1
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Wu Z, Huang X, Huang L, Zhang X. 102-Plex Approach for Accurate and Multiplexed Proteome Quantification. Anal Chem 2024; 96:1402-1409. [PMID: 38215345 DOI: 10.1021/acs.analchem.3c03036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Hyperplexing approaches have been aimed to meet the demand for large-scale proteomic analyses. Currently, the analysis capacity has expanded to up to 54 samples within a single experiment by utilizing different isotopic and isobaric reagent combinations. In this report, we propose a super multiplexed approach to enable the analysis of up to 102 samples in a single experiment, by the combination of our recently developed TAG-TMTpro and TAG-IBT16 labeling. We systematically investigated the identification and quantification performance of the 102-plex approach using the mixtures of E. coli and HeLa peptides. Our results revealed that all labeling series demonstrated accurate and reliable quantification performance. The combination of TAG-IBT16 and TAG-TMTpro approaches expands the multiplexing capacity to 102 plexes, providing a more multiplexed quantification method for even larger-scale proteomic analysis. Data are available via ProteomeXchange with the identifier PXD042398.
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Affiliation(s)
- Zhen Wu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xirui Huang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lin Huang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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2
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Bowser BL, Patterson KL, Robinson RA. Evaluating cPILOT Data toward Quality Control Implementation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1741-1752. [PMID: 37459602 DOI: 10.1021/jasms.3c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Multiplexing enables the monitoring of hundreds to thousands of proteins in quantitative proteomics analyses and increases sample throughput. In most mass-spectrometry-based proteomics workflows, multiplexing is achieved by labeling biological samples with heavy isotopes via precursor isotopic labeling or isobaric tagging. Enhanced multiplexing strategies, such as combined precursor isotopic labeling and isobaric tagging (cPILOT), combine multiple technologies to afford an even higher sample throughput. Critical to enhanced multiplexing analyses is ensuring that analytical performance is optimal and that missingness of sample channels is minimized. Automation of sample preparation steps and use of quality control (QC) metrics can be incorporated into multiplexing analyses and reduce the likelihood of missing information, thus maximizing the amount of usable quantitative data. Here, we implemented QC metrics previously developed in our laboratory to evaluate a 36-plex cPILOT experiment that encompassed 144 mouse samples of various tissue types, time points, genotypes, and biological replicates. The evaluation focuses on the use of a sample pool generated from all samples in the experiment to monitor the daily instrument performance and to provide a means for data normalization across sample batches. Our results show that tracking QC metrics enabled the quantification of ∼7000 proteins in each sample batch, of which ∼70% had minimal missing values across up to 36 sample channels. Implementation of QC metrics for future cPILOT studies as well as other enhanced multiplexing strategies will help yield high-quality data sets.
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Affiliation(s)
- Bailey L Bowser
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Khiry L Patterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã As Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Memory & Alzheimer's Center, Nashville, Tennessee 37212, United States
- Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Nashville, Tennessee 37232, United States
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3
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Bowser BL, Robinson RAS. Enhanced Multiplexing Technology for Proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:379-400. [PMID: 36854207 DOI: 10.1146/annurev-anchem-091622-092353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The identification of thousands of proteins and their relative levels of expression has furthered understanding of biological processes and disease and stimulated new systems biology hypotheses. Quantitative proteomics workflows that rely on analytical assays such as mass spectrometry have facilitated high-throughput measurements of proteins partially due to multiplexing. Multiplexing allows proteome differences across multiple samples to be measured simultaneously, resulting in more accurate quantitation, increased statistical robustness, reduced analysis times, and lower experimental costs. The number of samples that can be multiplexed has evolved from as few as two to more than 50, with studies involving more than 10 samples being denoted as enhanced multiplexing or hyperplexing. In this review, we give an update on emerging multiplexing proteomics techniques and highlight advantages and limitations for enhanced multiplexing strategies.
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Affiliation(s)
- Bailey L Bowser
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
- Department of Neurology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Memory and Alzheimer's Center, Nashville, Tennessee, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Brain Institute, Vanderbilt School of Medicine, Nashville, Tennessee, USA
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4
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Liang Y, Truong T, Saxton AJ, Boekweg H, Payne SH, Van Ry PM, Kelly RT. HyperSCP: Combining Isotopic and Isobaric Labeling for Higher Throughput Single-Cell Proteomics. Anal Chem 2023; 95:8020-8027. [PMID: 37167627 PMCID: PMC10246935 DOI: 10.1021/acs.analchem.3c00906] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Recent developments in mass spectrometry-based single-cell proteomics (SCP) have resulted in dramatically improved sensitivity, yet the relatively low measurement throughput remains a limitation. Isobaric and isotopic labeling methods have been separately applied to SCP to increase throughput through multiplexing. Here we combined both forms of labeling to achieve multiplicative scaling for higher throughput. Two-plex stable isotope labeling of amino acids in cell culture (SILAC) and isobaric tandem mass tag (TMT) labeling enabled up to 28 single cells to be analyzed in a single liquid chromatography-mass spectrometry (LC-MS) analysis, in addition to carrier, reference, and negative control channels. A custom nested nanowell chip was used for nanoliter sample processing to minimize sample losses. Using a 145-min total LC-MS cycle time, ∼280 single cells were analyzed per day. This measurement throughput could be increased to ∼700 samples per day with a high-duty-cycle multicolumn LC system producing the same active gradient. The labeling efficiency and achievable proteome coverage were characterized for multiple analysis conditions.
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Affiliation(s)
- Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Aubrianna J Saxton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Hannah Boekweg
- Department of Biology, Brigham Young University, Provo, Utah 84602, United States
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, Utah 84602, United States
| | - Pam M Van Ry
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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5
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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: 14] [Impact Index Per Article: 14.0] [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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6
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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: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [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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7
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Wu Z, Shen Y, Zhang X. TAG-TMTpro, a Hyperplexing Quantitative Approach for High-Throughput Proteomic Studies. Anal Chem 2022; 94:12565-12569. [PMID: 36066113 DOI: 10.1021/acs.analchem.2c02099] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isobaric labeling is the most widely used multiplexing quantitative approach in proteomic studies, enabling the comparison of up to 18 samples in a single MS analysis. Expanding the multiplexing capacity is of great necessity for high-throughput proteomic studies. Herein, we establish a novel TAG-TMTpro approach by introducing Ala or Gly residues to peptides prior to TMTpro labeling, which is able to triple the quantitative capacity of TMTpro. We systematically evaluated the Boc-Ala-OSu and Boc-Gly-OSu reaction and optimized the conditions for labeling, side-product elimination, and Boc deprotection. We validated the identification and quantification performance using E. coli and HeLa cell lysates. We demonstrated that the TAG-TMTpro approach resulted in good identification reproducibility and reliable quantitative accuracy. The TAG-TMTpro is able to triple the multiplexing capacity of TMTpro reagents and is a versatile quantitative approach for high-throughput proteomic studies. Data are available via ProteomeXchange with identifier PXD033711.
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Affiliation(s)
- Zhen Wu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yi Shen
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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8
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Quantitative proteomics to study aging in rabbit spleen tissues. Exp Gerontol 2022; 167:111908. [PMID: 35932934 DOI: 10.1016/j.exger.2022.111908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/04/2022]
Abstract
Aging is a process that occurs in tissues and across species, leading to the degradation of many biological processes. We previously demonstrated that rabbits are a feasible model for studying aging due to their genetic homology and relatively short lifespan in comparison to humans. We utilized a cPILOT multiplexing strategy to identify proteomic changes in spleen tissues of young, middle, and old aged rabbits. We identified 63 proteins that change significantly (p < 0.05) with age and notably these proteins relate to nucleotide and RNA binding, DNA repair, actin regulation, and immune system pathways. Here, we explore the implications of aging in the spleen and demonstrate the utility of a rabbit model to understand aging processes.
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9
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Burt RA, Alghusen IM, John Ephrame S, Villar MT, Artigues A, Slawson C. Mapping the O-GlcNAc Modified Proteome: Applications for Health and Disease. Front Mol Biosci 2022; 9:920727. [PMID: 35664676 PMCID: PMC9161079 DOI: 10.3389/fmolb.2022.920727] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/02/2022] [Indexed: 01/03/2023] Open
Abstract
O-GlcNAc is a pleotropic, enigmatic post-translational modification (PTM). This PTM modifies thousands of proteins differentially across tissue types and regulates diverse cellular signaling processes. O-GlcNAc is implicated in numerous diseases, and the advent of O-GlcNAc perturbation as a novel class of therapeutic underscores the importance of identifying and quantifying the O-GlcNAc modified proteome. Here, we review recent advances in mass spectrometry-based proteomics that will be critical in elucidating the role of this unique glycosylation system in health and disease.
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Affiliation(s)
- Rajan A. Burt
- University of Kansas Medical Center, Medical Scientist Training Program (MSTP), Kansas, KS, United States
| | - Ibtihal M. Alghusen
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
| | - Sophiya John Ephrame
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
| | - Maria T. Villar
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
| | - Antonio Artigues
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
| | - Chad Slawson
- University of Kansas Medical Center, Medical Scientist Training Program (MSTP), Kansas, KS, United States
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
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10
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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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11
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Espino JA, King CD, Jones LM, Robinson RAS. In Vivo Fast Photochemical Oxidation of Proteins Using Enhanced Multiplexing Proteomics. Anal Chem 2020; 92:7596-7603. [PMID: 32383586 PMCID: PMC7815197 DOI: 10.1021/acs.analchem.0c00174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
In vivo fast photochemical oxidation of proteins
(IV-FPOP) is a hydroxyl radical protein footprinting method used to
study protein structure and protein–protein interactions. Oxidatively
modified proteins by IV-FPOP are analyzed by mass spectrometry (MS),
and the extent of oxidation is quantified by label-free MS. Peptide
oxidation changes yield useful information about protein structure,
due to changes in solvent accessibility. However, the sample size
necessary for animal studies requires increased sample preparation
and instrument time. Here, we report the combined application of IV-FPOP
and the enhanced multiplexing strategy combined precursor isotopic
labeling and isobaric tagging (cPILOT) for higher-throughput analysis
of oxidative modifications in C. elegans. Key differences
in the performance of label-free MS and cPILOT were identified. The
addition of oxygen (+16) was the most abundant modification identified
among all known possible FPOP modifications. This study presents IV-FPOP
coupled with enhanced multiplexing strategies such as cPILOT to increase
throughput of studies seeking to examine oxidative protein modifications.
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Affiliation(s)
- Jessica A Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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12
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Aggarwal S, Kumar A, Jamwal S, Midha MK, Talukdar NC, Yadav AK. HyperQuant-A Computational Pipeline for Higher Order Multiplexed Quantitative Proteomics. ACS OMEGA 2020; 5:10857-10867. [PMID: 32455206 PMCID: PMC7240821 DOI: 10.1021/acsomega.0c00515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Quantitative proteomics has evolved considerably over the last decade with the advent of higher order multiplexing (HOM) techniques. With the development of methods such as-multitagging, cPILOT, hyperplexing, BONPlex, and MITNCAT, the HOM technique is rapidly taking the center stage in multiplexed quantitative proteomics. These studies combined MS1 and MS2 labels in a single experiment enabling higher sample throughput. While HOM is highly promising, the computational analysis is still a big challenge, as the available tools cannot harness its power completely. We have developed a new quantitative pipeline, HyperQuant to aid in accurately quantitating complex HOM data. The pipeline uses identification results from either MaxQuant or any other search engine and quantitation results from QuantWizIQ. The Mapper and Combiner modules of HyperQuant allow facile integration of the labeled data, along with peptide spectrum match (PSM) intensity/ratio integration for proteins, respectively, for each PSM label combination. This also includes appropriate combination of replicates/fractions before summarizing the protein intensity/ratio, leading to robust quantitation. To the best of our knowledge, this is the first tool for the quantitation of HOM data with flexibility for any combination of MS1 and MS2 labels. We demonstrate its utility in analyzing two 18-plex data sets from the hyperplexing and the BONplex studies. The tool is open source and freely available for noncommercial use. HyperQuant is a highly valuable tool that will help in advancing the field of multiplexed quantitative proteomics.
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Affiliation(s)
- Suruchi Aggarwal
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
- Division
of Life Sciences, Institute of Advanced
Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
- Department
of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam 781001, India
| | - Ajay Kumar
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Shilpa Jamwal
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Mukul Kumar Midha
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Narayan Chandra Talukdar
- Division
of Life Sciences, Institute of Advanced
Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
- Department
of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam 781001, India
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
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13
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Quantitative proteomics to study aging in rabbit liver. Mech Ageing Dev 2020; 187:111227. [PMID: 32126221 DOI: 10.1016/j.mad.2020.111227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 01/24/2020] [Accepted: 02/27/2020] [Indexed: 12/23/2022]
Abstract
Aging globally effects cellular and organismal metabolism across a range of mammalian species, including humans and rabbits. Rabbits (Oryctolagus cuniculus are an attractive model system of aging due to their genetic similarity with humans and their short lifespans. This model can be used to understand metabolic changes in aging especially in major organs such as liver where we detected pronounced variations in fat metabolism, mitochondrial dysfunction, and protein degradation. Such changes in the liver are consistent across several mammalian species however in rabbits the downstream effects of these changes have not yet been explored. We have applied proteomics to study changes in the liver proteins from young, middle, and old age rabbits using a multiplexing cPILOT strategy. This resulted in the identification of 2,586 liver proteins, among which 45 proteins had significant p < 0.05) changes with aging. Seven proteins were differentially-expressed at all ages and include fatty acid binding protein, aldehyde dehydrogenase, enoyl-CoA hydratase, 3-hydroxyacyl CoA dehydrogenase, apolipoprotein C3, peroxisomal sarcosine oxidase, adhesion G-protein coupled receptor, and glutamate ionotropic receptor kinate. Insights to how alterations in metabolism affect protein expression in liver have been gained and demonstrate the utility of rabbit as a model of aging.
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14
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King CD, Robinson RAS. Evaluating Combined Precursor Isotopic Labeling and Isobaric Tagging Performance on Orbitraps To Study the Peripheral Proteome of Alzheimer's Disease. Anal Chem 2020; 92:2911-2916. [PMID: 31940168 PMCID: PMC7932850 DOI: 10.1021/acs.analchem.9b01974] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Combined precursor isotopic labeling and isobaric tagging (cPILOT) is an enhanced multiplexing strategy currently capable of analyzing up to 24 samples simultaneously. This capability is especially helpful when studying multiple tissues and biological replicates in models of disease, such as Alzheimer's disease (AD). Here, cPILOT was used to study proteomes from heart, liver, and brain tissues in a late-stage amyloid precursor protein/presenilin-1 (APP/PS-1) human transgenic double-knock-in mouse model of AD. The original global cPILOT assay developed on an Orbitrap Velos instrument was transitioned to an Orbitrap Fusion Lumos instrument. The advantages of faster scan rates, lower limits of detection, and synchronous precursor selection on the Fusion Lumos afford greater numbers of isobarically tagged peptides to be quantified in comparison to the Orbitrap Velos. Parameters such as LC gradient, m/z isolation window, dynamic exclusion, targeted mass analyses, and synchronous precursor scan were optimized leading to >600 000 PSMs, corresponding to 6074 proteins. Overall, these studies inform of system-wide changes in brain, heart, and liver proteins from a mouse model of AD.
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Affiliation(s)
- Christina D King
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Renã A S Robinson
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
- Department of Neurology , Vanderbilt University Medical Center , Nashville , Tennessee 37232 , United States
- Vanderbilt Memory & Alzheimer's Center , Vanderbilt University Medical Center , Nashville , Tennessee 37212 , United States
- Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37232 , United States
- Vanderbilt Brain Institute , Vanderbilt University , Nashville , Tennessee 37232 , United States
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15
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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16
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Aggarwal S, Talukdar NC, Yadav AK. Advances in Higher Order Multiplexing Techniques in Proteomics. J Proteome Res 2019; 18:2360-2369. [DOI: 10.1021/acs.jproteome.9b00228] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Suruchi Aggarwal
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Faridabad − Gurgaon Expressway, Faridabad, Haryana 121001, India
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
- Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam 781001, India
| | - Narayan C. Talukdar
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
- Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam 781001, India
| | - Amit K. Yadav
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Faridabad − Gurgaon Expressway, Faridabad, Haryana 121001, India
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Affiliation(s)
- Albert B. Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A. S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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Frost DC, Rust CJ, Robinson RAS, Li L. Increased N,N-Dimethyl Leucine Isobaric Tag Multiplexing by a Combined Precursor Isotopic Labeling and Isobaric Tagging Approach. Anal Chem 2018; 90:10664-10669. [PMID: 30095893 DOI: 10.1021/acs.analchem.8b01301] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Multiplex isobaric tags have become valuable tools for high-throughput quantitative analysis of complex biological samples in discovery-based proteomics studies. Hybrid labeling strategies that pair stable isotope mass difference labeling with multiplex isobaric tag-based quantification further facilitate these studies by greatly increasing multiplexing capability. In this work, we present a cost-effective chemical labeling approach that couples duplex stable isotope dimethyl labeling with our custom 12-plex N,N-dimethyl leucine (DiLeu) isobaric tags in a combined precursor isotopic labeling and isobaric tagging (cPILOT) strategy that is compatible with a wide variety of biological samples and permits 24-plex quantification in a single LC-MS/MS experiment. We demonstrate the utility of the DiLeu cPILOT approach by labeling yeast digests and performing proof-of-principle quantification experiments on the Orbitrap Fusion Lumos.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53705 , United States
| | - Clayton J Rust
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Renã A S Robinson
- Department of Chemistry , Vanderbilt University , 5423 Stevenson Center , Nashville , Tennessee 37235 , 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 , 1101 University Avenue , Madison , Wisconsin 53706 , United States
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King CD, Singh D, Holden K, Govan AB, Keith SA, Ghazi A, Robinson RA. Proteomic identification of virulence-related factors in young and aging C. elegans infected with Pseudomonas aeruginosa. J Proteomics 2018; 181:92-103. [DOI: 10.1016/j.jprot.2018.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 03/26/2018] [Accepted: 04/09/2018] [Indexed: 12/16/2022]
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King CD, Dudenhoeffer JD, Gu L, Evans AR, Robinson RAS. Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT). J Vis Exp 2017. [PMID: 28518113 DOI: 10.3791/55406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
There is an increasing demand to analyze many biological samples for disease understanding and biomarker discovery. Quantitative proteomics strategies that allow simultaneous measurement of multiple samples have become widespread and greatly reduce experimental costs and times. Our laboratory developed a technique called combined precursor isotopic labeling and isobaric tagging (cPILOT), which enhances sample multiplexing of traditional isotopic labeling or isobaric tagging approaches. Global cPILOT can be applied to samples originating from cells, tissues, bodily fluids, or whole organisms and gives information on relative protein abundances across different sample conditions. cPILOT works by 1) using low pH buffer conditions to selectively dimethylate peptide N-termini and 2) using high pH buffer conditions to label primary amines of lysine residues with commercially-available isobaric reagents (see Table of Materials/Reagents). The degree of sample multiplexing available is dependent on the number of precursor labels used and the isobaric tagging reagent. Here, we present a 12-plex analysis using light and heavy dimethylation combined with six-plex isobaric reagents to analyze 12 samples from mouse tissues in a single analysis. Enhanced multiplexing is helpful for reducing experimental time and cost and more importantly, allowing comparison across many sample conditions (biological replicates, disease stage, drug treatments, genotypes, or longitudinal time-points) with less experimental bias and error. In this work, the global cPILOT approach is used to analyze brain, heart, and liver tissues across biological replicates from an Alzheimer's disease mouse model and wild-type controls. Global cPILOT can be applied to study other biological processes and adapted to increase sample multiplexing to greater than 20 samples.
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Affiliation(s)
| | | | | | - Adam R Evans
- Large Molecule Analytical Development, Pharmaceutical Development & Manufacturing Science, Janssen Research and Development
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21
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Dyer RR, Gu L, Robinson RAS. S-Nitrosylation in Alzheimer’s Disease Using Oxidized Cysteine-Selective cPILOT. NEUROMETHODS 2017. [DOI: 10.1007/978-1-4939-7119-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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22
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Robinson RAS, Amin B, Guest PC. Multiplexing Biomarker Methods, Proteomics and Considerations for Alzheimer’s Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 974:21-48. [DOI: 10.1007/978-3-319-52479-5_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Gu L, Robinson RAS. Proteomic approaches to quantify cysteine reversible modifications in aging and neurodegenerative diseases. Proteomics Clin Appl 2016; 10:1159-1177. [PMID: 27666938 DOI: 10.1002/prca.201600015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/13/2016] [Accepted: 09/23/2016] [Indexed: 01/11/2023]
Abstract
Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling, and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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Gu L, Robinson RAS. High-throughput endogenous measurement of S-nitrosylation in Alzheimer's disease using oxidized cysteine-selective cPILOT. Analyst 2016; 141:3904-15. [PMID: 27152368 PMCID: PMC4904844 DOI: 10.1039/c6an00417b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reversible cysteine modifications play important physiological roles such as modulating enzymatic catalysis, maintaining redox homeostasis and conducting cellular signaling. These roles can be critical in the context of disease. Oxidative modifications such as S-nitrosylation (SNO) are signatures of neurodestruction in conditions of oxidative stress however are also indicators of neuroprotection and normal signaling in cellular environments with low concentrations of reactive oxygen and nitrogen species. SNO is a dynamic and low abundance modification and requires sensitive and selective analytical methods for its detection in biological tissues. Here we present an enhanced multiplexing strategy to study SNO in complex mixtures arising from tissues. This method, termed oxidized cysteine-selective cPILOT (OxcyscPILOT), allows simultaneous analysis of SNO-modified peptides in 12 samples. OxcyscPILOT has three primary steps: (1) blocking of free thiols by a cysteine-reactive reagent, (2) enrichment of peptides containing SNO on a solid phase resin, and (3) isotopic labeling and isobaric tagging of enriched peptides on the solid phase resin. This approach offers the advantage of allowing total protein abundance levels to be measured simultaneously with endogenous SNO levels and measurement of SNO levels across four biological replicates in a single analysis. Furthermore, the relative amount of SNO on a specific cysteine site can also be determined. A well-known model of Alzheimer's disease, the APP/PS-1 transgenic mouse model, was selected for demonstration of the method as several SNO-modified proteins have previously been reported in brain and synaptosomes from AD subjects. OxcyscPILOT analysis resulted in identification of 138 SNO-modified cysteines in brain homogenates that correspond to 135 proteins. Many of these SNO-modified proteins were only present in wild-type or AD mice, whereas 93 proteins had SNO signals in both WT and AD. Pathway analysis links SNO-modified proteins to various biological pathways especially metabolism and signal transduction, consistent with previous reports in the literature. The OxcyscPILOT strategy provides enhanced multiplexing capability to current redox proteomics methods to study oxidative modifications of cysteine.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Castillo MJ, McShane AJ, Cai M, Shen Y, Wang L, Yao X. Nonisotopic reagents for a cost-effective increase in sample throughput of targeted quantitative proteomics. Anal Chem 2015; 87:9209-16. [PMID: 26291548 DOI: 10.1021/acs.analchem.5b01727] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The new technology of ultrathroughput MS (uMS) transforms the intrinsic capability of analyte multiplexing in mass spectrometry (MS) to sample multiplexing. Core technological advantages of uMS rely on the decoupled use of isotopic quantitation reference and nonisotopic mass coding of samples. These advantages include: (1) high sample-throughput potential, (2) utilization of minimal amounts of expensive stable isotopes for the quantitation reference, and (3) unleashing of the open-source exploration of the chemical structure diversity of nonisotopic reagents to significantly enhance the MS detectability of analytes. A particular uMS method, ultrathroughput multiple reaction monitoring (uMRM), is reported for one-experiment quantitation of a surrogate peptide (SVILLGR) of prostate specific antigen (PSA) in multiple serum samples. Following derivatization of the pair of spiked, isotopic reference (SVILLGR*) and endogenous, native peptide in each sample, all samples were pooled for a step of simultaneous enrichment and cleanup of derivatized peptide pairs using immobilized antibody. The MS analysis of the pooled sample reported the quantity and sample origin of the surrogate peptide. Several analyses with different sample throughput were presented, with the highest being 15-in-1. Screening of nonisotopic reagents used combinatorial libraries of peptidyl compounds, and the reagent selection was based on the derivatization effectiveness and the capability of MS signal enhancement for the peptide. The precision, accuracy, and linearity of the uMRM MS technology were found to be comparable with standard isotope dilution MRM MS.
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Affiliation(s)
- Mary Joan Castillo
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Adam J McShane
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Min Cai
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Yuanyuan Shen
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Lei Wang
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Xudong Yao
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
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Greer T, Hao L, Nechyporenko A, Lee S, Vezina CM, Ricke WA, Marker PC, Bjorling DE, Bushman W, Li L. Custom 4-Plex DiLeu Isobaric Labels Enable Relative Quantification of Urinary Proteins in Men with Lower Urinary Tract Symptoms (LUTS). PLoS One 2015; 10:e0135415. [PMID: 26267142 PMCID: PMC4534462 DOI: 10.1371/journal.pone.0135415] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 07/21/2015] [Indexed: 12/19/2022] Open
Abstract
The relative quantification of proteins using liquid chromatography mass spectrometry (LC-MS) has allowed researchers to compile lists of potential disease markers. These complex quantitative workflows often include isobaric labeling of enzymatically-produced peptides to analyze their relative abundances across multiple samples in a single LC-MS run. Recent efforts by our lab have provided scientists with cost-effective alternatives to expensive commercial labels. Although the quantitative performance of these dimethyl leucine (DiLeu) labels has been reported using known ratios of complex protein and peptide standards, their potential in large-scale proteomics studies using a clinically relevant system has never been investigated. Our work rectifies this oversight by implementing 4-plex DiLeu to quantify proteins in the urine of aging human males who suffer from lower urinary tract symptoms (LUTS). Protein abundances in 25 LUTS and 15 control patients were compared, revealing that of the 836 proteins quantified, 50 were found to be differentially expressed (>20% change) and statistically significant (p-value <0.05). Gene ontology (GO) analysis of the differentiated proteins showed that many were involved in inflammatory responses and implicated in fibrosis. While confirmation of individual protein abundance changes would be required to verify protein expression, this study represents the first report using the custom isobaric label, 4-plex DiLeu, to quantify protein abundances in a clinically relevant system.
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Affiliation(s)
- Tyler Greer
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ling Hao
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anatoliy Nechyporenko
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sanghee Lee
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chad M. Vezina
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Will A. Ricke
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Paul C. Marker
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dale E. Bjorling
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Wade Bushman
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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27
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Frost DC, Greer T, Xiang F, Liang Z, Li L. Development and characterization of novel 8-plex DiLeu isobaric labels for quantitative proteomics and peptidomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1115-24. [PMID: 25981542 PMCID: PMC4837894 DOI: 10.1002/rcm.7201] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/05/2015] [Accepted: 03/22/2015] [Indexed: 05/08/2023]
Abstract
RATIONALE Relative quantification of proteins via their enzymatically digested peptide products determines disease biomarker candidate lists in discovery studies. Isobaric label-based strategies using TMT and iTRAQ allow for up to 10 samples to be multiplexed in one experiment, but their expense limits their use. The demand for cost-effective tagging reagents capable of multiplexing many samples led us to develop an 8-plex version of our isobaric labeling reagent, DiLeu. METHODS The original 4-plex DiLeu reagent was extended to an 8-plex set by coupling isotopic variants of dimethylated leucine to an alanine balance group designed to offset the increasing mass of the label's reporter group. Tryptic peptides from a single protein digest, a protein mixture digest, and Saccharomyces cerevisiae lysate digest were labeled with 8-plex DiLeu and analyzed via nanospray liquid chromatography/tandem mass spectrometry (nanoLC/MS(2) ) on a Q-Exactive Orbitrap mass spectrometer. Characteristics of 8-plex DiLeu-labeled peptides, including quantitative accuracy and fragmentation, were examined. RESULTS An 8-plex set of DiLeu reagents with 1 Da spaced reporters was synthesized at a yield of 36%. The average cost to label eight 100 µg peptide samples was calculated to be approximately $15. Normalized collision energy tests on the Q-Exactive revealed that a higher-energy collisional dissociation value of 27 generated the optimum number of high-quality spectral matches. Relative quantification of DiLeu-labeled peptides yielded normalized median ratios accurate to within 12% of their expected values. CONCLUSIONS Cost-effective 8-plex DiLeu reagents can be synthesized and applied to relative peptide and protein quantification. These labels increase the multiplexing capacity of our previous 4-plex implementation without requiring high-resolution instrumentation to resolve reporter ion signals.
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Affiliation(s)
| | - Tyler Greer
- Department of Chemistry, University of Wisconsin–Madison
| | - Feng Xiang
- School of Pharmacy, University of Wisconsin–Madison
| | - Zhidan Liang
- School of Pharmacy, University of Wisconsin–Madison
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin–Madison
- Department of Chemistry, University of Wisconsin–Madison
- Address reprint requests to: Dr. Lingjun Li, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI 53705, USA. . Phone: (608) 265-8491, Fax: (608) 262-5345
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Cao Z, Evans AR, Robinson RAS. MS(3)-based quantitative proteomics using pulsed-Q dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1025-1030. [PMID: 26044269 DOI: 10.1002/rcm.7192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 01/31/2015] [Accepted: 03/08/2015] [Indexed: 06/04/2023]
Abstract
RATIONALE Isobaric tagging reagents, such as tandem mass tags (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ), are high-throughput methods that allow the analysis of multiple samples simultaneously, which reduces instrument time and error. Accuracy and precision of isobaric tags are limited, however, in tandem mass spectrometry (MS/MS) acquisition due to co-isolation and co-fragmentation of neighboring peptide peaks in precursor scans. Here we present a MS(3) method using pulsed-Q dissociation (PQD) in ion trap and Orbitrap instrumentation as a means to improve ratio distortion and maintain high numbers of identified and quantified proteins. METHODS Mouse brain protein digests were labeled with TMT-128, 129, 130, 131 reagents, mixed in the following molar ratios 1:1:2:5, respectively, and analyzed using HCD-MS(3) and PQD-MS(3) methods. The most intense fragment ion (termed as HCD-MS(3)-top ion or PQD-MS(3)-top ion) or y1 ion (i.e., lysine-TMT tag ion; termed as HCD-MS(3)-y1 or PQD-MS(3)-y1) in collision-induced dissociation (CID) MS/MS was selected for MS(3). RESULTS Calculated protein ratios obtained in HCD-MS(3)-top ion and PQD-MS(3)-top ion, HCD-MS(3)-y1, and PQD-MS(3)-y1 are accurate and PQD-MS(3) methods resulted in higher numbers of identified and quantified peptide spectral counts and proteins. CONCLUSIONS PQD-MS(3) methods increase the amount of MS/MS spectra collected and number of quantified proteins and are accessible to those researchers with not only an orbitrap but also an ion trap mass spectrometer.
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Affiliation(s)
- Zhiyun Cao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Adam R Evans
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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Evans AR, Gu L, Guerrero R, Robinson RAS. Global cPILOT analysis of the APP/PS-1 mouse liver proteome. Proteomics Clin Appl 2015; 9:872-84. [PMID: 25620666 DOI: 10.1002/prca.201400149] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/20/2014] [Accepted: 01/21/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE A quantitative proteomics strategy called combined precursor isotopic labeling and isobaric tagging (cPILOT) was designed to discover alterations in the amyloid precursor protein/presenilin-1 (APP/PS-1) mouse liver proteome. The multiplexing strategy allows simultaneous quantitation of 12 samples in a single experiment. EXPERIMENTAL DESIGN For cPILOT samples, six APP/PS-1 and six heterozygous mouse livers were modified using precursor dimethylation (pH 2.5) followed by isobaric tagging (pH 8.0). Samples were pooled, fractioned with strong cation exchange, and analyzed using RPLC-MS(3) for protein identification and relative quantitation. In order to increase proteome coverage, a two-tiered data collection strategy was employed. Six duplex precursor dimethylation experiments were also performed to verify cPILOT protein quantitation. RESULTS The combination of cPILOT with precursor dimethylation data resulted in 2437 total liver proteins identified and 77 differentially expressed proteins in APP/PS-1 liver. Differentially expressed proteins are involved in metabolic processes such as B-oxidation, pyruvate metabolism, and glucose regulation. CONCLUSIONS AND CLINICAL RELEVANCE cPILOT expands protein quantitation using isobaric tags and can be applied to any clinical laboratory interested in enhanced multiplexing strategies. Differentially expressed proteins in APP/PS-1 mouse liver suggest the potential use of ketone bodies to alleviate metabolic dysregulation in Alzheimer's disease brain. Our work also suggests alterations in the alanine cycle potentially leading to hyperammonia production, may contribute to Alzheimer's disease pathogenesis.
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Affiliation(s)
- Adam R Evans
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rodolfo Guerrero
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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Gu L, Evans AR, Robinson RAS. Sample multiplexing with cysteine-selective approaches: cysDML and cPILOT. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:615-630. [PMID: 25588721 DOI: 10.1007/s13361-014-1059-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/22/2014] [Accepted: 11/22/2014] [Indexed: 06/04/2023]
Abstract
Cysteine-selective proteomics approaches simplify complex protein mixtures and improve the chance of detecting low abundant proteins. It is possible that cysteinyl-peptide/protein enrichment methods could be coupled to isotopic labeling and isobaric tagging methods for quantitative proteomics analyses in as few as two or up to 10 samples, respectively. Here we present two novel cysteine-selective proteomics approaches: cysteine-selective dimethyl labeling (cysDML) and cysteine-selective combined precursor isotopic labeling and isobaric tagging (cPILOT). CysDML is a duplex precursor quantification technique that couples cysteinyl-peptide enrichment with on-resin stable-isotope dimethyl labeling. Cysteine-selective cPILOT is a novel 12-plex workflow based on cysteinyl-peptide enrichment, on-resin stable-isotope dimethyl labeling, and iodoTMT tagging on cysteine residues. To demonstrate the broad applicability of the approaches, we applied cysDML and cPILOT methods to liver tissues from an Alzheimer's disease (AD) mouse model and wild-type (WT) controls. From the cysDML experiments, an average of 850 proteins were identified and 594 were quantified, whereas from the cPILOT experiment, 330 and 151 proteins were identified and quantified, respectively. Overall, 2259 unique total proteins were detected from both cysDML and cPILOT experiments. There is tremendous overlap in the proteins identified and quantified between both experiments, and many proteins have AD/WT fold-change values that are within ~20% error. A total of 65 statistically significant proteins are differentially expressed in the liver proteome of AD mice relative to WT. The performance of cysDML and cPILOT are demonstrated and advantages and limitations of using multiple duplex experiments versus a single 12-plex experiment are highlighted.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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31
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Frost DC, Greer T, Li L. High-resolution enabled 12-plex DiLeu isobaric tags for quantitative proteomics. Anal Chem 2014; 87:1646-54. [PMID: 25405479 PMCID: PMC4318621 DOI: 10.1021/ac503276z] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Multiplex
isobaric tags (e.g., tandem mass tags (TMT) and isobaric
tags for relative and absolute quantification (iTRAQ)) are a valuable
tool for high-throughput mass spectrometry based quantitative proteomics.
We have developed our own multiplex isobaric tags, DiLeu, that feature
quantitative performance on par with commercial offerings but can
be readily synthesized in-house as a cost-effective alternative. In
this work, we achieve a 3-fold increase in the multiplexing capacity
of the DiLeu reagent without increasing structural complexity by exploiting
mass defects that arise from selective incorporation of 13C, 15N, and 2H stable isotopes in the reporter
group. The inclusion of eight new reporter isotopologues that differ
in mass from the existing four reporters by intervals of 6 mDa yields
a 12-plex isobaric set that preserves the synthetic simplicity and
quantitative performance of the original implementation. We show that
the new reporter variants can be baseline-resolved in high-resolution
higher-energy C-trap dissociation (HCD) spectra, and we demonstrate
accurate 12-plex quantitation of a DiLeu-labeled Saccharomyces
cerevisiae lysate digest via high-resolution nano
liquid chromatography–tandem mass spectrometry (nanoLC–MS2) analysis on an Orbitrap Elite mass spectrometer.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin , 777 Highland Avenue, Madison, Wisconsin 53705, United States
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Ren RJ, Dammer EB, Wang G, Seyfried NT, Levey AI. Proteomics of protein post-translational modifications implicated in neurodegeneration. Transl Neurodegener 2014; 3:23. [PMID: 25671099 PMCID: PMC4323146 DOI: 10.1186/2047-9158-3-23] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/21/2014] [Indexed: 11/18/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics has developed into a battery of approaches that is exceedingly adept at identifying with high mass accuracy and precision any of the following: oxidative damage to proteins (redox proteomics), phosphorylation (phosphoproteomics), ubiquitination (diglycine remnant proteomics), protein fragmentation (degradomics), and other posttranslational modifications (PTMs). Many studies have linked these PTMs to pathogenic mechanisms of neurodegeneration. To date, identifying PTMs on specific pathology-associated proteins has proven to be a valuable step in the evaluation of functional alteration of proteins and also elucidates biochemical and structural explanations for possible pathophysiological mechanisms of neurodegenerative diseases. This review provides an overview of methods applicable to the identification and quantification of PTMs on proteins and enumerates historic, recent, and potential future research endeavours in the field of proteomics furthering the understanding of PTM roles in the pathogenesis of neurodegeneration.
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Affiliation(s)
- Ru-Jing Ren
- />Department of Neurology,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Eric B Dammer
- />Department of Biochemistry, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Gang Wang
- />Department of Pharmacology, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Nicholas T Seyfried
- />Department of Neurology,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
- />Department of Biochemistry, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
- />Emory Proteomics Service Center, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Allan I Levey
- />Department of Neurology,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
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Cao Z, Yende S, Kellum JA, Angus DC, Robinson RAS. Proteomics reveals age-related differences in the host immune response to sepsis. J Proteome Res 2013; 13:422-32. [PMID: 24266763 DOI: 10.1021/pr400814s] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sepsis is commonly caused by community-acquired pneumonia (CAP) and may develop into severe sepsis, characterized by multiple organ failure. The risk of severe sepsis among CAP patients and subsequent mortality increases sharply after the age of 65. The molecular mechanisms associated with this age-related risk are not fully understood. To better understand factors involved with increased incidence and mortality of severe sepsis in the elderly, we used a nested case-control study of patients enrolled in a multicenter observational cohort of 2320 participants with CAP. We identified a total of 39 CAP patients 50-65 and 70-85 years old who did or did not develop severe sepsis. Plasma samples were obtained on presentation to the emergency department and prior to therapeutic interventions. A semiquantitative plasma proteomics workflow was applied which incorporated tandem immunoaffinity depletion, iTRAQ labeling, strong cation exchange fractionation, and nanoflow liquid chromatography coupled to high-resolution mass spectrometry. In total, 772 proteins were identified, of which 58 proteins exhibit statistically significant differences in expression levels among patients with severe sepsis as a function of age. Differentially expressed proteins are involved in pathways such as acute phase response, coagulation signaling, atherosclerosis signaling, lipid metabolism, and production of nitric oxide and reactive oxygen species. This study provides insight into factors that may explain age-related differences in incidence of severe sepsis in the elderly.
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Affiliation(s)
- Zhiyun Cao
- Department of Chemistry and ‡The Clinical Research, Investigation, and Systems Modeling of Acute Illness (CRISMA) Laboratory and Department of Critical Care Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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