- Research Institute for Sustainable Chemistry (RISC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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10
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Zhao P, Zare RN, Chen H. Absolute Quantitation of Oxidizable Peptides by Coulometric Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2398-2407. [PMID: 31429055 DOI: 10.1007/s13361-019-02299-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/15/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
Quantitation methods for peptides using mass spectrometry have advanced rapidly. These methods rely on using standard and/or isotope-labeled peptides, which might be difficult or expensive to synthesize. To tackle this challenge, we present a new approach for absolute quantitation without the use of standards or calibration curves based on coulometry combined with mass spectrometry (MS). In this approach, which we call coulometric mass spectrometry (CMS), the mass spectrum of a target peptide containing one or more tyrosine residues is recorded before and after undergoing electrochemical oxidation. We record the total integrated oxidation current from the electrochemical measurement, which according to the Faraday's Law of coulometry, provides the number of moles of oxidized peptide. The ion intensity ratio of the target peptide before and after oxidation provides an excellent estimate of the fraction of the peptide that has been oxidized, from which the total amount of peptide is calculated. The striking strength of CMS is that it needs no standard peptide, but CMS does require the peptide to contain a known number of oxidizable groups. To illustrate the power of this method, we analyzed various tyrosine-containing peptides such as GGYR, DRVY, oxytocin, [Arg8]-vasotocin and angiotensinogen 1-14 with a quantification error ranging from - 7.5 to + 2.4%. This approach is also applicable to quantifying phosphopeptides and could be useful in proteomics research.
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Affiliation(s)
- Pengyi Zhao
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, CA, 94305-5080, USA.
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
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11
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Li G, Ma F, Cao Q, Zheng Z, DeLaney K, Liu R, Li L. Nanosecond photochemically promoted click chemistry for enhanced neuropeptide visualization and rapid protein labeling. Nat Commun 2019; 10:4697. [PMID: 31619683 PMCID: PMC6795811 DOI: 10.1038/s41467-019-12548-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 09/17/2019] [Indexed: 12/28/2022] Open
Abstract
Comprehensive protein identification and concomitant structural probing of proteins are of great biological significance. However, this is challenging to accomplish simultaneously in one confined space. Here, we develop a nanosecond photochemical reaction (nsPCR)-based click chemistry, capable of structural probing of proteins and enhancing their identifications through on-demand removal of surrounding matrices within nanoseconds. The nsPCR is initiated using a photoactive compound, 2-nitrobenzaldehyde (NBA), and is examined by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). Benefiting from the on-demand matrix-removal effect, this nsPCR strategy enables enhanced neuropeptide identification and visualization from complex tissue samples such as mouse brain tissue. The design shows great promise for structural probing of proteins up to 155 kDa due to the exclusive accessibility of nsPCR to primary amine groups, as demonstrated by its general applicability using a series of proteins with various lysine residues from multiple sample sources, with accumulated labeling efficiencies greater than 90%. Mass spectrometry-based quantitative proteomics aim to identify and quantify proteins from complex biological samples. Here, the authors developed a method for simultaneous high-throughput protein labelling and on-demand matrix removal within nanoseconds.
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Affiliation(s)
- Gongyu Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Fengfei Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Qinjingwen Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Zhen Zheng
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Rui Liu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA. .,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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12
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Zhong X, Frost DC, Li L. High-Resolution Enabled 5-plex Mass Defect-Based N, N-Dimethyl Leucine Tags for Quantitative Proteomics. Anal Chem 2019; 91:7991-7995. [PMID: 31135137 DOI: 10.1021/acs.analchem.9b01691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A mass defect-based labeling strategy provides high accuracy as an MS1-centric quantification method, avoiding the ratio compression that affects isobaric label-based reporter ion quantification. We have developed cost-effective 5-plex mass defect N, N-dimethyl leucine (mdDiLeu) tags for quantification of various biological samples with increased multiplexing at a given resolving power afforded by the addition of mass difference isotopologues. The combination of mass difference and mass defect produces two labeled peak clusters separated by 5 Da in MS1 spectra that are detected as five isotopic peaks at high resolution with mass differences of 15, 17, and 18 mDa per tag. Synthesis of each of the 5-plex mdDiLeu tags is accomplished by a single straightforward reaction step, making it accessible to any lab. To demonstrate 5-plex mdDiLeu for quantitative proteomics, we perform proof-of-principle experiments of mdDiLeu-labeled Saccharomyces cerevisiae lysate digest on an Orbitrap Fusion Lumos mass spectrometer.
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Affiliation(s)
- Xiaofang Zhong
- School of Pharmacy , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53705 , United States
| | - Dustin C Frost
- School of Pharmacy , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53705 , United States
| | - Lingjun Li
- School of Pharmacy , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53705 , United States.,Department of Chemistry , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53706 , United States
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13
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Zhao XE, He Y, Zhu S, Xu Y, You J, Bai Y, Liu H. Stable isotope labeling derivatization and magnetic dispersive solid phase extraction coupled with UHPLC-MS/MS for the measurement of brain neurotransmitters in post-stroke depression rats administrated with gastrodin. Anal Chim Acta 2019; 1051:73-81. [DOI: 10.1016/j.aca.2018.11.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022]
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14
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Chen B, Feng Y, Frost DC, Zhong X, Buchberger AR, Johnson J, Xu M, Kim M, Puccetti D, Diamond C, Ikonomidou C, Li L. Quantitative Glycomic Analysis by Mass-Defect-Based Dimethyl Pyrimidinyl Ornithine (DiPyrO) Tags and High-Resolution Mass Spectrometry. Anal Chem 2018; 90:7817-7823. [PMID: 29779369 DOI: 10.1021/acs.analchem.8b00548] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We recently developed a novel amine-reactive mass-defect-based chemical tag, dimethyl pyrimidinyl ornithine (DiPyrO), for quantitative proteomic analysis at the MS1 level. In this work, we further extend the application of the DiPyrO tag, which provides amine group reactivity, optical detection capability, and improved electrospray sensitivity, to quantify N-linked glycans enzymatically released from glycoproteins in the glycosylamine form. Duplex DiPyrO tags that differ in mass by 45.3 mDa were used to label the glycosylamine moieties of freshly released N-glycosylamines from glycoprotein standards and human serum proteins. We demonstrate that both MALDI-LTQ-Orbitrap and nano-HILIC LC/MS/MS Fusion Lumos Orbitrap platforms are capable of resolving the singly or multiply charged N-glycans labeled with mass-defect DiPyrO tags. Dynamic range of quantification, based on MS1 peak intensities, was evaluated across 2 orders of magnitude. With optimized N-glycan release conditions, glycosylamine labeling conditions, and MS acquisition parameters, the N-glycan profiles and abundances in human serum proteins of cancer patients before and after chemotherapy were compared. Moreover, this study also opens a door for using well-developed amine-reactive tags for relative quantification of glycans, which could be widely applied.
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