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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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2
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Steigerwald S, Sinha A, Fort KL, Zeng WF, Niu L, Wichmann C, Kreutzmann A, Mourad D, Aizikov K, Grinfeld D, Makarov A, Mann M, Meier F. Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis. Mol Cell Proteomics 2024; 23:100713. [PMID: 38184013 PMCID: PMC10851225 DOI: 10.1016/j.mcpro.2024.100713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024] Open
Abstract
Optimizing data-independent acquisition methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here, we describe a real-time full mass range implementation of the phase-constrained spectrum deconvolution method (ΦSDM) for Orbitrap mass spectrometry that increases mass resolving power without increasing scan time. Comparing its performance to the standard enhanced Fourier transformation signal processing revealed that the increased resolving power of ΦSDM is beneficial in areas of high peptide density and comes with a greater ability to resolve low-abundance signals. In a standard 2 h analysis of a 200 ng HeLa digest, this resulted in an increase of 16% in the number of quantified peptides. As the acquisition speed becomes even more important when using fast chromatographic gradients, we further applied ΦSDM methods to a range of shorter gradient lengths (21, 12, and 5 min). While ΦSDM improved identification rates and spectral quality in all tested gradients, it proved particularly advantageous for the 5 min gradient. Here, the number of identified protein groups and peptides increased by >15% in comparison to enhanced Fourier transformation processing. In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.
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Affiliation(s)
- Sophia Steigerwald
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kyle L Fort
- Thermo Fisher Scientific (GmbH), Bremen, Germany
| | - Wen-Feng Zeng
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lili Niu
- Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christoph Wichmann
- Department Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | | | | | | | - Matthias Mann
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Florian Meier
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Functional Proteomics, Jena University Hospital, Jena, Germany.
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3
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Shi Y, Chen J, Cai L, Zhang X, Chen Z, Yang J, Jiang Y, Lu Y. Uncovering the Hidden World of Aqueous Humor Proteins for Discovery of Biomarkers for Marfan Syndrome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303161. [PMID: 38088571 PMCID: PMC10853735 DOI: 10.1002/advs.202303161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Ectopia lentis is a hallmark of Marfan syndrome (MFS), a genetic connective tissue disorder affecting 1/5000 to 1/10 000 individuals worldwide. Early detection in ophthalmology clinics and timely intervention of cardiovascular complications can be lifesaving. In this study, a modified proteomics workflow with liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based data-independent acquisition (DIA) and field asymmetric ion mobility spectrometry (FAIMS) to profile the proteomes of aqueous humor (AH) and lens tissue from MFS children with ectopia lentis is utilized. Over 2300 and 2938 comparable proteins are identified in AH and the lens capsule, respectively. Functional enrichment analyses uncovered dysregulation of complement and coagulation-related pathways, collagen binding, and cell adhesion in MFS. Through weighted correlation network analysis (WGCNA) and machine learning, distinct modules associated with clinical traits are constructed and a unique biomarker panel (Q14376, Q99972, P02760, Q07507; gene names: GALE, MYOC, AMBP, DPT) is defined. These biomarkers are further validated using advanced parallel reaction monitoring (PRM) in an independent patient cohort. The results provide novel insights into the proteome characterization of ectopia lentis and offer a promising approach for developing a valuable biomarker panel to aid in the early diagnosis of Marfan syndrome via AH proteome.
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Affiliation(s)
- Yumeng Shi
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Jiahui Chen
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Lei Cai
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Xueling Zhang
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Zexu Chen
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Jin Yang
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Yongxiang Jiang
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Yi Lu
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
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4
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Ma M, Li M, Zhu Y, Zhao Y, Wu F, Wang Z, Feng Y, Chiang HY, Patankar MS, Chang C, Li L. 6-Plex mdSUGAR Isobaric-Labeling Guide Fingerprint Embedding for Glycomics Analysis. Anal Chem 2023; 95:17637-17645. [PMID: 37982459 PMCID: PMC10794169 DOI: 10.1021/acs.analchem.3c03342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Glycans are vital biomolecules with diverse functions in biological processes. Mass spectrometry (MS) has become the most widely employed technology for glycomics studies. However, in the traditional data-dependent acquisition mode, only a subset of the abundant ions during MS1 scans are isolated and fragmented in subsequent MS2 events, which reduces reproducibility and prevents the measurement of low-abundance glycan species. Here, we reported a new method termed 6-plex mdSUGAR isobaric-labeling guide fingerprint embedding (MAGNI), to achieve multiplexed, quantitative, and targeted glycan analysis. The glycan peak signature was embedded by a triplicate-labeling strategy with a 6-plex mdSUGAR tag, and using ultrahigh-resolution mass spectrometers, the low-abundance glycans that carry the mass fingerprints can be recognized on the MS1 spectra through an in-house developed software tool, MAGNIFinder. These embedded unique fingerprints can guide the selection and fragmentation of targeted precursor ions and further provide rich information on glycan structures. Quantitative analysis of two standard glycoproteins demonstrated the accuracy and precision of MAGNI. Using this approach, we identified 304 N-glycans in two ovarian cancer cell lines. Among them, 65 unique N-glycans were found differentially expressed, which indicates a distinct glycosylation pattern for each cell line. Remarkably, 31 N-glycans can be quantified in only 1 × 103 cells, demonstrating the high sensitivity of our method. Taken together, our MAGNI method offers a useful tool for low-abundance N-glycan characterization and is capable of determining small quantitative differences in N-glycan profiling. Therefore, it will be beneficial to the field of glycobiology and will expand our understanding of glycosylation.
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Affiliation(s)
- Min Ma
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Miyang Li
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Yinlong Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yingyi Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Feixuan Wu
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Zicong Wang
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Yu Feng
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Hung-Yu Chiang
- Biophysics Program, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Manish S. Patankar
- Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin–Madison, Madison, Wisconsin 53705, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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5
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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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Abstract
Accurate protein quantification is key to identifying protein markers, regulatory relationships between proteins, and pathophysiological mechanisms. Realizing this potential requires sensitive and deep protein analysis of a large number of samples. Toward this goal, proteomics throughput can be increased by parallelizing the analysis of both precursors and samples using multiplexed data independent acquisition (DIA) implemented by the plexDIA framework: https://plexDIA.slavovlab.net. Here we demonstrate the improved precisions of retention time estimates within plexDIA and how this enables more accurate protein quantification. plexDIA has demonstrated multiplicative gains in throughput, and these gains may be substantially amplified by improving the multiplexing reagents, data acquisition, and interpretation. We discuss future directions for advancing plexDIA, which include engineering optimized mass-tags for high-plexDIA, introducing isotopologous carriers, and developing algorithms that utilize the regular structures of plexDIA data to improve sensitivity, proteome coverage, and quantitative accuracy. These advances in plexDIA will increase the throughput of functional proteomic assays, including quantifying protein conformations, turnover dynamics, modifications states and activities. The sensitivity of these assays will extend to single-cell analysis, thus enabling functional single-cell protein analysis.
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Affiliation(s)
- Jason Derks
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, Massachusetts 02115, United States
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, Massachusetts 02115, United States
- Parallel Squared Technology Institute, Watertown, Massachusetts 02472, United States
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7
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Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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8
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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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Derks J, Leduc A, Wallmann G, Huffman RG, Willetts M, Khan S, Specht H, Ralser M, Demichev V, Slavov N. Increasing the throughput of sensitive proteomics by plexDIA. Nat Biotechnol 2023; 41:50-59. [PMID: 35835881 PMCID: PMC9839897 DOI: 10.1038/s41587-022-01389-w] [Citation(s) in RCA: 86] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/13/2022] [Indexed: 01/22/2023]
Abstract
Current mass spectrometry methods enable high-throughput proteomics of large sample amounts, but proteomics of low sample amounts remains limited in depth and throughput. To increase the throughput of sensitive proteomics, we developed an experimental and computational framework, called plexDIA, for simultaneously multiplexing the analysis of peptides and samples. Multiplexed analysis with plexDIA increases throughput multiplicatively with the number of labels without reducing proteome coverage or quantitative accuracy. By using three-plex non-isobaric mass tags, plexDIA enables quantification of threefold more protein ratios among nanogram-level samples. Using 1-hour active gradients, plexDIA quantified ~8,000 proteins in each sample of labeled three-plex sets and increased data completeness, reducing missing data more than twofold across samples. Applied to single human cells, plexDIA quantified ~1,000 proteins per cell and achieved 98% data completeness within a plexDIA set while using ~5 minutes of active chromatography per cell. These results establish a general framework for increasing the throughput of sensitive and quantitative protein analysis.
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Affiliation(s)
- Jason Derks
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA.
| | - Andrew Leduc
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Georg Wallmann
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - R Gray Huffman
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | | | - Saad Khan
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Harrison Specht
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | | | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA.
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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] [MESH Headings] [Grants] [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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11
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Beller NC, Hummon AB. Advances in stable isotope labeling: dynamic labeling for spatial and temporal proteomic analysis. Mol Omics 2022; 18:579-590. [PMID: 35723214 PMCID: PMC9378559 DOI: 10.1039/d2mo00077f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The field of proteomics is continually improving, requiring the development of new quantitative methods. Stable isotope labeling in cell culture (SILAC) is a metabolic labeling technique originating in the early 2000s. By incorporating isotopically labeled amino acids into the media used for cell culture, unlabeled versus labeled cells can be differentiated by the mass spectrometer. Traditional SILAC labeling has been expanded to pulsed applications allowing for a new quantitative dimension of proteomics - temporal analysis. The complete introduction of Heavy SILAC labeling chased with surplus unlabeled medium mimics traditional pulse-chase experiments and allows for the loss of heavy signal to track proteomic changes over time. In a similar fashion, pulsed SILAC (pSILAC) monitors the initial incorporation of a heavy label across a period of time, which allows for the rate of protein label integration to be assessed. These innovative techniques have aided in inspiring numerous SILAC-based temporal and spatial labeling applications, including super SILAC, spike-in SILAC, spatial SILAC, and a revival in label multiplexing. This review reflects upon the evolution of SILAC and the pulsed SILAC application, introduces advances in SILAC labeling, and proposes future perspectives for this novel and exciting field.
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Affiliation(s)
- Nicole C Beller
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA, 43210.
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA, 43210.
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA, 43210
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12
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Multiplexed quantitative neuropeptidomics via DiLeu isobaric tagging. Methods Enzymol 2022; 663:235-257. [DOI: 10.1016/bs.mie.2021.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Sauer CS, Phetsanthad A, Riusech OL, Li L. Developing mass spectrometry for the quantitative analysis of neuropeptides. Expert Rev Proteomics 2021; 18:607-621. [PMID: 34375152 PMCID: PMC8522511 DOI: 10.1080/14789450.2021.1967146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Neuropeptides are signaling molecules originating in the neuroendocrine system that can act as neurotransmitters and hormones in many biochemical processes. Their exact function is difficult to characterize, however, due to dependence on concentration, post-translational modifications, and the presence of other comodulating neuropeptides. Mass spectrometry enables sensitive, accurate, and global peptidomic analyses that can profile neuropeptide expression changes to understand their roles in many biological problems, such as neurodegenerative disorders and metabolic function. AREAS COVERED We provide a brief overview of the fundamentals of neuropeptidomic research, limitations of existing methods, and recent progress in the field. This review is focused on developments in mass spectrometry and encompasses labeling strategies, post-translational modification analysis, mass spectrometry imaging, and integrated multi-omic workflows, with discussion emphasizing quantitative advancements. EXPERT OPINION Neuropeptidomics is critical for future clinical research with impacts in biomarker discovery, receptor identification, and drug design. While advancements are being made to improve sensitivity and accuracy, there is still room for improvement. Better quantitative strategies are required for clinical analyses, and these methods also need to be amenable to mass spectrometry imaging, post-translational modification analysis, and multi-omics to facilitate understanding and future treatment of many diseases.
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Affiliation(s)
- Christopher S. Sauer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Olga L. Riusech
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075, USA
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Tian X, de Vries MP, Permentier HP, Bischoff R. The Isotopic Ac-IP Tag Enables Multiplexed Proteome Quantification in Data-Independent Acquisition Mode. Anal Chem 2021; 93:8196-8202. [PMID: 34053216 PMCID: PMC8209779 DOI: 10.1021/acs.analchem.1c00453] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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Data-independent
acquisition (DIA) is an increasingly used approach
for quantitative proteomics. However, most current isotope labeling
strategies are not suitable for DIA as they lead to more complex MS2
spectra or severe ratio distortion. As a result, DIA suffers from
a lower throughput than data-dependent acquisition (DDA) due to a
lower level of multiplexing. Herein, we synthesized an isotopically
labeled acetyl-isoleucine-proline (Ac-IP) tag for multiplexed quantification
in DIA. Differentially labeled peptides have distinct precursor ions
carrying the quantitative information but identical MS2 spectra since
the isotopically labeled Ac-Ile part leaves as a neutral loss upon
collision-induced dissociation, while fragmentation of the peptide
backbone generates regular fragment ions for identification. The Ac-IP-labeled
samples can be analyzed using general DIA liquid chromatography–mass
spectrometry settings, and the data obtained can be processed with
established approaches. Relative quantification requires deconvolution
of the isotope envelope of the respective precursor ions. Suitability
of the Ac-IP tag is demonstrated with a triplex-labeled yeast proteome
spiked with bovine serum albumin that was mixed at 10:5:1 ratios,
resulting in measured ratios of 9.7:5.3:1.1.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Hjalmar P Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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15
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Chen Z, Yu Q, Yu Q, Johnson J, Shipman R, Zhong X, Huang J, Asthana S, Carlsson C, Okonkwo O, Li L. In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease. Mol Cell Proteomics 2021; 20:100081. [PMID: 33862227 PMCID: PMC8724636 DOI: 10.1016/j.mcpro.2021.100081] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 01/22/2023] Open
Abstract
As the body fluid that directly interchanges with the extracellular fluid of the central nervous system (CNS), cerebrospinal fluid (CSF) serves as a rich source for CNS-related disease biomarker discovery. Extensive proteome profiling has been conducted for CSF, but studies aimed at unraveling site-specific CSF N-glycoproteome are lacking. Initial efforts into site-specific N-glycoproteomics study in CSF yield limited coverage, hindering further experimental design of glycosylation-based disease biomarker discovery in CSF. In the present study, we have developed an N-glycoproteomic approach that combines enhanced N-glycopeptide sequential enrichment by hydrophilic interaction chromatography (HILIC) and boronic acid enrichment with electron transfer and higher-energy collision dissociation (EThcD) for large-scale intact N-glycopeptide analysis. The application of the developed approach to the analyses of human CSF samples enabled identifications of a total of 2893 intact N-glycopeptides from 511 N-glycosites and 285 N-glycoproteins. To our knowledge, this is the largest site-specific N-glycoproteome dataset reported for CSF to date. Such dataset provides molecular basis for a better understanding of the structure-function relationships of glycoproteins and their roles in CNS-related physiological and pathological processes. As accumulating evidence suggests that defects in glycosylation are involved in Alzheimer's disease (AD) pathogenesis, in the present study, a comparative in-depth N-glycoproteomic analysis was conducted for CSF samples from healthy control and AD patients, which yielded a comparable N-glycoproteome coverage but a distinct expression pattern for different categories of glycoforms, such as decreased fucosylation in AD CSF samples. Altered glycosylation patterns were detected for a number of N-glycoproteins including alpha-1-antichymotrypsin, ephrin-A3 and carnosinase CN1 etc., which serve as potentially interesting targets for further glycosylation-based AD study and may eventually lead to molecular elucidation of the role of glycosylation in AD progression.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Richard Shipman
- Department of Applied Science, University of Wisconsin-Stout, Menomonie, Wisconsin, USA
| | - Xiaofang Zhong
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Sanjay Asthana
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Cynthia Carlsson
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Ozioma Okonkwo
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA.
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16
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Zhang S, Di Y, Yao J, Wang Y, Shu H, Yan G, Zhang L, Lu H. Mass defect-based carbonyl activated tags (mdCATs) for multiplex data-independent acquisition proteome quantification. Chem Commun (Camb) 2021; 57:737-740. [DOI: 10.1039/d0cc06493a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A novel eight-plex mass-defect-based carbonyl activated tag (mdCAT) has been designed for DIA quantification for the first time.
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Affiliation(s)
- Siwen Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Yi Di
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Jun Yao
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Yingjie Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Chinese Academy of Sciences
| | - Hong Shu
- Department of Clinical Laboratory
- Cancer Hospital of Guangxi Medical University
- Nanning
- China
| | - Guoquan Yan
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research
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17
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Tian X, de Vries MP, Permentier HP, Bischoff R. A Versatile Isobaric Tag Enables Proteome Quantification in Data-Dependent and Data-Independent Acquisition Modes. Anal Chem 2020; 92:16149-16157. [PMID: 33256395 PMCID: PMC7745205 DOI: 10.1021/acs.analchem.0c03858] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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Quantifying proteins based on peptide-coupled
reporter ions is
a multiplexed quantitative strategy in proteomics that alleviates
the problem of ratio distortion caused by peptide cofragmentation,
as commonly observed in other reporter-ion-based approaches, such
as TMT and iTRAQ. Data-independent acquisition (DIA) is an attractive
alternative to data-dependent acquisition (DDA) due to its better
reproducibility. While multiplexed labeling is widely used in DDA,
it is rarely used in DIA, presumably because current approaches lead
to more complex MS2 spectra, severe ratio distortion, or to a reduction
in quantification accuracy and precision. Herein, we present a versatile
acetyl-alanine-glycine (Ac-AG) tag that conceals quantitative information
in isobarically labeled peptides and reveals it upon tandem MS in
the form of peptide-coupled reporter ions. Since the peptide-coupled
reporter ion is precursor-specific while fragment ions of the peptide
backbone originating from different labeling channels are identical,
the Ac-AG tag is compatible with both DDA and DIA. By isolating the
monoisotopic peak of the precursor ion in DDA, intensities of the
peptide-coupled reporter ions represent the relative ratios between
constituent samples, whereas in DIA, the ratio can be inferred after
deconvoluting the peptide-coupled reporter ion isotopes. The proteome
quantification capability of the Ac-AG tag was demonstrated by triplex
labeling of a yeast proteome spiked with bovine serum albumin (BSA)
over a 10-fold dynamic range. Within this complex proteomics background,
BSA spiked at 1:5:10 ratios was detected at ratios of 1.00:4.87:10.13
in DDA and 1.16:5.20:9.64 in DIA.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 16, 9713 AV Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Hjalmar P Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 16, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 16, 9713 AV Groningen, The Netherlands
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