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Pandeswari PB, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv 2018; 9:313-344. [PMID: 35521579 PMCID: PMC9059502 DOI: 10.1039/c8ra07200k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022] Open
Abstract
Owing to rapid growth in the elucidation of genome sequences of various organisms, deducing proteome sequences has become imperative, in order to have an improved understanding of biological processes. Since the traditional Edman method was unsuitable for high-throughput sequencing and also for N-terminus modified proteins, mass spectrometry (MS) based methods, mainly based on soft ionization modes: electrospray ionization and matrix-assisted laser desorption/ionization, began to gain significance. MS based methods were adaptable for high-throughput studies and applicable for sequencing N-terminus blocked proteins/peptides too. Consequently, over the last decade a new discipline called 'proteomics' has emerged, which encompasses the attributes necessary for high-throughput identification of proteins. 'Proteomics' may also be regarded as an offshoot of the classic field, 'biochemistry'. Many protein sequencing and proteomic investigations were successfully accomplished through MS dependent sequence elucidation of 'short proteolytic peptides (typically: 7-20 amino acid residues), which is called the 'shotgun' or 'bottom-up (BU)' approach. While the BU approach continues as a workhorse for proteomics/protein sequencing, attempts to sequence intact proteins without proteolysis, called the 'top-down (TD)' approach started, due to ambiguities in the BU approach, e.g., protein inference problem, identification of proteoforms and the discovery of posttranslational modifications (PTMs). The high-throughput TD approach (TD proteomics) is yet in its infancy. Nevertheless, TD characterization of purified intact proteins has been useful for detecting PTMs. With the hope to overcome the pitfalls of BU and TD strategies, another concept called the 'middle-down (MD)' approach was put forward. Similar to BU, the MD approach also involves proteolysis, but in a restricted manner, to produce 'longer' proteolytic peptides than the ones usually obtained in BU studies, thereby providing better sequence coverage. In this regard, special proteases (OmpT, Sap9, IdeS) have been used, which can cleave proteins to produce longer proteolytic peptides. By reviewing ample evidences currently existing in the literature that is predominantly on PTM characterization of histones and antibodies, herein we highlight salient features of the MD approach. Consequently, we are inclined to claim that the MD concept might have widespread applications in future for various research areas, such as clinical, biopharmaceuticals (including PTM analysis) and even for general/routine characterization of proteins including therapeutic proteins, but not just limited to analysis of histones or antibodies.
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Affiliation(s)
- P Boomathi Pandeswari
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
| | - Varatharajan Sabareesh
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
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2
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Srzentić K, Zhurov KO, Lobas AA, Nikitin G, Fornelli L, Gorshkov MV, Tsybin YO. Chemical-Mediated Digestion: An Alternative Realm for Middle-down Proteomics? J Proteome Res 2018; 17:2005-2016. [PMID: 29722266 DOI: 10.1021/acs.jproteome.7b00834] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein digestion in mass spectrometry (MS)-based bottom-up proteomics targets mainly lysine and arginine residues, yielding primarily 0.6-3 kDa peptides for the proteomes of organisms of all major kingdoms. Recent advances in MS technology enable analysis of complex mixtures of increasingly longer (>3 kDa) peptides in a high-throughput manner supporting the development of a middle-down proteomics (MDP) approach. Generating longer peptides is a paramount step in launching an MDP pipeline, but the quest for the selection of a cleaving agent that would provide the desired 3-15 kDa peptides remains open. Recent bioinformatics studies have shown that cleavage at the rarely occurring amino acid residues such as methionine (Met), tryptophan (Trp), or cysteine (Cys) would be suitable for MDP approach. Interestingly, chemical-mediated proteolytic cleavages uniquely allow targeting these rare amino acids, for which no specific proteolytic enzymes are known. Herein, as potential candidates for MDP-grade proteolysis, we have investigated the performance of chemical agents previously reported to target primarily Met, Trp, and Cys residues: CNBr, BNPS-Skatole (3-bromo-3-methyl-2-(2-nitrophenyl)sulfanylindole), and NTCB (2-nitro-5-thiobenzoic acid), respectively. Figures of merit such as digestion reproducibility, peptide size distribution, and occurrence of side reactions are discussed. The NTCB-based MDP workflow has demonstrated particularly attractive performance, and NTCB is put forward here as a potential cleaving agent for further MDP development.
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Affiliation(s)
- Kristina Srzentić
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | | | - Anna A Lobas
- V. L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Leninsky Prospect 38 , Moscow 119334 , Russia
| | - Gennady Nikitin
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | - Luca Fornelli
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Leninsky Prospect 38 , Moscow 119334 , Russia.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy per. , Dolgoprudny, Moscow 141707 , Russia
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park , Lausanne 1015 , Switzerland
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3
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Sanders JD, Greer SM, Brodbelt JS. Integrating Carbamylation and Ultraviolet Photodissociation Mass Spectrometry for Middle-Down Proteomics. Anal Chem 2017; 89:11772-11778. [DOI: 10.1021/acs.analchem.7b03396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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4
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Cotham VC, Horton AP, Lee J, Georgiou G, Brodbelt JS. Middle-Down 193-nm Ultraviolet Photodissociation for Unambiguous Antibody Identification and its Implications for Immunoproteomic Analysis. Anal Chem 2017; 89:6498-6504. [PMID: 28517930 DOI: 10.1021/acs.analchem.7b00564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) has emerged as a powerful tool within the growing field of immunoproteomics, which aims to understand antibody-mediated immunity at the molecular-level based on the direct determination of serological antibody repertoire. To date, these methods have relied on the use of high-resolution bottom-up proteomic strategies that require effective sampling and characterization of low abundance peptides derived from the antigen-binding domains of polyclonal antibody mixtures. Herein, we describe a method that uses restricted Lys-C enzymatic digestion to increase the average mass of proteolytic IgG peptides (≥4.5 kDa) and produce peptides which uniquely derive from single antibody species. This enhances the capacity to discriminate between very similar antibodies present within polyclonal mixtures. Furthermore, our use of 193-nm ultraviolet photodissociation (UVPD) improves spectral coverage of the antibody sequence relative to conventional collision- and electron-based fragmentation methods. We apply these methods to both a monoclonal and an antibody mixture. By identifying from a database search of approximately 15 000 antibody sequences those which compose the mixture, we demonstrate the analytical potential of middle-down UVPD for MS-based serological repertoire analysis.
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Affiliation(s)
- Victoria C Cotham
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Andrew P Horton
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jiwon Lee
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - George Georgiou
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
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5
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Cristobal A, Marino F, Post H, van den Toorn HWP, Mohammed S, Heck AJR. Toward an Optimized Workflow for Middle-Down Proteomics. Anal Chem 2017; 89:3318-3325. [PMID: 28233997 PMCID: PMC5362747 DOI: 10.1021/acs.analchem.6b03756] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Mass
spectrometry (MS)-based proteomics workflows can crudely be
classified into two distinct regimes, targeting either relatively
small peptides (i.e., 0.7 kDa < Mw <
3.0 kDa) or small to medium sized intact proteins (i.e., 10 kDa < Mw < 30 kDa), respectively, termed bottom-up
and top-down proteomics. Recently, a niche has started to be explored
covering the analysis of middle-range peptides (i.e., 3.0 kDa < Mw < 10 kDa), aptly termed middle-down proteomics.
Although middle-down proteomics can follow, in principle, a modular
workflow similar to that of bottom-up proteomics, we hypothesized
that each of these modules would benefit from targeted optimization
to improve its overall performance in the analysis of middle-range
sized peptides. Hence, to generate middle-range sized peptides from
cellular lysates, we explored the use of the proteases Asp-N and Glu-C
and a nonenzymatic acid induced cleavage. To increase the depth of
the proteome, a strong cation exchange (SCX) separation, carefully
tuned to improve the separation of longer peptides, combined with
reversed phase-liquid chromatography (RP-LC) using columns packed
with material possessing a larger pore size, was used. Finally, after
evaluating the combination of potentially beneficial MS settings,
we also assessed the peptide fragmentation techniques, including higher-energy
collision dissociation (HCD), electron-transfer dissociation (ETD),
and electron-transfer combined with higher-energy collision dissociation
(EThcD), for characterization of middle-range sized peptides. These
combined
improvements clearly improve the detection and sequence coverage of
middle-range peptides and should guide researchers to explore further
how middle-down proteomics may lead to an improved proteome coverage,
beneficial for, among other things, the enhanced analysis of (co-occurring)
post-translational modifications.
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Affiliation(s)
- Alba Cristobal
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Fabio Marino
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Henk W P van den Toorn
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Departments of Chemistry and Biochemistry, University of Oxford , New Biochemistry Building, South Parks Road, Oxford, OX1 3QU Oxfordshire, United Kingdom
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
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Abstract
OBJECTIVES Mass spectrometry-based proteomics enables near-comprehensive protein expression profiling. We aimed to compare quantitatively the relative expression levels of thousands of proteins across 5 pancreatic cell lines. METHODS Using tandem mass tags (TMT10-plex), we profiled the global proteomes of 5 cell lines in duplicate in a single multiplexed experiment. We selected cell lines commonly used in pancreatic research: CAPAN-1, HPAC, HPNE, PANC1, and PaSCs. In addition, we examined the effects of different proteases (Lys-C and Lys-C plus trypsin) on the dataset depth. RESULTS We quantified over 8000 proteins across the 5 cell lines. Analysis of variance testing of cell lines within each data set resulted in over 1400 statistically significant differences in protein expression levels. Comparing the data sets, 10% more proteins and 30% more peptides were identified in the Lys-C/trypsin data set than in the Lys-C-only data set. The correlation coefficient of quantified proteins common between the data sets was greater than 0.85. CONCLUSIONS We illustrate protein level differences across pancreatic cell lines. In addition, we highlight the advantages of Lys-C/trypsin over Lys-C-only digests for discovery proteomics. These data sets provide a valuable resource of cell line-dependent peptide and protein differences for future targeted analyses, including those investigating on- or off-target drug effects across cell lines.
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7
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Sweredoski MJ, Moradian A, Raedle M, Franco C, Hess S. High Resolution Parallel Reaction Monitoring with Electron Transfer Dissociation for Middle-Down Proteomics. Anal Chem 2015; 87:8360-6. [DOI: 10.1021/acs.analchem.5b01542] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Michael J. Sweredoski
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Annie Moradian
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Matthias Raedle
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
- Hochschule Weihenstephan-Triesdorf, University of Applied Sciences, Faculty of Biotechnology and Bioinformatic, Am Hofgarten 4, 85354 Freising, Germany
| | - Catarina Franco
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sonja Hess
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
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8
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Valkevich E, Sanchez NA, Ge Y, Strieter ER. Middle-down mass spectrometry enables characterization of branched ubiquitin chains. Biochemistry 2014; 53:4979-89. [PMID: 25023374 PMCID: PMC4372068 DOI: 10.1021/bi5006305] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/09/2014] [Indexed: 12/22/2022]
Abstract
Protein ubiquitylation, one of the most prevalent post-translational modifications in eukaryotes, is involved in regulating nearly every cellular signaling pathway. The vast functional range of ubiquitylation has largely been attributed to the formation of a diverse array of polymeric ubiquitin (polyUb) chains. Methods that enable the characterization of these diverse chains are necessary to fully understand how differences in structure relate to function. Here, we describe a method for the detection of enzymatically derived branched polyUb conjugates in which a single Ub subunit is modified by two Ub molecules at distinct lysine residues. Using a middle-down mass spectrometry approach in which restricted trypsin-mediated digestion is coupled with mass spectrometric analysis, we characterize the polyUb chains produced by bacterial effector E3 ligases NleL (non-Lee-encoded effector ligase from enterohemorrhagic Escherichia coli O157:H7) and IpaH9.8 (from Shigella flexneri). Because Ub is largely intact after minimal trypsinolysis, multiple modifications on a single Ub moiety can be detected. Analysis of NleL- and IpaH9.8-derived polyUb chains reveals branch points are present in approximately 10% of the overall chain population. When unanchored, well-defined polyUb chains are added to reaction mixtures containing NleL, longer chains are more likely to be modified internally, forming branch points rather than extending from the end of the chain. These results suggest that middle-down mass spectrometry can be used to assess the extent to which branched polyUb chains are formed by various enzymatic systems and potentially evaluate the presence of these atypical conjugates in cell and tissue extracts.
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Affiliation(s)
- Ellen
M. Valkevich
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nicholas A. Sanchez
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department
of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin—Madison, 1300 University Avenue, Madison, Wisconsin 53706, United States
| | - Eric R. Strieter
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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9
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Cannon JR, Cammarata M, Robotham SA, Cotham VC, Shaw JB, Fellers RT, Early BP, Thomas PM, Kelleher NL, Brodbelt JS. Ultraviolet photodissociation for characterization of whole proteins on a chromatographic time scale. Anal Chem 2014; 86:2185-92. [PMID: 24447299 PMCID: PMC3958131 DOI: 10.1021/ac403859a] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/21/2014] [Indexed: 02/01/2023]
Abstract
Intact protein characterization using mass spectrometry thus far has been achieved at the cost of throughput. Presented here is the application of 193 nm ultraviolet photodissociation (UVPD) for top down identification and characterization of proteins in complex mixtures in an online fashion. Liquid chromatographic separation at the intact protein level coupled with fast UVPD and high-resolution detection resulted in confident identification of 46 unique sequences compared to 44 using HCD from prepared Escherichia coli ribosomes. Importantly, nearly all proteins identified in both the UVPD and optimized HCD analyses demonstrated a substantial increase in confidence in identification (as defined by an average decrease in E value of ∼40 orders of magnitude) due to the higher number of matched fragment ions. Also shown is the potential for high-throughput characterization of intact proteins via liquid chromatography (LC)-UVPD-MS of molecular weight-based fractions of a Saccharomyces cerevisiae lysate. In total, protein products from 215 genes were identified and found in 292 distinct proteoforms, 168 of which contained some type of post-translational modification.
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Affiliation(s)
- Joe R. Cannon
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Michael
B. Cammarata
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Scott A. Robotham
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Victoria C. Cotham
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Jared B. Shaw
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Ryan T. Fellers
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Bryan P. Early
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Paul M. Thomas
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Jennifer S. Brodbelt
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
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