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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: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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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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53
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Li H, Sheng Y, McGee W, Cammarata M, Holden D, Loo JA. Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry. Anal Chem 2017; 89:2731-2738. [PMID: 28192979 DOI: 10.1021/acs.analchem.6b02377] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS) has played an increasingly important role in the identification and structural and functional characterization of proteins. In particular, the use of tandem mass spectrometry has afforded one of the most versatile methods to acquire structural information for proteins and protein complexes. The unique nature of electron capture dissociation (ECD) for cleaving protein backbone bonds while preserving noncovalent interactions has made it especially suitable for the study of native protein structures. However, the intra- and intermolecular interactions stabilized by hydrogen bonds and salt bridges can hinder the separation of fragments even with preactivation, which has become particularly problematic for the study of large macromolecular proteins and protein complexes. Here, we describe the capabilities of another activation method, 30 eV electron ionization dissociation (EID), for the top-down MS characterization of native protein-ligand and protein-protein complexes. Rich structural information that cannot be delivered by ECD can be generated by EID. EID allowed for the comparison of the gas-phase and the solution-phase structural stability and unfolding process of human carbonic anhydrase I (HCA-I). In addition, the EID fragmentation patterns reflect the structural similarities and differences among apo-, Zn-, and Cu,Zn-superoxide dismutase (SOD1) dimers. In particular, the structural changes due to Cu-binding and a point mutation (G41D) were revealed by EID-MS. The performance of EID was also compared to that of 193 nm ultraviolet photodissociation (UVPD), which allowed us to explore their qualitative similarities and differences as potential valuable tools for the MS study of native proteins and protein complexes.
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Affiliation(s)
- Huilin Li
- Department of Biological Chemistry, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States
| | - Yuewei Sheng
- Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California , Los Angeles, California 90095, United States
| | - William McGee
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Michael Cammarata
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Dustin Holden
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California , Los Angeles, California 90095, United States
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54
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Holden DD, Brodbelt JS. Improving Performance Metrics of Ultraviolet Photodissociation Mass Spectrometry by Selective Precursor Ejection. Anal Chem 2016; 89:837-846. [PMID: 28105830 DOI: 10.1021/acs.analchem.6b03777] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Confident protein identifications derived from high-throughput bottom-up and top-down proteomics workflows depend on acquisition of thousands of tandem mass spectrometry (MS/MS) spectra with adequate signal-to-noise and accurate mass assignments of the fragment ions. Ultraviolet photodissociation (UVPD) using 193 nm photons has proven to be well-suited for activation and fragmentation of peptides and proteins in ion trap mass spectrometers, but the spectral signal-to-noise ratio (S/N) is typically lower than that obtained from collisional activation methods. The lower S/N is attributed to the dispersion of ion current among numerous fragment ion channels (a,b,c,x,y,z ions). In addition, frequently UVPD is performed such that a relatively large population of precursor ions remains undissociated after the UV photoactivation period in order to prevent overdissociation into small uninformative or internal fragment ions. Here we report a method to improve spectral S/N and increase the accuracy of mass assignments of UVPD mass spectra via resonance ejection of undissociated precursor ions after photoactivation. This strategy, termed precursor ejection UVPD or PE-UVPD, allows the ion trap to be filled with more ions prior to UVPD while at the same time alleviating the space charge problems that would otherwise contribute to the skewing of mass assignments and reduction of S/N. Here we report the performance gains by implementation of PE-UVPD for peptide analysis in an ion trap mass spectrometer.
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Affiliation(s)
- Dustin D Holden
- 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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55
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Yan J, Zhou M, Gilbert JD, Wolff JJ, Somogyi Á, Pedder RE, Quintyn RS, Morrison LJ, Easterling ML, Paša-Tolić L, Wysocki VH. Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Anal Chem 2016; 89:895-901. [DOI: 10.1021/acs.analchem.6b03986] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jing Yan
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joshua D. Gilbert
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Árpád Somogyi
- OSU
Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Royston S. Quintyn
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lindsay J. Morrison
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Ljiljana Paša-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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