1
|
Dhenin J, Dupré M, Druart K, Krick A, Mauriac C, Chamot-Rooke J. A multiparameter optimization in middle-down analysis of monoclonal antibodies by LC-MS/MS. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4909. [PMID: 36822210 DOI: 10.1002/jms.4909] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
In antibody-based drug research, a complete characterization of antibody proteoforms covering both the amino acid sequence and all posttranslational modifications remains a major concern. The usual mass spectrometry-based approach to achieve this goal is bottom-up proteomics, which relies on the digestion of antibodies but does not allow the diversity of proteoforms to be assessed. Middle-down and top-down approaches have recently emerged as attractive alternatives but are not yet mastered and thus used in routine by many analytical chemistry laboratories. The work described here aims at providing guidelines to achieve the best sequence coverage for the fragmentation of intact light and heavy chains generated from a simple reduction of intact antibodies using Orbitrap mass spectrometry. Three parameters were found crucial to this aim: the use of an electron-based activation technique, the multiplex selection of precursor ions of different charge states, and the combination of replicates.
Collapse
Affiliation(s)
- Jonathan Dhenin
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Mass Spectrometry for Biology, Paris, 75015, France
- Université Paris Cité, Sorbonne Paris Cité, Paris, France
- DMPK, Sanofi, Chilly-Mazarin, 91385, France
| | - Mathieu Dupré
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Mass Spectrometry for Biology, Paris, 75015, France
| | - Karen Druart
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Mass Spectrometry for Biology, Paris, 75015, France
| | | | | | - Julia Chamot-Rooke
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Mass Spectrometry for Biology, Paris, 75015, France
| |
Collapse
|
2
|
Jeong K, Babović M, Gorshkov V, Kim J, Jensen ON, Kohlbacher O. FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts. Nat Commun 2022; 13:4407. [PMID: 35906205 PMCID: PMC9338294 DOI: 10.1038/s41467-022-31922-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
The detailed analysis and structural characterization of proteoforms by top-down proteomics (TDP) has gained a lot of interest in biomedical research. Data-dependent acquisition (DDA) of intact proteins is non-trivial due to the diversity and complexity of proteoforms. Dedicated acquisition methods thus have the potential to greatly improve TDP. Here, we present FLASHIda, an intelligent online data acquisition algorithm for TDP that ensures the real-time selection of high-quality precursors of diverse proteoforms. FLASHIda combines fast charge deconvolution algorithms and machine learning-based quality assessment for optimal precursor selection. In an analysis of E. coli lysate, FLASHIda increases the number of unique proteoform level identifications from 800 to 1500 or generates a near-identical number of identifications in one third of the instrument time when compared to standard DDA mode. Furthermore, FLASHIda enables sensitive mapping of post-translational modifications and detection of chemical adducts. As a software extension module to the instrument, FLASHIda can be readily adopted for TDP studies of complex samples to enhance proteoform identification rates.
Collapse
Affiliation(s)
- Kyowon Jeong
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
| | - Maša Babović
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Odense, Denmark
| | - Vladimir Gorshkov
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Odense, Denmark
| | - Jihyung Kim
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Sand 14, 72076, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Odense, Denmark
| | - Oliver Kohlbacher
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
- Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Str. 9, 72076, Tübingen, Germany.
| |
Collapse
|
3
|
Lu L, Scalf M, Shortreed MR, Smith LM. Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1319-1325. [PMID: 33754701 PMCID: PMC8783543 DOI: 10.1021/jasms.0c00462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Top-down proteomics is a key mass spectrometry-based technology for comprehensive analysis of proteoforms. Proteoforms exhibit multiple high charge states and isotopic forms in full MS scans. The dissociation behavior of proteoforms in different charge states and subjected to different collision energies is highly variable. The current widely employed data-dependent acquisition (DDA) method selects a narrow m/z range (corresponding to a single proteoform charge state) for dissociation from the most abundant precursors. We describe here Mesh, a novel dissociation strategy, to dissociate multiple charge states of one proteoform with multiple collision energies. We show that the Mesh strategy has the potential to generate fragment ions with improved sequence coverage and improve identification ratios in top-down proteomic analyses of complex samples. The strategy is implemented within an open-source instrument control software program named MetaDrive to perform real time deconvolution and precursor selection.
Collapse
Affiliation(s)
- Lei Lu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Michael R. Shortreed
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
- Corresponding Author Phone: (608) 263-2594. Fax: (608) 265-6780.
| |
Collapse
|
4
|
Dupré M, Duchateau M, Malosse C, Borges-Lima D, Calvaresi V, Podglajen I, Clermont D, Rey M, Chamot-Rooke J. Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination. J Proteome Res 2020; 20:202-211. [PMID: 32929970 DOI: 10.1021/acs.jproteome.0c00351] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The current technique used for microbial identification in hospitals is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, it suffers from important limitations, in particular, for closely related species or when the database used for the identification lacks the appropriate reference. In this work, we set up a liquid chromatography (LC)-MS/MS top-down proteomics platform, which aims at discriminating closely related pathogenic bacteria through the identification of specific proteoforms. Using Escherichia coli as a model, all steps of the workflow were optimized: protein extraction, on-line LC separation, MS method, and data analysis. Using optimized parameters, about 220 proteins, corresponding to more than 500 proteoforms, could be identified in a single run. We then used this platform for the discrimination of enterobacterial pathogens undistinguishable by MALDI-TOF, although leading to very different clinical outcomes. For each pathogen, we identified specific proteoforms that could potentially be used as biomarkers. We also improved the characterization of poorly described bacterial strains. Our results highlight the advantage of addressing proteoforms rather than peptides for accurate bacterial characterization and qualify top-down proteomics as a promising tool in clinical microbiology. Data are available via ProteomeXchange with the identifier PXD019247.
Collapse
Affiliation(s)
- Mathieu Dupré
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Christian Malosse
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Diogo Borges-Lima
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Valeria Calvaresi
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Isabelle Podglajen
- Microbiology Department, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75015, France
| | - Dominique Clermont
- Collection of the Institut Pasteur (CIP), Institut Pasteur, Paris 75015, France
| | - Martial Rey
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| |
Collapse
|
5
|
Liyang Z, Xinling Z. Optimization design of automatic filing system of financial management information under the background of information technology development. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2020. [DOI: 10.3233/jifs-179504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Zheng Liyang
- School of Economics and Management, Inner Mongolia Agricultural University, Hohhot Inner Mongolia, China
| | - Zhang Xinling
- School of Economics and Management, Inner Mongolia Agricultural University, Hohhot Inner Mongolia, China
| |
Collapse
|
6
|
Huguet R, Mullen C, Srzentić K, Greer JB, Fellers RT, Zabrouskov V, Syka JEP, Kelleher NL, Fornelli L. Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms. Anal Chem 2019; 91:15732-15739. [PMID: 31714757 DOI: 10.1021/acs.analchem.9b03925] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the recent technological advances in Fourier transform mass spectrometry (FTMS) instrumentation, top-down proteomics (TDP) is currently mostly applied to the characterization of proteoforms <30 kDa due to the poor performance of high-resolution FTMS for the analysis of larger proteoforms and the high complexity of intact proteomes in the 30-60 kDa mass range. Here, we propose a novel data acquisition method based on ion-ion proton transfer, herein termed proton transfer charge reduction (PTCR), to investigate large proteoforms of Pseudomonas aeruginosa in a high-throughput fashion. We designed a targeted data acquisition strategy, named tPTCR, which applies two consecutive gas phase fractionation steps for obtaining intact precursor masses: first, a narrow (1.5 m/z-wide) quadrupole filter m/z transmission window is used to select a subset of charge states from all ionized proteoform cations; second, this aliquot of protein cations is subjected to PTCR in order to reduce their average charge state: upon m/z analysis in an Orbitrap, proteoform mass spectra with minimal m/z peak overlap and easy-to-interpret charge state distributions are obtained, simplifying the proteoform mass calculation. Subsequently, the same quadrupole-selected narrow m/z region of analytes is subjected to collisional dissociation to obtain proteoform sequence information, which used in combination with intact mass information leads to proteoform identification through an off-line database search. The newly proposed method was benchmarked against the previously developed "medium/high" data-dependent acquisition strategy and doubled the number of UniProt entries and proteoforms >30 kDa identified on the liquid chromatography time scale.
Collapse
Affiliation(s)
- Romain Huguet
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Christopher Mullen
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Kristina Srzentić
- Thermo Fisher Scientific , 790 Memorial Drive, Suite 2D , Cambridge , Massachusetts 02139 , United States
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - John E P Syka
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Luca Fornelli
- Department of Biology , University of Oklahoma , 730 Van Vleet Oval , Norman , Oklahoma 73071 , United States
| |
Collapse
|
7
|
Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, LeDuc RD, Liu X, Payne SH, Sun L, Thomas PM, Tucholski T, Wang Z, Wu S, Wu Z, Yu D, Shortreed MR, Smith LM. Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics 2019; 19:e1800361. [PMID: 31050378 PMCID: PMC6602557 DOI: 10.1002/pmic.201800361] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/07/2019] [Indexed: 12/29/2022]
Abstract
A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post-translational modifications. In top-down proteomic analyses, proteoforms are identified and quantified through mass spectrometric analysis of intact proteins. Recent technological developments have enabled comprehensive proteoform analyses in complex samples, and an increasing number of laboratories are adopting top-down proteomic workflows. In this review, some recent advances are outlined and current challenges and future directions for the field are discussed.
Collapse
Affiliation(s)
- Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Robert J Millikin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Cell and Regenerative Biology and Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemistry and Molecular Biosciences and the Division of Hematology and Oncology, Northwestern University, Evanston, IL, 60208, USA
| | - Richard D LeDuc
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT, 84602
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| |
Collapse
|
8
|
Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, Friedewald J, Kelleher NL. A comprehensive pipeline for translational top-down proteomics from a single blood draw. Nat Protoc 2019; 14:119-152. [PMID: 30518910 DOI: 10.1038/s41596-018-0085-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Top-down proteomics (TDP) by mass spectrometry (MS) is a technique by which intact proteins are analyzed. It has become increasingly popDesalting and concentrating GELFrEEular in translational research because of the value of characterizing distinct proteoforms of intact proteins. Compared to bottom-up proteomics (BUP) strategies, which measure digested peptide mixtures, TDP provides highly specific molecular information that avoids the bioinformatic challenge of protein inference. However, the technique has been difficult to implement widely because of inherent limitations of existing sample preparation methods and instrumentation. Recent improvements in proteoform pre-fractionation and the availability of high-resolution benchtop mass spectrometers have made it possible to use high-throughput TDP for the analysis of complex clinical samples. Here, we provide a comprehensive protocol for analysis of a common sample type in translational research: human peripheral blood mononuclear cells (PBMCs). The pipeline comprises multiple workflows that can be treated as modular by the reader and used for various applications. First, sample collection and cell preservation are described for two clinical biorepository storage schemes. Cell lysis and proteoform pre-fractionation by gel-eluted liquid fractionation entrapment electrophoresis are then described. Importantly, instrument setup and liquid chromatography-tandem MS are described for TDP analyses, which rely on high-resolution Fourier-transform MS. Finally, data processing and analysis are described using two different, application-dependent software tools: ProSight Lite for targeted analyses of one or a few proteoforms and TDPortal for high-throughput TDP in discovery mode. For a single sample, the minimum completion time of the entire experiment is 72 h.
Collapse
Affiliation(s)
- Timothy K Toby
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Kristina Srzentić
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Caroline J DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Josh Levitsky
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - John Friedewald
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Neil L Kelleher
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA. .,National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA.
| |
Collapse
|
9
|
Shliaha PV, Gibb S, Gorshkov V, Jespersen MS, Andersen GR, Bailey D, Schwartz J, Eliuk S, Schwämmle V, Jensen ON. Maximizing Sequence Coverage in Top-Down Proteomics By Automated Multimodal Gas-Phase Protein Fragmentation. Anal Chem 2018; 90:12519-12526. [DOI: 10.1021/acs.analchem.8b02344] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pavel V. Shliaha
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Sebastian Gibb
- Department of Anesthesiology and Intensive Care, University Medicine Greifswald, Greifswald 17489, Germany
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Malena Schack Jespersen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Gregers R. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Derek Bailey
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Jacob Schwartz
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Shannon Eliuk
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
10
|
Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, LeDuc RD, Westphall MS, Thomas PM, Kelleher NL, Coon JJ. The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins. Anal Chem 2018; 90:8553-8560. [PMID: 29924586 DOI: 10.1021/acs.analchem.8b01638] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High-throughput top-down proteomic experiments directly identify proteoforms in complex mixtures, making high quality tandem mass spectra necessary to deeply characterize proteins with many sources of variation. Collision-based dissociation methods offer expedient data acquisition but often fail to extensively fragment proteoforms for thorough analysis. Electron-driven dissociation methods are a popular alternative approach, especially for precursor ions with high charge density. Combining infrared photoactivation concurrent with electron transfer dissociation (ETD) reactions, i.e., activated ion ETD (AI-ETD), can significantly improve ETD characterization of intact proteins, but benefits of AI-ETD have yet to be quantified in high-throughput top-down proteomics. Here, we report the first application of AI-ETD to LC-MS/MS characterization of intact proteins (<20 kDa), highlighting improved proteoform identification the method offers over higher energy-collisional dissociation (HCD), standard ETD, and ETD followed by supplemental HCD activation (EThcD). We identified 935 proteoforms from 295 proteins from human colorectal cancer cell line HCT116 using AI-ETD compared to 1014 proteoforms, 915 proteoforms, and 871 proteoforms with HCD, ETD, and EThcD, respectively. Importantly, AI-ETD outperformed each of the three other methods in MS/MS success rates and spectral quality metrics (e.g., sequence coverage achieved and proteoform characterization scores). In all, this four-method analysis offers the most extensive comparisons to date and demonstrates that AI-ETD both increases identifications over other ETD methods and improves proteoform characterization via higher sequence coverage, positioning it as a premier method for high-throughput top-down proteomics.
Collapse
Affiliation(s)
| | - Jacek W Sikora
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Henrique S Seckler
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Richard D LeDuc
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | | | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Joshua J Coon
- Morgridge Institute for Research , Madison , Wisconsin 53706 , United States
| |
Collapse
|
11
|
Kachuk C, Doucette AA. The benefits (and misfortunes) of SDS in top-down proteomics. J Proteomics 2018; 175:75-86. [DOI: 10.1016/j.jprot.2017.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/19/2017] [Accepted: 03/03/2017] [Indexed: 12/18/2022]
|
12
|
Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
13
|
Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, 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
| |
Collapse
|
14
|
Kar UK, Simonian M, Whitelegge JP. Integral membrane proteins: bottom-up, top-down and structural proteomics. Expert Rev Proteomics 2017; 14:715-723. [PMID: 28737967 DOI: 10.1080/14789450.2017.1359545] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a disproportionately large segment of the proteome, technical developments need timely review. Areas covered: Publically available resources such as Pubmed were surveyed. Bottom-up proteomics analyses now allow efficient extraction and digestion such that membrane protein coverage is essentially complete, making up around one third of the proteome. However, this coverage relies upon hydrophilic loop regions while transmembrane domains are generally poorly covered in peptide-based strategies. Top-down mass spectrometry where the intact membrane protein is fragmented in the gas phase gives good coverage in transmembrane regions, and membrane fractions are yielding to high-throughput top-down proteomics. Exciting progress in native mass spectrometry of membrane protein complexes is providing insights into subunit stoichiometry and lipid binding, and cross-linking strategies are contributing critical in-vivo information. Expert commentary: It is clear from the literature that integral membrane proteins have yielded to advanced techniques in protein chemistry and mass spectrometry, with applications limited only by the imagination of investigators. Key advances toward translation to the clinic are emphasized.
Collapse
Affiliation(s)
- Upendra K Kar
- a Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Margaret Simonian
- b NPI-Semel Institute , University of California Los Angeles , Los Angeles , CA , USA
| | - Julian P Whitelegge
- b NPI-Semel Institute , University of California Los Angeles , Los Angeles , CA , USA
| |
Collapse
|
15
|
Xiao K, Yu F, Fang H, Xue B, Liu Y, Li Y, Tian Z. Are neutral loss and internal product ions useful for top-down protein identification? J Proteomics 2017; 160:21-27. [DOI: 10.1016/j.jprot.2017.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 10/19/2022]
|
16
|
Top-Down Proteomics and Farm Animal and Aquatic Sciences. Proteomes 2016; 4:proteomes4040038. [PMID: 28248248 PMCID: PMC5260971 DOI: 10.3390/proteomes4040038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/25/2016] [Accepted: 12/05/2016] [Indexed: 01/16/2023] Open
Abstract
Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.
Collapse
|
17
|
Fornelli L, Durbin KR, Fellers RT, Early BP, Greer JB, LeDuc RD, Compton PD, Kelleher NL. Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer. J Proteome Res 2016; 16:609-618. [PMID: 28152595 DOI: 10.1021/acs.jproteome.6b00698] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, developments in high resolution mass spectrometry have enabled the high throughput analysis of intact proteins from complex proteomes, leading to the identification of thousands of proteoforms. Several previous reports on top-down proteomics (TDP) relied on hybrid ion trap-Fourier transform mass spectrometers combined with data-dependent acquisition strategies. To further reduce TDP to practice, we use a quadrupole-Orbitrap instrument coupled with software for proteoform-dependent data acquisition to identify and characterize nearly 2000 proteoforms at a 1% false discovery rate from human fibroblasts. By combining a 3 m/z isolation window with short transients to improve specificity and signal-to-noise for proteoforms >30 kDa, we demonstrate improving proteome coverage by capturing 439 proteoforms in the 30-60 kDa range. Three different data acquisition strategies were compared and resulted in the identification of many proteoforms not observed in replicate data-dependent experiments. Notably, the data set is reported with updated metrics and tools including a new viewer and assignment of permanent proteoform record identifiers for inclusion of highly characterized proteoforms (i.e., those with C-scores >40) in a repository curated by the Consortium for Top-Down Proteomics.
Collapse
Affiliation(s)
- Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Kenneth R Durbin
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Bryan P Early
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| |
Collapse
|
18
|
Durbin KR, Fornelli L, Fellers RT, Doubleday PF, Narita M, Kelleher NL. Quantitation and Identification of Thousands of Human Proteoforms below 30 kDa. J Proteome Res 2016; 15:976-82. [PMID: 26795204 PMCID: PMC4794255 DOI: 10.1021/acs.jproteome.5b00997] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins. We extended the coverage of the label-free technique, achieving differential analysis of whole proteins <30 kDa from the proteomes of growing and senescent human fibroblasts. By integrating improved control software with more instrument time allocated for quantitation of intact ions, we were able to collect protein data between the two cell states, confidently comparing 1577 proteoform levels. To then identify and characterize proteoforms, our advanced acquisition software, named Autopilot, employed enhanced identification efficiency in identifying 1180 unique Swiss-Prot accession numbers at 1% false-discovery rate. This coverage of the low mass proteome is equivalent to the largest previously reported but was accomplished in 23% of the total acquisition time. By maximizing both the number of quantified proteoforms and their identification rate in an integrated software environment, this work significantly advances proteoform-resolved analyses of complex systems.
Collapse
Affiliation(s)
- Kenneth R. Durbin
- Departments of Chemistry and Molecular Biosciences, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Ryan T. Fellers
- Departments of Chemistry and Molecular Biosciences, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Peter F. Doubleday
- Departments of Chemistry and Molecular Biosciences, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, U.K
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular Biosciences, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
| |
Collapse
|
19
|
Riley NM, Mullen C, Weisbrod CR, Sharma S, Senko MW, Zabrouskov V, Westphall MS, Syka JEP, Coon JJ. Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:520-31. [PMID: 26589699 PMCID: PMC4758868 DOI: 10.1007/s13361-015-1306-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/29/2015] [Accepted: 11/05/2015] [Indexed: 05/11/2023]
Abstract
Electron transfer dissociation (ETD) is a valuable tool for protein sequence analysis, especially for the fragmentation of intact proteins. However, low product ion signal-to-noise often requires some degree of signal averaging to achieve high quality MS/MS spectra of intact proteins. Here we describe a new implementation of ETD on the newest generation of quadrupole-Orbitrap-linear ion trap Tribrid, the Orbitrap Fusion Lumos, for improved product ion signal-to-noise via ETD reactions on larger precursor populations. In this new high precursor capacity ETD implementation, precursor cations are accumulated in the center section of the high pressure cell in the dual pressure linear ion trap prior to charge-sign independent trapping, rather than precursor ion sequestration in only the back section as is done for standard ETD. This new scheme increases the charge capacity of the precursor accumulation event, enabling storage of approximately 3-fold more precursor charges. High capacity ETD boosts the number of matching fragments identified in a single MS/MS event, reducing the need for spectral averaging. These improvements in intra-scan dynamic range via reaction of larger precursor populations, which have been previously demonstrated through custom modified hardware, are now available on a commercial platform, offering considerable benefits for intact protein analysis and top down proteomics. In this work, we characterize the advantages of high precursor capacity ETD through studies with myoglobin and carbonic anhydrase.
Collapse
Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | | | - Seema Sharma
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | | | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| |
Collapse
|
20
|
Birner-Gruenberger R, Breinbauer R. Weighing the proteasome for covalent modifications. ACTA ACUST UNITED AC 2016; 22:315-6. [PMID: 25794435 DOI: 10.1016/j.chembiol.2015.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Posttranslational modifications (PTMs) control protein function, but established peptide-based proteomic methods often fail to provide a comprehensive view of PTMs. In this issue of Chemistry & Biology, Gersch et al. describe an efficient combination of chromatographic separation and top-down mass spectrometry that together with an intuitive visualization tool allowed them to screen the proteasome for PTMs and covalently binding inhibitors.
Collapse
Affiliation(s)
- Ruth Birner-Gruenberger
- Research Unit Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University Graz, and Omics Center Graz, BioTechMed-Graz, A-8010 Graz, Austria
| | - Rolf Breinbauer
- Institute of Organic Chemistry, Graz University of Technology, A-8010 Graz, Austria.
| |
Collapse
|
21
|
Sun RX, Luo L, Wu L, Wang RM, Zeng WF, Chi H, Liu C, He SM. pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification. Anal Chem 2016; 88:3082-90. [DOI: 10.1021/acs.analchem.5b03963] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Rui-Xiang Sun
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Lan Luo
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Wu
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui-Min Wang
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Feng Zeng
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Chi
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Chao Liu
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Si-Min He
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| |
Collapse
|
22
|
Lorenzatto KR, Kim K, Ntai I, Paludo GP, Camargo de Lima J, Thomas PM, Kelleher NL, Ferreira HB. Top Down Proteomics Reveals Mature Proteoforms Expressed in Subcellular Fractions of the Echinococcus granulosus Preadult Stage. J Proteome Res 2015; 14:4805-14. [PMID: 26465659 DOI: 10.1021/acs.jproteome.5b00642] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Echinococcus granulosus is the causative agent of cystic hydatid disease, a neglected zoonosis responsible for high morbidity and mortality. Several molecular mechanisms underlying parasite biology remain poorly understood. Here, E. granulosus subcellular fractions were analyzed by top down and bottom up proteomics for protein identification and characterization of co-translational and post-translational modifications (CTMs and PTMs, respectively). Nuclear and cytosolic extracts of E. granulosus protoscoleces were fractionated by 10% GELFrEE and proteins under 30 kDa were analyzed by LC-MS/MS. By top down analysis, 186 proteins and 207 proteoforms were identified, of which 122 and 52 proteoforms were exclusively detected in nuclear and cytosolic fractions, respectively. CTMs were evident as 71% of the proteoforms had methionine excised and 47% were N-terminal acetylated. In addition, in silico internal acetylation prediction coupled with top down MS allowed the characterization of 9 proteins differentially acetylated, including histones. Bottom up analysis increased the overall number of identified proteins in nuclear and cytosolic fractions to 154 and 112, respectively. Overall, our results provided the first description of the low mass proteome of E. granulosus subcellular fractions and highlighted proteoforms with CTMs and PTMS whose characterization may lead to another level of understanding about molecular mechanisms controlling parasitic flatworm biology.
Collapse
Affiliation(s)
- Karina R Lorenzatto
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Kyunggon Kim
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Ioanna Ntai
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Gabriela P Paludo
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Jeferson Camargo de Lima
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrique B Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| |
Collapse
|
23
|
Riley NM, Westphall MS, Coon JJ. Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins. Anal Chem 2015; 87:7109-16. [PMID: 26067513 PMCID: PMC9488116 DOI: 10.1021/acs.analchem.5b00881] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here we report the first implementation of activated ion electron transfer dissociation (AI-ETD) for top down protein characterization, showing that AI-ETD definitively extends the m/z range over which ETD can be effective for fragmentation of intact proteins. AI-ETD, which leverages infrared photon bombardment concurrent to the ETD reaction to mitigate nondissociative electron transfer, was performed using a novel multipurpose dissociation cell that can perform both beam-type collisional dissociation and ion-ion reactions on an ion trap-Orbitrap hybrid mass spectrometer. AI-ETD increased the number of c- and z-type product ions for all charge states over ETD alone, boosting product ion yield by nearly 4-fold for low charge density precursors. AI-ETD also outperformed HCD, generating more matching fragments for all proteins at all charge states investigated. In addition to generating more unique fragment ions, AI-ETD provided greater protein sequence coverage compared to both HCD and ETD. In all, the effectiveness of AI-ETD across the entirety of the m/z spectrum demonstrates its efficacy for robust fragmentation of intact proteins.
Collapse
Affiliation(s)
- Nicholas M. Riley
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Michael S. Westphall
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706, United States
| |
Collapse
|
24
|
Durbin KR, Skinner OS, Fellers RT, Kelleher NL. Analyzing internal fragmentation of electrosprayed ubiquitin ions during beam-type collisional dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:782-7. [PMID: 25716753 PMCID: PMC4401654 DOI: 10.1007/s13361-015-1078-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/31/2014] [Accepted: 12/31/2014] [Indexed: 05/11/2023]
Abstract
Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis.
Collapse
Affiliation(s)
- Kenneth R Durbin
- Departments of Chemistry and Molecular Biosciences, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | | | | | | |
Collapse
|
25
|
Petras D, Heiss P, Süssmuth RD, Calvete JJ. Venom Proteomics of Indonesian King Cobra, Ophiophagus hannah: Integrating Top-Down and Bottom-Up Approaches. J Proteome Res 2015; 14:2539-56. [DOI: 10.1021/acs.jproteome.5b00305] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Daniel Petras
- Institut
für Chemie, Technische Universität Berlin, Müller-Breslau-Straße
10, 10623 Berlin, Germany
| | - Paul Heiss
- Institut
für Chemie, Technische Universität Berlin, Müller-Breslau-Straße
10, 10623 Berlin, Germany
| | - Roderich D. Süssmuth
- Institut
für Chemie, Technische Universität Berlin, Müller-Breslau-Straße
10, 10623 Berlin, Germany
| | - Juan J. Calvete
- Laboratorio
de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, 46010 Valencia, Spain
| |
Collapse
|
26
|
Skinner OS, Catherman AD, Early BP, Thomas PM, Compton PD, Kelleher NL. Fragmentation of integral membrane proteins in the gas phase. Anal Chem 2014; 86:4627-34. [PMID: 24689519 PMCID: PMC4018139 DOI: 10.1021/ac500864w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 04/01/2014] [Indexed: 11/28/2022]
Abstract
Integral membrane proteins (IMPs) are of great biophysical and clinical interest because of the key role they play in many cellular processes. Here, a comprehensive top down study of 152 IMPs and 277 soluble proteins from human H1299 cells including 11 087 fragments obtained from collisionally activated dissociation (CAD), 6452 from higher-energy collisional dissociation (HCD), and 2981 from electron transfer dissociation (ETD) shows their great utility and complementarity for the identification and characterization of IMPs. A central finding is that ETD is ∼2-fold more likely to cleave in soluble regions than threshold fragmentation methods, whereas the reverse is observed in transmembrane domains with an observed ∼4-fold bias toward CAD and HCD. The location of charges just prior to dissociation is consistent with this directed fragmentation: protons remain localized on basic residues during ETD but easily mobilize along the backbone during collisional activation. The fragmentation driven by these protons, which is most often observed in transmembrane domains, both is of higher yield and occurs over a greater number of backbone cleavage sites. Further, while threshold dissociation events in transmembrane domains are on average 10.1 (CAD) and 9.2 (HCD) residues distant from the nearest charge site (R, K, H, N-terminus), fragmentation is strongly influenced by the N- or C-terminal position relative to that site: the ratio of observed b- to y-fragments is ∼1:3 if the cleavage occurs >7 residues N-terminal and ∼3:1 if it occurs >7 residues C-terminal to the nearest basic site. Threshold dissociation products driven by a mobilized proton appear to be strongly dependent on not only relative position of a charge site but also N- or C-terminal directionality of proton movement.
Collapse
Affiliation(s)
| | | | - Bryan P. Early
- Departments
of Chemistry
and Molecular Biosciences, the Chemistry of Life Processes Institute,
the Proteomics Center of Excellence, and the Robert H. Lurie Comprehensive
Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Paul M. Thomas
- Departments
of Chemistry
and Molecular Biosciences, the Chemistry of Life Processes Institute,
the Proteomics Center of Excellence, and the Robert H. Lurie Comprehensive
Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Philip D. Compton
- Departments
of Chemistry
and Molecular Biosciences, the Chemistry of Life Processes Institute,
the Proteomics Center of Excellence, and the Robert H. Lurie Comprehensive
Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments
of Chemistry
and Molecular Biosciences, the Chemistry of Life Processes Institute,
the Proteomics Center of Excellence, and the Robert H. Lurie Comprehensive
Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
27
|
Catherman AD, Skinner OS, Kelleher NL. Top Down proteomics: facts and perspectives. Biochem Biophys Res Commun 2014; 445:683-93. [PMID: 24556311 PMCID: PMC4103433 DOI: 10.1016/j.bbrc.2014.02.041] [Citation(s) in RCA: 319] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/10/2014] [Indexed: 12/29/2022]
Abstract
The rise of the "Top Down" method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious "inference" problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.
Collapse
Affiliation(s)
- Adam D Catherman
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States
| | - Owen S Skinner
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States.
| |
Collapse
|