1
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Xiang P, Liyu A, Kwon Y, Hu D, Williams SM, Veličković D, Markillie LM, Chrisler WB, Paša-Tolić L, Zhu Y. Spatial Proteomics toward Subcellular Resolution by Coupling Deep Ultraviolet Laser Ablation with Nanodroplet Sample Preparation. ACS MEASUREMENT SCIENCE AU 2023; 3:459-468. [PMID: 38145026 PMCID: PMC10740121 DOI: 10.1021/acsmeasuresciau.3c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/17/2023] [Accepted: 09/22/2023] [Indexed: 12/26/2023]
Abstract
Multiplexed molecular profiling of tissue microenvironments, or spatial omics, can provide critical insights into cellular functions and disease pathology. The coupling of laser microdissection with mass spectrometry-based proteomics has enabled deep and unbiased mapping of >1000 proteins. However, the throughput of laser microdissection is often limited due to tedious two-step procedures, sequential laser cutting, and sample collection. The two-step procedure also hinders the further improvement of spatial resolution to <10 μm as needed for subcellular proteomics. Herein, we developed a high-throughput and high-resolution spatial proteomics platform by seamlessly coupling deep ultraviolet (DUV) laser ablation (LA) with nanoPOTS (Nanodroplet Processing in One pot for Trace Samples)-based sample preparation. We demonstrated the DUV-LA system can quickly isolate and collect tissue samples at a throughput of ∼30 spots/min and a spatial resolution down to 2 μm from a 10 μm thick human pancreas tissue section. To improve sample recovery, we developed a proximity aerosol collection approach by placing DMSO droplets close to LA spots. We demonstrated the DUV-LA-nanoPOTS platform can detect an average of 1312, 1533, and 1966 proteins from ablation spots with diameters of 7, 13, and 19 μm, respectively. In a proof-of-concept study, we isolated and profiled two distinct subcellular regions of the pancreas tissue revealed by hematoxylin and eosin (H&E) staining. Quantitative proteomics revealed proteins specifically enriched to subcellular compartments.
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Affiliation(s)
- Piliang Xiang
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Andrey Liyu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Yumi Kwon
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Dehong Hu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Sarah M. Williams
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Lye Meng Markillie
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - William B. Chrisler
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Department
of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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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: 13] [Impact Index Per Article: 13.0] [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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Patterson KL, Arul AB, Choi MJ, Oliver NC, Whitaker MD, Bodrick AC, Libby JB, Hansen S, Dumitrescu L, Gifford KA, Jefferson AL, Hohman TJ, Robinson RAS. Establishing Quality Control Procedures for Large-Scale Plasma Proteomics Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37163770 DOI: 10.1021/jasms.3c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Proteomics research has been transformed due to high-throughput liquid chromatography (LC-MS/MS) tandem mass spectrometry instruments combined with highly sophisticated automated sample preparation and multiplexing workflows. However, scaling proteomics experiments to large sample cohorts (hundreds to thousands) requires thoughtful quality control (QC) protocols. Robust QC protocols can help with reproducibility, quantitative accuracy, and provide opportunities for more decisive troubleshooting. Our laboratory conducted a plasma proteomics study of a cohort of N = 335 patient samples using tandem mass tag (TMTpro) 16-plex batches. Over the course of a 10-month data acquisition period for this cohort we collected 271 pooled QC LC-MS/MS result files obtained from MS/MS analysis of a patient-derived pooled plasma sample, representative of the entire cohort population. This sample was tagged with TMTzero or TMTpro reagents and used to inform the daily performance of the LC-MS/MS instruments and to allow within and across sample batch normalization. Analytical variability of a number of instrumental and data analysis metrics including protein and peptide identifications, peptide spectral matches (PSMs), number of obtained MS/MS spectra, average peptide abundance, percent of peptides with a Δ m/z between ±0.003 Da, percent of MS/MS spectra obtained at the maximum injection time, and the retention time of selected tracking peptides were evaluated to help inform the design of a robust LC-MS/MS QC workflow for use in future cohort studies. This study also led to general tips for using selected metrics to inform real-time troubleshooting of LC-MS/MS performance issues with daily QC checks.
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Affiliation(s)
- Khiry L Patterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nekesa C Oliver
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Marsalas D Whitaker
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Angel C Bodrick
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, Meharry Medical College, Nashville, Tennessee 37208, United States
| | - Julia B Libby
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Shania Hansen
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Logan Dumitrescu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Katherine A Gifford
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Angela L Jefferson
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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6
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Wu Z, Xiang W, Huang L, Li S, Zhang X. Hyperplexing Approaches for up to 45-Plex Quantitative Proteomic Analysis. Anal Chem 2023; 95:5169-5175. [PMID: 36917635 DOI: 10.1021/acs.analchem.3c00237] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Isobaric labeling has emerged as an indispensable quantitative proteomic approach for its unprecedented multiplexing capacity in a single analysis. Currently, different hyperplexing approaches have been developed to meet the demand for the increasing sample size in large-scale cohort analysis. In this report, we present a tribrid hyperplexing approach by the combinatorial use of three types of isobaric reagents, a novel isobaric tag 16-plex (IBT16) reagent and the widely used tandem mass tag (TMT; TMT11) and TMTpro (TMT18) reagents. After the determination of labeling efficiency and the optimization of testing conditions, we systematically evaluated the identification and quantification performance of the three labeling reagents in both independent and combinatorial manners using the mixtures of E. coli and HeLa peptides with different ratios. Our results reveal that the three reagents are quite similar in all testing aspects despite some differences, and the combination use of the three reagents could expand the multiplexing capacity to up to 45-plex. Furthermore, we conclude the advantages of IBT16 in the combination use and the preferred combinations for different practical applications. Data are available via ProteomeXchange with identifier PXD037498.
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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
| | - Weirong Xiang
- 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
| | - Shuwei Li
- Nanjing Apollomics Biotech Inc., Nanjing, Jiangsu 210033, China.,China Pharmaceutical University, Nanjing, Jiangsu 210009, 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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7
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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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8
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Park J, Yu F, Fulcher JM, Williams SM, Engbrecht K, Moore RJ, Clair GC, Petyuk V, Nesvizhskii AI, Zhu Y. Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics. Anal Chem 2023; 95:1888-1898. [PMID: 36637389 DOI: 10.1021/acs.analchem.2c03739] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
There is a growing demand to develop high-throughput and high-sensitivity mass spectrometry methods for single-cell proteomics. The commonly used isobaric labeling-based multiplexed single-cell proteomics approach suffers from distorted protein quantification due to co-isolated interfering ions during MS/MS fragmentation, also known as ratio compression. We reasoned that the use of MS3-based quantification could mitigate ratio compression and provide better quantification. However, previous studies indicated reduced proteome coverages in the MS3 method, likely due to long duty cycle time and ion losses during multilevel ion selection and fragmentation. Herein, we described an improved MS acquisition method for MS3-based single-cell proteomics by employing a linear ion trap to measure reporter ions. We demonstrated that linear ion trap can increase the proteome coverages for single-cell-level peptides with even higher gain obtained via the MS3 method. The optimized real-time search MS3 method was further applied to study the immune activation of single macrophages. Among a total of 126 single cells studied, over 1200 and 1000 proteins were quantifiable when at least 50 and 75% nonmissing data were required, respectively. Our evaluation also revealed several limitations of the low-resolution ion trap detector for multiplexed single-cell proteomics and suggested experimental solutions to minimize their impacts on single-cell analysis.
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Affiliation(s)
- Junho Park
- Department of Pharmacology, School of Medicine, CHA University, Seongnam-si, Gyeonggi-do, Seongnam 13488, Republic of Korea
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109-1382, United States
| | - James M Fulcher
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kristin Engbrecht
- Nuclear, Chemistry, and Biology Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Vladislav Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109-1382, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-1382, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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9
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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: 27] [Impact Index Per Article: 13.5] [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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10
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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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11
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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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12
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Xing S, Pai A, Wu R, Lu Y. NHS-Ester Tandem Labeling in One Pot Enables 48-Plex Quantitative Proteomics. Anal Chem 2021; 93:12827-12832. [PMID: 34529408 DOI: 10.1021/acs.analchem.1c01314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stable-isotope labeling strategies are extensively used for multiplex quantitative proteomics. Hybrid-isotope labeling strategies that combine the use of isotopic mass difference labeling and isobaric tags can greatly increase sample multiplexity. In this work, we present a novel hybrid-isotope labeling approach that we termed NHS-ester tandem labeling in one pot (NETLOP). We first optimized 16-plex isobaric TMTpro labeling of lysine residues followed by 2-plex or 3-plex isotopic mTRAQ labeling of peptide N-termini, both of which with commercially available NHS-ester reactive reagents. We then demonstrated the utility of the NETLOP approach by labeling HeLa cell samples and performing proof-of-principle quantitative 32-plex and 48-plex proteomic analyses, each in a single LC-MS/MS experiment. Compared to current hybrid-isotope labeling methods, our NETLOP approach requires no sample cleanup between different labeling steps to minimize sample loss, induces no retention time shifts that compromise quantification accuracy, can be adapted to other NHS-ester isotopic labeling reagents to further increase multiplexity, and is compatible with samples from any origin in a wide array of biological and clinical proteomics applications.
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Affiliation(s)
- Sansi Xing
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Akshat Pai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Ruilin Wu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Yu Lu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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13
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Miles HN, Delafield DG, Li L. Recent Developments and Applications of Quantitative Proteomics Strategies for High-Throughput Biomolecular Analyses in Cancer Research. RSC Chem Biol 2021; 4:1050-1072. [PMID: 34430874 PMCID: PMC8341969 DOI: 10.1039/d1cb00039j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/18/2021] [Indexed: 12/28/2022] Open
Abstract
Innovations in medical technology and dedicated focus from the scientific community have inspired numerous treatment strategies for benign and invasive cancers. While these improvements often lend themselves to more positive prognoses and greater patient longevity, means for early detection and severity stratification have failed to keep pace. Detection and validation of cancer-specific biomarkers hinges on the ability to identify subtype-specific phenotypic and proteomic alterations and the systematic screening of diverse patient groups. For this reason, clinical and scientific research settings rely on high throughput and high sensitivity mass spectrometry methods to discover and quantify unique molecular perturbations in cancer patients. Discussed within is an overview of quantitative proteomics strategies and a summary of recent applications that enable revealing potential biomarkers and treatment targets in prostate, ovarian, breast, and pancreatic cancer in a high throughput manner.
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Affiliation(s)
- Hannah N. Miles
- School of Pharmacy, University of Wisconsin-Madison777 Highland AvenueMadisonWI53705-2222USA+1-608-262-5345+1-608-265-8491
| | | | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison777 Highland AvenueMadisonWI53705-2222USA+1-608-262-5345+1-608-265-8491
- Department of Chemistry, University of Wisconsin-MadisonMadisonWI53706USA
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14
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Delafield DG, Li L. Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation. Mol Cell Proteomics 2021; 20:100054. [PMID: 32576592 PMCID: PMC8724918 DOI: 10.1074/mcp.r120.002095] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/13/2022] Open
Abstract
Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. Mass-spectrometry-based strategies for glycomic quantitation have grown to include metabolic incorporation of stable isotopes, deposition of mass difference and mass defect isotopic labels, and isobaric chemical labeling, providing researchers with ample tools for accurate and robust quantitation. Beyond this, workflows have been designed to harness instrument capability for label-free quantification, and numerous software packages have been developed to facilitate reliable spectrum scoring. In this review, we present and highlight the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification.
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Affiliation(s)
- Daniel G Delafield
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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15
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Proteome-wide and matrisome-specific alterations during human pancreas development and maturation. Nat Commun 2021; 12:1020. [PMID: 33589611 PMCID: PMC7884717 DOI: 10.1038/s41467-021-21261-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/19/2021] [Indexed: 01/31/2023] Open
Abstract
The extracellular matrix (ECM) is unique to each tissue and capable of guiding cell differentiation, migration, morphology, and function. The ECM proteome of different developmental stages has not been systematically studied in the human pancreas. In this study, we apply mass spectrometry-based quantitative proteomics strategies using N,N-dimethyl leucine isobaric tags to delineate proteome-wide and ECM-specific alterations in four age groups: fetal (18-20 weeks gestation), juvenile (5-16 years old), young adults (21-29 years old) and older adults (50-61 years old). We identify 3,523 proteins including 185 ECM proteins and quantify 117 of them. We detect previously unknown proteome and matrisome features during pancreas development and maturation. We also visualize specific ECM proteins of interest using immunofluorescent staining and investigate changes in ECM localization within islet or acinar compartments. This comprehensive proteomics analysis contributes to an improved understanding of the critical roles that ECM plays throughout human pancreas development and maturation.
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16
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Derivatization-based sample-multiplexing for enhancing throughput in liquid chromatography/tandem mass spectrometry quantification of metabolites: an overview. J Chromatogr A 2020; 1634:461679. [DOI: 10.1016/j.chroma.2020.461679] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/02/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022]
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17
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Wei P, Hao L, Thomas S, Buchberger AR, Steinke L, Marker PC, Ricke WA, Li L. Urinary Amine Metabolomics Characterization with Custom 12-Plex Isobaric DiLeu Labeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1854-1860. [PMID: 32678615 PMCID: PMC7484200 DOI: 10.1021/jasms.0c00110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Lower urinary tract symptoms (LUTS) is common in aging males. Disease etiology is largely unknown but likely includes inflammation and age-related changes in steroid hormones. Diagnosis is currently based on subjective symptom scores, and mainstay treatments can be ineffective and bothersome. Biomarker discovery efforts could facilitate objective diagnostic criteria for personalized medicine and new potential druggable pathways. To identify urine metabolite markers specific to hormone-induced bladder outlet obstruction, we applied our custom synthesized multiplex isobaric tags to monitor the development of bladder outlet obstruction across time in an experimental mouse model of LUTS. Mouse urine samples were collected before treatment and after 2, 4, and 8 weeks of steroid hormone treatment and subsequently analyzed by nanoflow ultrahigh-performance liquid chromatography coupled to tandem mass spectrometry. Accurate and high-throughput quantification of amine-containing metabolites was achieved by 12-plex DiLeu isobaric labeling. Metandem, a novel online software tool for large-scale isobaric labeling-based metabolomics, was used for identification and relative quantification of labeled metabolites. A total of 59 amine-containing metabolites were identified and quantified, 9 of which were changed significantly by the hormone treatment. Metabolic pathway analyses showed that three metabolic pathways were potentially disrupted. Among them, the arginine and proline metabolism pathway was significantly dysregulated both in this model and in a prior analysis of LUTS patient samples. Proline and citrulline were significantly changed in both samples and serve as attractive candidate biomarkers. The 12-plex DiLeu isobaric labeling with Metandem data processing presents an accessible and efficient workflow for an amine-containing metabolome study in biological specimens.
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Affiliation(s)
- Pingli Wei
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ling Hao
- Department of Chemistry, George Washington University, Washington, DC, 20052, USA
| | - Samuel Thomas
- Molecular and Environmental Toxicology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Amanda Rae Buchberger
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Laura Steinke
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Paul C. Marker
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - William A. Ricke
- Molecular and Environmental Toxicology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Molecular and Environmental Toxicology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Corresponding Author: Prof. Lingjun Li, School of Pharmacy & Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI 53705, . Phone: (608)265-8491, Fax: (608)262-5345
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18
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Frost DC, Feng Y, Li L. 21-plex DiLeu Isobaric Tags for High-Throughput Quantitative Proteomics. Anal Chem 2020; 92:8228-8234. [PMID: 32401496 DOI: 10.1021/acs.analchem.0c00473] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Isobaric tags enable multiplexed quantitative analysis of many biological samples in a single LC-MS/MS experiment. As a cost-effective alternative to expensive commercial isobaric tagging reagents, we developed our own custom N,N-dimethylleucine "DiLeu" isobaric tags for quantitative proteomics. Here, we present a new generation of DiLeu tags that achieves 21-plex quantification in high-resolution HCD MS/MS spectra via distinct reporter ions that differ in mass from each other by a minimum of 3 mDa. The 21-plex set retains the compact tag structure and existing isotopologues of the 12-plex set but includes nine new reporter variants formulated with unique configurations of 13C, 15N, and 2H stable isotopes, each synthesized in-house via a stepwise N-monomethylation synthesis strategy using readily available reagents. Thus, multiplexing capacity is expanded significantly, while preserving the performance and low cost of the previous implementation. We show that 21-plex DiLeu tags generate strong reporter ions following HCD fragmentation of labeled peptides acquired on Orbitrap platforms at a minimum of 60,000 resolving power (at 400 m/z), and we demonstrate accurate 21-plex quantification of labeled K562 human cell line protein digests via single-shot nanoLC-MS/MS analysis on a Q Exactive HF system.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yu Feng
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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19
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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
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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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20
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Wang Z, Yu K, Tan H, Wu Z, Cho JH, Han X, Sun H, Beach TG, Peng J. 27-Plex Tandem Mass Tag Mass Spectrometry for Profiling Brain Proteome in Alzheimer's Disease. Anal Chem 2020; 92:7162-7170. [PMID: 32343560 PMCID: PMC8176402 DOI: 10.1021/acs.analchem.0c00655] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Multiplexed isobaric labeling methods, such as tandem mass tags (TMT), remarkably improve the throughput of quantitative mass spectrometry. Here, we present a 27-plex TMT method coupled with two-dimensional liquid chromatography (LC/LC) for extensive peptide fractionation and high-resolution tandem mass spectrometry (MS/MS) for peptide quantification and then apply the method to profile the complex human brain proteome of Alzheimer's disease (AD). The 27-plex method combines multiplexed capacities of the 11-plex and the 16-plex TMT, as the peptides labeled by the two TMT sets display different mass and hydrophobicity, which can be well separated in LC-MS/MS. We first systematically optimized the protocol for the newly developed 16-plex TMT, including labeling reaction, desalting, and MS conditions, and then directly compared the 11-plex and 16-plex methods by analyzing the same human AD samples. Both methods yielded similar proteome coverage, analyzing >100 000 peptides in >10 000 human proteins. Furthermore, the 11-plex and 16-plex samples were mixed for a 27-plex assay, resulting in more than 8000 protein measurements within the same MS time. The 27-plex results are highly consistent with those of the individual 11-plex and 16-plex TMT analyses. We also used these proteomics data sets to compare the AD brain with the nondementia controls, discovering major AD-related proteins and revealing numerous novel protein alterations enriched in the pathways of amyloidosis, immunity, mitochondrial, and synaptic functions. Overall, our data strongly demonstrate that this new 27-plex strategy is highly feasible for routine large-scale proteomic analysis.
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Affiliation(s)
- Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Contribute equally
| | - Kaiwen Yu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Contribute equally
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Contribute equally
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xian Han
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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21
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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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22
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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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23
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Dayon L, Affolter M. Progress and pitfalls of using isobaric mass tags for proteome profiling. Expert Rev Proteomics 2020; 17:149-161. [PMID: 32067523 DOI: 10.1080/14789450.2020.1731309] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: Quantitative proteomics using mass spectrometry is performed via label-free or label-based approaches. Labeling strategies rely on the incorporation of stable heavy isotopes by metabolic, enzymatic, or chemical routes. Isobaric labeling uses chemical labels of identical masses but of different fragmentation behaviors to allow the relative quantitative comparison of peptide/protein abundances between biological samples.Areas covered: We have carried out a systematic review on the use of isobaric mass tags in proteomic research since their inception in 2003. We focused on their quantitative performances, their multiplexing evolution, as well as their broad use for relative quantification of proteins in pre-clinical models and clinical studies. Current limitations, primarily linked to the quantitative ratio distortion, as well as state-of-the-art and emerging solutions to improve their quantitative readouts are discussed.Expert opinion: The isobaric mass tag technology offers a unique opportunity to compare multiple protein samples simultaneously, allowing higher sample throughput and internal relative quantification for improved trueness and precision. Large studies can be performed when shared reference samples are introduced in multiple experiments. The technology is well suited for proteome profiling in the context of proteomic discovery studies.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne, Switzerland
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24
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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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25
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Gräwe C, Makowski MM, Vermeulen M. PAQMAN: Protein-nucleic acid affinity quantification by MAss spectrometry in nuclear extracts. Methods 2019; 184:70-77. [PMID: 31857188 DOI: 10.1016/j.ymeth.2019.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 12/01/2022] Open
Abstract
In recent years, various mass spectrometry-based approaches have been developed to determine global protein-DNA binding specificities using DNA affinity purifications from crude nuclear extracts. However, these assays are semi-quantitative and do not provide information about interaction affinities. We recently developed a technology that we call Protein-nucleic acid Affinity Quantification by MAss spectrometry in Nuclear extracts or PAQMAN, that can be used to determine apparent affinities between multiple nuclear proteins and a nucleic acid sequence of interest in one experiment. In PAQMAN, a series of affinity purifications with increasing bait concentrations and fixed amounts of crude nuclear extracts are combined with isobaric stable isotope labeling and quantitative mass spectrometry to generate Hill-like Kd curves for dozens of proteins in a single experiment. Here, we apply PAQMAN to determine apparent affinities for a genetic variant, rs36115365-C, which regulates TERT expression and is associated with an increased risk to develop various malignancies. Furthermore, we describe a detailed protocol for this method including important quality checks.
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Affiliation(s)
- Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Matthew M Makowski
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands.
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26
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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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27
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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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28
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Lacerda MPF, Marcelino MY, Lourencetti NMS, Neto ÁB, Gattas EA, Mendes-Giannini MJS, Fusco-Almeida AM. Methodologies and Applications of Proteomics for Study of Yeast Strains: An Update. Curr Protein Pept Sci 2019; 20:893-906. [PMID: 31322071 DOI: 10.2174/1389203720666190715145131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022]
Abstract
Yeasts are one of the mostly used microorganisms as models in several studies. A wide range of applications in different processes can be attributed to their intrinsic characteristics. They are eukaryotes and therefore valuable expression hosts that require elaborate post-translational modifications. Their arsenal of proteins has become a valuable biochemical tool for the catalysis of several reactions of great value to the food (beverages), pharmaceutical and energy industries. Currently, the main challenge in systemic yeast biology is the understanding of the expression, function and regulation of the protein pool encoded by such microorganisms. In this review, we will provide an overview of the proteomic methodologies used in the analysis of yeasts. This research focuses on the advantages and improvements in their most recent applications with an understanding of the functionality of the proteins of these microorganisms, as well as an update of the advances of methodologies employed in mass spectrometry.
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Affiliation(s)
- Maria Priscila F Lacerda
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Mônica Yonashiro Marcelino
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Natália M S Lourencetti
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Álvaro Baptista Neto
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | - Edwil A Gattas
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | | | - Ana Marisa Fusco-Almeida
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
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Xu Y, Sun L, Wang X, Zhu S, You J, Zhao XE, Bai Y, Liu H. Integration of stable isotope labeling derivatization and magnetic dispersive solid phase extraction for measurement of neurosteroids by in vivo microdialysis and UHPLC-MS/MS. Talanta 2019; 199:97-106. [DOI: 10.1016/j.talanta.2019.02.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/28/2019] [Accepted: 02/03/2019] [Indexed: 12/12/2022]
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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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Bąchor R, Waliczek M, Stefanowicz P, Szewczuk Z. Trends in the Design of New Isobaric Labeling Reagents for Quantitative Proteomics. Molecules 2019; 24:molecules24040701. [PMID: 30781343 PMCID: PMC6412310 DOI: 10.3390/molecules24040701] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 12/23/2022] Open
Abstract
Modern mass spectrometry is one of the most frequently used methods of quantitative proteomics, enabling determination of the amount of peptides in a sample. Although mass spectrometry is not inherently a quantitative method due to differences in the ionization efficiency of various analytes, the application of isotope-coded labeling allows relative quantification of proteins and proteins. Over the past decade, a new method for derivatization of tryptic peptides using isobaric labels has been proposed. The labels consist of reporter and balanced groups. They have the same molecular weights and chemical properties, but differ in the distribution of stable heavy isotopes. These tags are designed in such a way that during high energy collision induced dissociation (CID) by tandem mass spectrometry, the isobaric tag is fragmented in the specific linker region, yielding reporter ions with different masses. The mass shifts among the reporter groups are compensated by the balancing groups so that the overall mass is the same for all forms of the reagent. Samples of peptides are labeled with the isobaric mass tags in parallel and combined for analysis. Quantification of individual peptides is achieved by comparing the intensity of reporter ions in the tandem mass (MS/MS) spectra. Isobaric markers have found a wide range of potential applications in proteomics. However, the currently available isobaric labeling reagents have some drawbacks, such as high cost of production, insufficient selectivity of the derivatization, and relatively limited enhancement of sensitivity of the analysis. Therefore, efforts have been devoted to the development of new isobaric markers with increased usability. The search for new isobaric markers is focused on developing a more selective method of introducing a tag into a peptide molecule, increasing the multiplexicity of markers, lowering the cost of synthesis, and increasing the sensitivity of measurement by using ionization tags containing quaternary ammonium salts. Here, the trends in the design of new isobaric labeling reagents for quantitative proteomics isobaric derivatization strategies in proteomics are reviewed, with a particular emphasis on isobaric ionization tags. The presented review focused on different types of isobaric reagents used in quantitative proteomics, their chemistry, and advantages offer by their application.
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Affiliation(s)
- Remigiusz Bąchor
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
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Zhong X, Yu Q, Ma F, Frost DC, Lu L, Chen Z, Zetterberg H, Carlsson C, Okonkwo O, Li L. HOTMAQ: A Multiplexed Absolute Quantification Method for Targeted Proteomics. Anal Chem 2019; 91:2112-2119. [PMID: 30608134 PMCID: PMC6379083 DOI: 10.1021/acs.analchem.8b04580] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Absolute quantification in targeted proteomics is challenging due to a variety of factors, including low specificity in complex backgrounds, limited analytical throughput, and wide dynamic range. To address these problems, we developed a hybrid offset-triggered multiplex absolute quantification (HOTMAQ) strategy that combines cost-effective mass difference and isobaric tags to enable simultaneous construction of an internal standard curve in the MS1 precursor scan, real-time identification of peptides at the MS2 level, and mass offset-triggered accurate quantification of target proteins in synchronous precursor selection (SPS)-MS3 spectra. This approach increases the analytical throughput of targeted quantitative proteomics by up to 12-fold. The HOTMAQ strategy was employed to verify candidate protein biomarkers in preclinical Alzheimer's disease with high accuracy. The greatly enhanced throughput and quantitative performance, paired with sample flexibility, makes HOTMAQ broadly applicable to targeted peptidomics, proteomics, and phosphoproteomics.
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Affiliation(s)
- Xiaofang Zhong
- School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Qinying Yu
- School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Fengfei Ma
- School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Dustin C Frost
- School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Lei Lu
- School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Zhengwei Chen
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Sahlgrenska Academy , University of Gothenburg , S-431 80 , Gothenburg , Sweden
- Clinical Neurochemistry Laboratory , Sahlgrenska University Hospital , S-431 80 , Mölndal , Sweden
- Department of Molecular Neuroscience , UCL Institute of Neurology , Queen Square, London , WC1N 3BG , U.K
- UK Dementia Research Institute at UCL , London , WC1N 3BG , U.K
| | - Cynthia Carlsson
- School of Medicine and Public Health , University of Wisconsin , Madison , Wisconsin 53705 , United States
| | - Ozioma Okonkwo
- School of Medicine and Public Health , University of Wisconsin , 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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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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Huang T, Armbruster MR, Coulton JB, Edwards JL. Chemical Tagging in Mass Spectrometry for Systems Biology. Anal Chem 2018; 91:109-125. [DOI: 10.1021/acs.analchem.8b04951] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tianjiao Huang
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - Michael R. Armbruster
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - John B. Coulton
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - James L. Edwards
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
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