1
|
Dunham SD, Brodbelt JS. Enhancing Top-Down Analysis of Proteins by Combining Ultraviolet Photodissociation (UVPD), Proton-Transfer Charge Reduction (PTCR), and Gas-Phase Fractionation to Alleviate the Impact of Nondissociated Precursor Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:255-265. [PMID: 38150423 DOI: 10.1021/jasms.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Recent advances in top-down mass spectrometry strategies continue to improve the analysis of intact proteins. 193 nm ultraviolet photodissociation (UVPD) is one method well-suited for top-down analysis. UVPD is often performed using relatively low photon flux in order to limit multiple-generation dissociation of fragment ions and maximize sequence coverage. Consequently, a large portion of the precursor ion survives the UVPD process, dominates the spectrum, and may impede identification of fragment ions. Here, we explore the isolation of subpopulations of fragment ions lower and higher than the precursor ion after UVPD as a means to eliminate the impact of the surviving precursor ion on the detection of low abundance fragment ions. This gas-phase fractionation method improved sequence coverage harvested from fragment ions found in the m/z regions lower and higher than the precursor by an average factor of 1.3 and 2.3, respectively. Combining this gas-phase fractionation method with proton transfer charge reduction (PTCR) further increased the sequence coverage obtained from these m/z regions by another factor of 1.3 and 1.4, respectively. Implementing a post-UVPD fractionation + PTCR strategy with six fractionation events resulted in a sequence coverage of 75% for enolase, the highest reported for 193 nm UVPD.
Collapse
Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
| |
Collapse
|
2
|
Bashyal A, Dunham SD, Brodbelt JS. Characterization of Unbranched Ubiquitin Tetramers by Combining Ultraviolet Photodissociation with Proton Transfer Charge Reduction Reactions. Anal Chem 2023; 95:14001-14008. [PMID: 37677053 DOI: 10.1021/acs.analchem.3c02618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Polyubiquitination is an important post-translational modification (PTM) that regulates various biological functions. The linkage sites and topologies of polyubiquitination chains are important factors in determining the fate of polyubiquitinated proteins. Characterization of polyubiquitin chains is the first step in understanding the biological functions of protein ubiquitination, but it is challenging owing to the repeating nature of the ubiquitin chains and the difficulty in deciphering linkage positions. Here, we combine ultraviolet photodissociation (UVPD) mass spectrometry and gas-phase proton transfer charge reduction (PTCR) to facilitate the assignment of product ions generated from Lys6-, Lys11-, Lys29-, Lys33-, Lys48-, and Lys63-linked ubiquitin tetramers. UVPD results in extensive fragmentation of intact proteins in a manner that allows the localization of PTMs. However, UVPD mass spectra of large proteins (>30 kDa) are often congested due to the overlapping isotopic distribution of highly charged fragment ions. UVPD + PTCR improved the identification of PTM-containing fragment ions, allowing the localization of linkage sites in all six tetramers analyzed. UVPD + PTCR also increased the sequence coverage obtained from the PTM-containing fragment ions in each of the four chains of each tetramer by 7 to 44% when compared to UVPD alone.
Collapse
Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sean D Dunham
- 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
| |
Collapse
|
3
|
Zemaitis KJ, Zhou M, Kew W, Paša-Tolić L. 193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:328-332. [PMID: 36622763 PMCID: PMC10084724 DOI: 10.1021/jasms.2c00302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
MALDI imaging allows for the near-cellular profiling of proteoforms directly from microbial, plant, and mammalian samples. Despite detecting hundreds of proteoforms, identification of unknowns with only intact mass information remains a distinct challenge, even with high mass resolving power and mass accuracy. To this end, many supplementary methods have been used to create experimental databases for accurate mass matching, including bulk or spatially resolved bottom-up and/or top-down proteomics. Herein, we describe the application of 193 nm ultraviolet photodissociation (UVPD) for fragmentation of quadrupole isolated singly charged ubiquitin (m/z 8565) by MALDI-UVPD on a UHMR HF Orbitrap. This platform permitted the high-resolution accurate mass measurement of not just terminal fragments but also large internal fragments. The outlined workflow demonstrates the feasibility of top-down analyses of isolated MALDI protein ions and the potential toward more comprehensive characterization of proteoforms in MALDI imaging applications.
Collapse
Affiliation(s)
- Kevin J Zemaitis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - William Kew
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| |
Collapse
|
4
|
Lanzillotti M, Brodbelt JS. Comparison of Top-Down Protein Fragmentation Induced by 213 and 193 nm UVPD. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:279-285. [PMID: 36594540 DOI: 10.1021/jasms.2c00288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The growing interest in advancing tandem mass spectrometry strategies for top-down proteomics has motivated efforts to optimize ion activation strategies for intact proteins, including the comparison of 193 and 213 nm wavelengths for ultraviolet photodissociation (UVPD). The present study focuses on the performance and outcomes of UVPD for five proteins, ubiquitin, cytochrome C, frataxin, myoglobin, and carbonic anhydrase, with an emphasis on evaluating the similarities and differences in fragmentation promoted by UVPD using 193 nm versus 213 nm photons. Mass spectra were collected as a function of the number of laser pulses, and precursor depletion levels were monitored and controlled to provide consistent energy deposition between 213 and 193 nm UVPD. Fragment ions were confirmed on the basis of their isotopic distributions in m/z space to preserve both charge state and abundance information and were classified on the basis of ion type and frequency. A large portion of the total fragment ion abundance was attributable to preferential cleavages, particularly ones adjacent to proline residues. These cleavages were examined on the basis of the backbone site and abundances, revealing that a and y-2 ions N-terminal to proline residues appeared at disproportionately high abundances in 213 nm UVPD spectra as compared to 193 nm UVPD spectra, highlighting one notable difference in the top-down spectra. We theorize that these fragments are formed more efficiently in 213 nm UVPD than in 193 nm UVPD due to increased absorption of 213 nm photons at the proline amide bond.
Collapse
Affiliation(s)
- Michael Lanzillotti
- 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
| |
Collapse
|
5
|
Dunham SD, Wei B, Lantz C, Loo JA, Brodbelt JS. Impact of Internal Fragments on Top-Down Analysis of Intact Proteins by 193 nm UVPD. J Proteome Res 2023; 22:170-181. [PMID: 36503236 DOI: 10.1021/acs.jproteome.2c00583] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
193 nm ultraviolet photodissociation (UVPD) allows high sequence coverage to be obtained for intact proteins using terminal fragments alone. However, internal fragments, those that contain neither N- nor C- terminus, are typically ignored, neglecting their potential to bolster characterization of intact proteins. Here, we explore internal fragments generated by 193 nm UVPD for proteins ranging in size from 17-47 kDa and using the ClipsMS algorithm to facilitate searches for internal fragments. Internal fragments were only retained if identified in multiple replicates in order to reduce spurious assignments and to explore the reproducibility of internal fragments generated by UVPD. Inclusion of internal fragment improved sequence coverage by an average of 18% and 32% for UVPD and HCD, respectively, across all proteins and charge states studied. However, only an average of 18% of UVPD internal fragments were identified in two out of three replicates relative to the average number identified across all replicates for all proteins studied. Conversely, for HCD, an average of 63% of internal fragments were retained across replicates. These trends reflect an increased risk of false-positive identifications and a need for caution when considering internal fragments for UVPD. Additionally, proton-transfer charge reduction (PTCR) reactions were performed following UVPD or HCD to assess the impact on internal fragment identifications, allowing up to 20% more fragment ions to be retained across multiple replicates. At this time, it is difficult to recommend the inclusion of the internal fragment when searching UVPD spectra without further work to develop strategies for reducing the possibilities of false-positive identifications. All mass spectra are available in the public repository jPOST with the accession number JPST001885.
Collapse
Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Benqian Wei
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Carter Lantz
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
6
|
Shields SWJ, Sanders JD, Brodbelt JS. Enhancing the Signal-to-Noise of Diagnostic Fragment Ions of Unsaturated Glycerophospholipids via Precursor Exclusion Ultraviolet Photodissociation Mass Spectrometry (PEx-UVPD-MS). Anal Chem 2022; 94:11352-11359. [PMID: 35917227 PMCID: PMC9484799 DOI: 10.1021/acs.analchem.2c02128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding and elucidating the diverse structures and functions of lipids has motivated the development of many innovative tandem mass spectrometry (MS/MS) strategies. Higher-energy activation methods, such as ultraviolet photodissociation (UVPD), generate unique fragment ions from glycerophospholipids that can be used to perform in-depth structural analysis and facilitate the deconvolution of isomeric lipid structures in complex samples. Although detailed characterization is central to the correlation of lipid structure to biological function, it is often impeded by the lack of sufficient instrument sensitivity for highly bioactive but low-abundance phospholipids. Here, we present precursor exclusion (PEx) UVPD, a simple yet powerful technique to enhance the signal-to-noise (S/N) of informative low-abundance fragment ions produced from UVPD of glycerophospholipids. Through the exclusion of the large population of undissociated precursor ions with an MS3 strategy, the S/N of diagnostic fragment ions from PC 18:0/18:2(9Z, 12Z) increased up to an average of 13x for PEx-UVPD compared to UVPD alone. These enhancements were extended to complex mixtures of lipids from bovine liver extract to confidently identify 35 unique structures using liquid chromatography PEx-UVPD. This methodology has the potential to advance lipidomics research by offering deeper structure elucidation and confident identification of biologically active lipids.
Collapse
Affiliation(s)
- Samuel W J Shields
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Sanders
- 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
| |
Collapse
|
7
|
Dunham SD, Sanders JD, Holden DD, Brodbelt JS. Improving the Center Section Sequence Coverage of Large Proteins Using Stepped-Fragment Ion Protection Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:446-456. [PMID: 35119856 DOI: 10.1021/jasms.1c00296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry has gained attention in recent years for its ability to provide high sequence coverage of intact proteins. However, secondary dissociation of fragment ions, in which fragment ions subjected to multiple laser pulses decompose into small products, is a common phenomenon during UVPD that contributes to limited coverage in the midsection of protein sequences. To counter secondary dissociation, a method involving the application of notched waveforms to modulate the trajectories of fragment ions away from the laser beam, termed fragment ion protection (FIP), was previously developed to reduce the probability of secondary dissociation. This, in turn, increased the number of identified large fragment ions. In the present study, FIP was applied to UVPD of large proteins ranging in size from 29 to 55 kDa, enhancing the abundances of large fragment ions. A stepped-FIP strategy was implemented in which UVPD mass spectra were collected using multiple different amplitudes of the FIP waveforms and then the results from the mass spectra were combined. By using stepped-FIP, the number of fragment ions in the midsections of the sequences increased for all proteins. For example, whereas no fragment ions were identified in the middle section of the sequence for glutamate dehydrogenase (55 kDa, 55+ charge state), 10 sequence ions were identified by using UVPD-FIP.
Collapse
Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Dustin D Holden
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| |
Collapse
|
8
|
Macias LA, Sipe SN, Santos IC, Bashyal A, Mehaffey MR, Brodbelt JS. Influence of Primary Structure on Fragmentation of Native-Like Proteins by Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2860-2873. [PMID: 34714071 PMCID: PMC8639798 DOI: 10.1021/jasms.1c00269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Analysis of native-like protein structures in the gas phase via native mass spectrometry and auxiliary techniques has become a powerful tool for structural biology applications. In combination with ultraviolet photodissociation (UVPD), native top-down mass spectrometry informs backbone flexibility, topology, hydrogen bonding networks, and conformational changes in protein structure. Although it is known that the primary structure affects dissociation of peptides and proteins in the gas phase, its effect on the types and locations of backbone cleavages promoted by UVPD and concomitant influence on structural characterization of native-like proteins is not well understood. Here, trends in the fragmentation of native-like proteins were evaluated by tracking the propensity of 10 fragment types (a, a+1, b, c, x, x+1, y, y-1, Y, and z) in relation to primary structure in a native-top down UVPD data set encompassing >9600 fragment ions. Differing fragmentation trends are reported for the production of distinct fragment types, attributed to a combination of both direct dissociation pathways from excited electronic states and those surmised to involve intramolecular vibrational energy redistribution after internal conversion. The latter pathways were systematically evaluated to evince the role of proton mobility in the generation of "CID-like" fragments through UVPD, providing pertinent insight into the characterization of native-like proteins. Fragmentation trends presented here are envisioned to enhance analysis of the protein higher-order structure or augment scoring algorithms in the high-throughput analysis of intact proteins.
Collapse
Affiliation(s)
- Luis A Macias
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sarah N Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês C Santos
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - M Rachel Mehaffey
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
9
|
Duselis EM, Panepinto MC, Syka JEP, Mullen C, D'Ippolito RA, English AM, Ugrin SA, Shabanowitz J, Hunt DF. Improved Sequence Analysis of Intact Proteins by Parallel Ion Parking during Electron Transfer Dissociation. Anal Chem 2021; 93:15728-15735. [PMID: 34788003 DOI: 10.1021/acs.analchem.1c03652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron transfer dissociation (ETD) is an analytically useful tool for primary structure interrogation of intact proteins, but its utility is limited by higher-order reactions with the products. To inhibit these higher-order reactions, first-generation fragment ions are kinetically excited by applying an experimentally tailored parallel ion parking waveform during ETD (ETD-PIP). In combination with subsequent ion/ion proton transfer reactions, precursor-to-product conversion was maximized as evidenced by the consumption of more than 90% of the 21 kDa Protein G precursor to form ETD product ions. The employment of ETD-PIP increased sequence coverage to 90% from 80% with standard ETD. Additionally, the inhibition of sequential electron transfers was reflected in the high number of complementary ion pairs from ETD-PIP (90%) compared to standard ETD (39%).
Collapse
Affiliation(s)
- Elizabeth M Duselis
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Maria C Panepinto
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - John E P Syka
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Robert A D'Ippolito
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - A Michelle English
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Scott A Ugrin
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Pathology, University of Virginia, Charlottesville, Virginia 22903, United States
| |
Collapse
|
10
|
Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
Collapse
Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
11
|
Wu Z, Jin Y, Chen B, Gugger MK, Wilkinson-Johnson CL, Tiambeng TN, Jin S, Ge Y. Comprehensive Characterization of the Recombinant Catalytic Subunit of cAMP-Dependent Protein Kinase by Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2561-2570. [PMID: 31792770 PMCID: PMC6922056 DOI: 10.1007/s13361-019-02341-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 05/22/2023]
Abstract
Reversible phosphorylation plays critical roles in cell growth, division, and signal transduction. Kinases which catalyze the transfer of γ-phosphate groups of nucleotide triphosphates to their substrates are central to the regulation of protein phosphorylation and are therefore important therapeutic targets. Top-down mass spectrometry (MS) presents unique opportunities to study protein kinases owing to its capabilities in comprehensive characterization of proteoforms that arise from alternative splicing, sequence variations, and post-translational modifications. Here, for the first time, we developed a top-down MS method to characterize the catalytic subunit (C-subunit) of an important kinase, cAMP-dependent protein kinase (PKA). The recombinant PKA C-subunit was expressed in Escherichia coli and successfully purified via his-tag affinity purification. By intact mass analysis with high resolution and high accuracy, four different proteoforms of the affinity-purified PKA C-subunit were detected, and the most abundant proteoform was found containing seven phosphorylations with the removal of N-terminal methionine. Subsequently, the seven phosphorylation sites of the most abundant PKA C-subunit proteoform were characterized simultaneously using tandem MS methods. Four sites were unambiguously identified as Ser10, Ser11, Ser18, and Ser30, and the remaining phosphorylation sites were localized to Ser2/Ser3, Ser358/Thr368, and Thr[215-224]Tyr in the PKA C-subunit sequence with a 20mer 6xHis-tag added at the N-terminus. Interestingly, four of these seven phosphorylation sites were located at the 6xHis-tag. Furthermore, we have performed dephosphorylation reaction by Lambda protein phosphatase and showed that all phosphorylations of the recombinant PKA C-subunit phosphoproteoforms were removed by this phosphatase.
Collapse
Affiliation(s)
- Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Morgan K Gugger
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Timothy N Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705, USA.
| |
Collapse
|
12
|
Sanders JD, Mullen C, Watts E, Holden DD, Syka JEP, Schwartz JC, Brodbelt JS. Enhanced Sequence Coverage of Large Proteins by Combining Ultraviolet Photodissociation with Proton Transfer Reactions. Anal Chem 2019; 92:1041-1049. [DOI: 10.1021/acs.analchem.9b04026] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher Mullen
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dustin D. Holden
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - John E. P. Syka
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jae C. Schwartz
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
13
|
Ugrin SA, English AM, Syka JEP, Bai DL, Anderson LC, Shabanowitz J, Hunt DF. Ion-Ion Proton Transfer and Parallel Ion Parking for the Analysis of Mixtures of Intact Proteins on a Modified Orbitrap Mass Analyzer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2163-2173. [PMID: 31392699 PMCID: PMC6805958 DOI: 10.1007/s13361-019-02290-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 05/09/2023]
Abstract
We have enabled parallel ion parking on a modified Orbitrap Elite™ as a way to control ion-ion proton transfer reactions via selective activation of a range of ions. The result is the concentration of the majority of ion current from multiple charge states of each precursor proteoform into a single charge state, maximizing signal intensity and increasing effective sensitivity compared to conventional MS1 spectra. These techniques were applied in an on-line HPLC, data-dependent MS/MS analysis of intact E. coli ribosomal proteins with HCD fragmentation. With one injection, all but two ribosomal proteins were selected for fragmentation and subsequently identified. The techniques described facilitate rapid identification of intact proteins in complex mixtures and an enhanced ability to observe proteins of low abundance.
Collapse
Affiliation(s)
- Scott A Ugrin
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - A Michelle English
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | | | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.
- Department of Pathology, University of Virginia, Charlottesville, VA, 22908, USA.
| |
Collapse
|
14
|
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: 123] [Impact Index Per Article: 24.6] [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, Wisconsin 53706, United States
| | - Robert J. Millikin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rachel M. Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lissa C. Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Ryan T. Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology and Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry and Molecular Biosciences and the Division of Hematology-Oncology, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard D. LeDuc
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University, Indianapolis, Indiana 46202, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Samuel H. Payne
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Paul M. Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Michael R. Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|