1
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Naryzhny S. Puzzle of Proteoform Variety-Where Is a Key? Proteomes 2024; 12:15. [PMID: 38804277 PMCID: PMC11130821 DOI: 10.3390/proteomes12020015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different.
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Affiliation(s)
- Stanislav Naryzhny
- B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Leningrad Region, Gatchina 188300, Russia
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2
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Cramer DAT, Yin V, Caval T, Franc V, Yu D, Wu G, Lloyd G, Langendorf C, Whisstock JC, Law RHP, Heck AJR. Proteoform-Resolved Profiling of Plasminogen Activation Reveals Novel Abundant Phosphorylation Site and Primary N-Terminal Cleavage Site. Mol Cell Proteomics 2024; 23:100696. [PMID: 38101751 PMCID: PMC10825491 DOI: 10.1016/j.mcpro.2023.100696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Plasminogen (Plg), the zymogen of plasmin (Plm), is a glycoprotein involved in fibrinolysis and a wide variety of other physiological processes. Plg dysregulation has been implicated in a range of diseases. Classically, human Plg is categorized into two types, supposedly having different functional features, based on the presence (type I) or absence (type II) of a single N-linked glycan. Using high-resolution native mass spectrometry, we uncovered that the proteoform profiles of human Plg (and Plm) are substantially more extensive than this simple binary classification. In samples derived from human plasma, we identified up to 14 distinct proteoforms of Plg, including a novel highly stoichiometric phosphorylation site at Ser339. To elucidate the potential functional effects of these post-translational modifications, we performed proteoform-resolved kinetic analyses of the Plg-to-Plm conversion using several canonical activators. This conversion is thought to involve at least two independent cleavage events: one to remove the N-terminal peptide and another to release the active catalytic site. Our analyses reveal that these processes are not independent but are instead tightly regulated and occur in a step-wise manner. Notably, N-terminal cleavage at the canonical site (Lys77) does not occur directly from intact Plg. Instead, an activation intermediate corresponding to cleavage at Arg68 is initially produced, which only then is further processed to the canonical Lys77 product. Based on our results, we propose a refined categorization for human Plg proteoforms. In addition, we reveal that the proteoform profile of human Plg is more extensive than that of rat Plg, which lacks, for instance, the here-described phosphorylation at Ser339.
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Affiliation(s)
- Dario A T Cramer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Centre, University of Utrecht, Utrecht, The Netherlands
| | - Victor Yin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Centre, University of Utrecht, Utrecht, The Netherlands
| | - Tomislav Caval
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Centre, University of Utrecht, Utrecht, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Centre, University of Utrecht, Utrecht, The Netherlands
| | - Dingyi Yu
- Mass Spectrometry Facility, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Guojie Wu
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Gordon Lloyd
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Christopher Langendorf
- Mass Spectrometry Facility, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Ruby H P Law
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Victoria, Australia.
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Centre, University of Utrecht, Utrecht, The Netherlands.
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3
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Casella C, Kiles F, Urquhart C, Michaud DS, Kirwa K, Corlin L. Methylomic, Proteomic, and Metabolomic Correlates of Traffic-Related Air Pollution in the Context of Cardiorespiratory Health: A Systematic Review, Pathway Analysis, and Network Analysis. TOXICS 2023; 11:1014. [PMID: 38133415 PMCID: PMC10748071 DOI: 10.3390/toxics11121014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/18/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
A growing body of literature has attempted to characterize how traffic-related air pollution (TRAP) affects molecular and subclinical biological processes in ways that could lead to cardiorespiratory disease. To provide a streamlined synthesis of what is known about the multiple mechanisms through which TRAP could lead to cardiorespiratory pathology, we conducted a systematic review of the epidemiological literature relating TRAP exposure to methylomic, proteomic, and metabolomic biomarkers in adult populations. Using the 139 papers that met our inclusion criteria, we identified the omic biomarkers significantly associated with short- or long-term TRAP and used these biomarkers to conduct pathway and network analyses. We considered the evidence for TRAP-related associations with biological pathways involving lipid metabolism, cellular energy production, amino acid metabolism, inflammation and immunity, coagulation, endothelial function, and oxidative stress. Our analysis suggests that an integrated multi-omics approach may provide critical new insights into the ways TRAP could lead to adverse clinical outcomes. We advocate for efforts to build a more unified approach for characterizing the dynamic and complex biological processes linking TRAP exposure and subclinical and clinical disease and highlight contemporary challenges and opportunities associated with such efforts.
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Affiliation(s)
- Cameron Casella
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
| | - Frances Kiles
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
| | - Catherine Urquhart
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
| | - Dominique S. Michaud
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
| | - Kipruto Kirwa
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
- Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
| | - Laura Corlin
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
- Department of Civil and Environmental Engineering, Tufts University School of Engineering, Medford, MA 02155, USA
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4
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Po A, Eyers CE. Top-Down Proteomics and the Challenges of True Proteoform Characterization. J Proteome Res 2023; 22:3663-3675. [PMID: 37937372 PMCID: PMC10696603 DOI: 10.1021/acs.jproteome.3c00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Top-down proteomics (TDP) aims to identify and profile intact protein forms (proteoforms) extracted from biological samples. True proteoform characterization requires that both the base protein sequence be defined and any mass shifts identified, ideally localizing their positions within the protein sequence. Being able to fully elucidate proteoform profiles lends insight into characterizing proteoform-unique roles, and is a crucial aspect of defining protein structure-function relationships and the specific roles of different (combinations of) protein modifications. However, defining and pinpointing protein post-translational modifications (PTMs) on intact proteins remains a challenge. Characterization of (heavily) modified proteins (>∼30 kDa) remains problematic, especially when they exist in a population of similarly modified, or kindred, proteoforms. This issue is compounded as the number of modifications increases, and thus the number of theoretical combinations. Here, we present our perspective on the challenges of analyzing kindred proteoform populations, focusing on annotation of protein modifications on an "average" protein. Furthermore, we discuss the technical requirements to obtain high quality fragmentation spectral data to robustly define site-specific PTMs, and the fact that this is tempered by the time requirements necessary to separate proteoforms in advance of mass spectrometry analysis.
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Affiliation(s)
- Allen Po
- Centre
for Proteome Research, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, Faculty of Health & Life
Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, Faculty of Health & Life
Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
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5
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Kitamura N, Galligan JJ. A global view of the human post-translational modification landscape. Biochem J 2023; 480:1241-1265. [PMID: 37610048 PMCID: PMC10586784 DOI: 10.1042/bcj20220251] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Post-translational modifications (PTMs) provide a rapid response to stimuli, finely tuning metabolism and gene expression and maintain homeostasis. Advances in mass spectrometry over the past two decades have significantly expanded the list of known PTMs in biology and as instrumentation continues to improve, this list will surely grow. While many PTMs have been studied in detail (e.g. phosphorylation, acetylation), the vast majority lack defined mechanisms for their regulation and impact on cell fate. In this review, we will highlight the field of PTM research as it currently stands, discussing the mechanisms that dictate site specificity, analytical methods for their detection and study, and the chemical tools that can be leveraged to define PTM regulation. In addition, we will highlight the approaches needed to discover and validate novel PTMs. Lastly, this review will provide a starting point for those interested in PTM biology, providing a comprehensive list of PTMs and what is known regarding their regulation and metabolic origins.
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Affiliation(s)
- Naoya Kitamura
- Department of Pharmacology and College of Pharmacy, University of Arizona, Tucson, Arizona 85721, U.S.A
| | - James J. Galligan
- Department of Pharmacology and College of Pharmacy, University of Arizona, Tucson, Arizona 85721, U.S.A
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6
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Guo Y, Cupp‐Sutton KA, Zhao Z, Anjum S, Wu S. Multidimensional Separations in Top-Down Proteomics. ANALYTICAL SCIENCE ADVANCES 2023; 4:181-203. [PMID: 38188188 PMCID: PMC10769458 DOI: 10.1002/ansa.202300016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/21/2023] [Accepted: 05/01/2023] [Indexed: 01/09/2024]
Abstract
Top-down proteomics (TDP) identifies, quantifies, and characterizes proteins at the intact proteoform level in complex biological samples to understand proteoform function and cellular mechanisms. However, analyzing complex biological samples using TDP is still challenging due to high sample complexity and wide dynamic range. High-resolution separation methods are often applied prior to mass spectrometry (MS) analysis to decrease sample complexity and increase proteomics throughput. These separation methods, however, may not be efficient enough to characterize low abundance intact proteins in complex samples. As such, multidimensional separation techniques (combination of two or more separation methods with high orthogonality) have been developed and applied that demonstrate improved separation resolution and more comprehensive identification in TDP. A suite of multidimensional separation methods that couple various types of liquid chromatography (LC), capillary electrophoresis (CE), and/or gel electrophoresis-based separation approaches have been developed and applied in TDP to analyze complex biological samples. Here, we reviewed multidimensional separation strategies employed for TDP, summarized current applications, and discussed the gaps that may be addressed in the future.
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Affiliation(s)
- Yanting Guo
- Department of Chemistry and BiochemistryUniversity of OklahomaOklahomaNormanUSA
| | | | - Zhitao Zhao
- Department of Chemistry and BiochemistryUniversity of OklahomaOklahomaNormanUSA
| | - Samin Anjum
- Department of Chemistry and BiochemistryUniversity of OklahomaOklahomaNormanUSA
| | - Si Wu
- Department of Chemistry and BiochemistryUniversity of OklahomaOklahomaNormanUSA
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7
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Self W, Awwad K, Savaryn JP, Schulz M. An immuno-enrichment free, validated quantification of tau protein in human CSF by LC-MS/MS. PLoS One 2022; 17:e0269157. [PMID: 35653415 PMCID: PMC9162344 DOI: 10.1371/journal.pone.0269157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Tau protein is a key target of interest in developing therapeutics for neurodegenerative diseases. Here, we sought to develop a method that quantifies extracellular tau protein concentrations in human cerebrospinal fluid (CSF) without antibody-based enrichment strategies. We demonstrate that the fit-for-purpose validated method in Alzheimer's Disease CSF is limited to quasi quantitative measures of tau surrogate peptides. We also provide evidence that CSF total Tau measures by LC-MS are feasible in the presence of monoclonal therapeutic antibodies in human CSF. Our Tau LC-MS/MS method is a translational bioanalytical tool for assaying target engagement and pharmacodynamics for anti-tau antibody drug development campaigns.
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Affiliation(s)
- Wade Self
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Khader Awwad
- DMPK-BA, Abbvie Germany GmbH Co KG, Ludwigshafen, Germany
| | - John Paul Savaryn
- DMPK-BA, Abbvie Inc, North Chicago, Illinois, United States of America
| | - Michael Schulz
- DMPK-BA, Abbvie Germany GmbH Co KG, Ludwigshafen, Germany
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8
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Kemper EK, Zhang Y, Dix MM, Cravatt BF. Global profiling of phosphorylation-dependent changes in cysteine reactivity. Nat Methods 2022; 19:341-352. [PMID: 35228727 PMCID: PMC8920781 DOI: 10.1038/s41592-022-01398-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/14/2022] [Indexed: 01/11/2023]
Abstract
Proteomics has revealed that the ~20,000 human genes engender a far greater number of proteins, or proteoforms, that are diversified in large part by post-translational modifications (PTMs). How such PTMs affect protein structure and function is an active area of research but remains technically challenging to assess on a proteome-wide scale. Here, we describe a chemical proteomic method to quantitatively relate serine/threonine phosphorylation to changes in the reactivity of cysteine residues, a parameter that can affect the potential for cysteines to be post-translationally modified or engaged by covalent drugs. Leveraging the extensive high-stoichiometry phosphorylation occurring in mitotic cells, we discover numerous cysteines that exhibit phosphorylation-dependent changes in reactivity on diverse proteins enriched in cell cycle regulatory pathways. The discovery of bidirectional changes in cysteine reactivity often occurring in proximity to serine/threonine phosphorylation events points to the broad impact of phosphorylation on the chemical reactivity of proteins and the future potential to create small-molecule probes that differentially target proteoforms with PTMs.
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Affiliation(s)
- Esther K Kemper
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Yuanjin Zhang
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Melissa M Dix
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin F Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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9
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Smith TG, Uzozie AC, Chen S, Lange PF. Robust unsupervised deconvolution of linear motifs characterizes 68 protein modifications at proteome scale. Sci Rep 2021; 11:22490. [PMID: 34795380 PMCID: PMC8602328 DOI: 10.1038/s41598-021-01971-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022] Open
Abstract
The local sequence context is the most fundamental feature determining the post-translational modification (PTM) of proteins. Recent technological improvements allow for the detection of new and less prevalent modifications. We found that established state-of-the-art algorithms for the detection of PTM motifs in complex datasets failed to keep up with this technological development and are no longer robust. To overcome this limitation, we developed RoLiM, a new linear motif deconvolution algorithm and webserver, that enables robust and unbiased identification of local amino acid sequence determinants in complex biological systems demonstrated here by the analysis of 68 modifications found across 30 tissues in the human draft proteome map. Furthermore, RoLiM analysis of a large-scale phosphorylation dataset comprising 30 kinase inhibitors of 10 protein kinases in the EGF signalling pathway identified prospective substrate motifs for PI3K and EGFR.
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Affiliation(s)
- Theodore G Smith
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Anuli C Uzozie
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Siyuan Chen
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Philipp F Lange
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada. .,Department of Computer Science, University of British Columbia, Vancouver, BC, Canada. .,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
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10
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Zhang Y, Wright MA, Saar KL, Challa P, Morgunov AS, Peter QAE, Devenish S, Dobson CM, Knowles TPJ. Machine learning-aided protein identification from multidimensional signatures. LAB ON A CHIP 2021; 21:2922-2931. [PMID: 34109955 PMCID: PMC8314522 DOI: 10.1039/d0lc01148g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
The ability to determine the identity of specific proteins is a critical challenge in many areas of cellular and molecular biology, and in medical diagnostics. Here, we present a macine learning aided microfluidic protein characterisation strategy that within a few minutes generates a three-dimensional fingerprint of a protein sample indicative of its amino acid composition and size and, thereby, creates a unique signature for the protein. By acquiring such multidimensional fingerprints for a set of ten proteins and using machine learning approaches to classify the fingerprints, we demonstrate that this strategy allows proteins to be classified at a high accuracy, even though classification using a single dimension is not possible. Moreover, we show that the acquired fingerprints correlate with the amino acid content of the samples, which makes it is possible to identify proteins directly from their sequence without requiring any prior knowledge about the fingerprints. These findings suggest that such a multidimensional profiling strategy can lead to the development of a novel method for protein identification in a microfluidic format.
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Affiliation(s)
- Yuewen Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Maya A Wright
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Kadi L Saar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, UK
| | - Pavankumar Challa
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Alexey S Morgunov
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Fluidic Analytics Ltd., Cambridge, UK
| | - Quentin A E Peter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | | | - Christopher M Dobson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, UK
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11
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Fulcher JM, Makaju A, Moore RJ, Zhou M, Bennett DA, De Jager PL, Qian WJ, Paša-Tolić L, Petyuk VA. Enhancing Top-Down Proteomics of Brain Tissue with FAIMS. J Proteome Res 2021; 20:2780-2795. [PMID: 33856812 PMCID: PMC8672206 DOI: 10.1021/acs.jproteome.1c00049] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Proteomic investigations of Alzheimer's and Parkinson's disease have provided valuable insights into neurodegenerative disorders. Thus far, these investigations have largely been restricted to bottom-up approaches, hindering the degree to which one can characterize a protein's "intact" state. Top-down proteomics (TDP) overcomes this limitation; however, it is typically limited to observing only the most abundant proteoforms and of a relatively small size. Therefore, fractionation techniques are commonly used to reduce sample complexity. Here, we investigate gas-phase fractionation through high-field asymmetric waveform ion mobility spectrometry (FAIMS) within TDP. Utilizing a high complexity sample derived from Alzheimer's disease (AD) brain tissue, we describe how the addition of FAIMS to TDP can robustly improve the depth of proteome coverage. For example, implementation of FAIMS with external compensation voltage (CV) stepping at -50, -40, and -30 CV could more than double the mean number of non-redundant proteoforms, genes, and proteome sequence coverage compared to without FAIMS. We also found that FAIMS can influence the transmission of proteoforms and their charge envelopes based on their size. Importantly, FAIMS enabled the identification of intact amyloid beta (Aβ) proteoforms, including the aggregation-prone Aβ1-42 variant which is strongly linked to AD. Raw data and associated files have been deposited to the ProteomeXchange Consortium via the MassIVE data repository with data set identifier PXD023607.
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Affiliation(s)
- James M Fulcher
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aman Makaju
- Life Sciences Mass Spectrometry Unit, Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Philip L De Jager
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Medical Center, New York, New York 10032, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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12
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021; 60:14738-14749. [DOI: 10.1002/anie.202013462] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
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13
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
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14
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Harrington CR, Yang GY, Levitsky J. Advances in Rejection Management: Prevention and Treatment. Clin Liver Dis 2021; 25:53-72. [PMID: 33978583 DOI: 10.1016/j.cld.2020.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Extended survival of liver transplant recipients has brought rejection management to the forefront of liver transplant research. This article discusses T-cell-mediated rejection, antibody-mediated rejection, and chronic rejection. We focus on the prevention and then discuss treatment options. Future directions of rejection management include biomarkers of rejection, which may allow for monitoring of patients who are considered high risk for rejection and detection of rejection before there is any clinical evidence to improve graft and patient survival. With improved graft life and survival of liver transplant recipients, the new frontier of rejection management focuses on immunosuppression minimization, withdrawal, and personalization.
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Affiliation(s)
- Claire R Harrington
- Department of Medicine, Northwestern University Feinberg School of Medicine, 676 North St. Clair Street, Suite 2330, Chicago, IL 60611, USA
| | - Guang-Yu Yang
- Department of Pathology, Northwestern University Feinberg School of Medicine, 251 E Huron St. Chicago, IL 60611, USA
| | - Josh Levitsky
- Division of Gastroenterology and Hepatology, Northwestern University Feinberg School of Medicine, 676 North St. Clair Street, Suite 1400, Chicago, IL 60611, USA; Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, 676 North St. Clair Street, Suite 1900, Chicago, IL 60611, USA.
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15
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Corbett JR, Robinson DE, Patrie SM. Robustness and Ruggedness of Isoelectric Focusing and Superficially Porous Liquid Chromatography with Fourier Transform Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:346-354. [PMID: 33274937 PMCID: PMC10476448 DOI: 10.1021/jasms.0c00355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An investigation of a multidimensional proteomics workflow composed of off-gel isoelectric focusing (IEF) and superficially porous liquid chromatography (SPLC) with Fourier transform mass spectrometry (FTMS) was completed in order to assess various figures of merit associated with intact protein measurements. Triplicate analysis performed at both high and low FTMS resolutions on the E. coli proteome resulted in ∼900 redundant proteoforms from 3 to 95 kDa. Normalization of the chromatographic axis to identified proteoforms enabled reproducible physicochemical property measurements between proteome replicates with inter-replicate variances of ±3 ppm mass error for proteoforms <30 kDa, ±1.1 Da for proteins >30 kDa, ±12 s retention time error, and ±0.21 pI units. The results for E. coli and standard proteins revealed a correlation between pI precision and proteoform abundance with species detected in multiple IEF fractions exhibiting pI precisions less than the theoretical resolution of the off-gel system (±0.05 vs ±0.17, respectively). Evaluation of differentially modified proteoforms of standard proteins revealed that high sample loads (100s μgrams) change the IEF pH gradient profile, leading to sample broadening that facilitates resolution of charged post-translational modifications (e.g., phosphorylation, sialylation). Despite the impact of sample load on IEF resolution, results on standard proteins measured directly or after being spiked into E. coli demonstrated that the reproducibility of the workflow permitted recombination of the MS signal across IEF fractions in a manner supporting the evaluation of three label-free quantitation metrics for intact protein studies (proteoforms, proteoform ratios, and protein) over 102-103 sample amount with low femtomole detection limits.
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Affiliation(s)
- John R Corbett
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
- Department of Bioengineering, UT Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Dana E Robinson
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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16
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Mehaffey MR, Xia Q, Brodbelt JS. Uniting Native Capillary Electrophoresis and Multistage Ultraviolet Photodissociation Mass Spectrometry for Online Separation and Characterization of Escherichia coli Ribosomal Proteins and Protein Complexes. Anal Chem 2020; 92:15202-15211. [PMID: 33156608 PMCID: PMC7788560 DOI: 10.1021/acs.analchem.0c03784] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With an overarching goal of characterizing the structure of every protein within a cell, identifying its interacting partners, and quantifying the dynamics of the states in which it exists, key developments are still necessary to achieve comprehensive native proteomics by mass spectrometry (MS). In practice, much work remains to optimize reliable online separation methods that are compatible with native MS and improve tandem MS (MS/MS) approaches with respect to when and how energy is deposited into proteins of interest. Herein, we utilize native capillary zone electrophoresis coupled with MS to characterize the proteoforms in the Escherichia coli 70S ribosome. The capabilities of 193 nm ultraviolet photodissociation (UVPD) to yield informative backbone sequence ions are compared to those of higher-energy collisional dissociation (HCD). To further improve sequence coverage values, a multistage MS/MS approach is implemented involving front-end collisional activation to disassemble protein complexes into constituent subunits that are subsequently individually isolated and activated by HCD or UVPD. In total, 48 of the 55 known E. coli ribosomal proteins are identified as 84 unique proteoforms, including 22 protein-metal complexes and 10 protein-protein complexes. Additionally, mapping metal-bound holo fragment ions resulting from UVPD of protein-metal complexes offers insight into the metal-binding sites.
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Affiliation(s)
- M Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Qiangwei Xia
- CMP Scientific Corporation, Brooklyn, New York, New York 11226, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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17
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Histone H1 Post-Translational Modifications: Update and Future Perspectives. Int J Mol Sci 2020; 21:ijms21165941. [PMID: 32824860 PMCID: PMC7460583 DOI: 10.3390/ijms21165941] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022] Open
Abstract
Histone H1 is the most variable histone and its role at the epigenetic level is less characterized than that of core histones. In vertebrates, H1 is a multigene family, which can encode up to 11 subtypes. The H1 subtype composition is different among cell types during the cell cycle and differentiation. Mass spectrometry-based proteomics has added a new layer of complexity with the identification of a large number of post-translational modifications (PTMs) in H1. In this review, we summarize histone H1 PTMs from lower eukaryotes to humans, with a particular focus on mammalian PTMs. Special emphasis is made on PTMs, whose molecular function has been described. Post-translational modifications in H1 have been associated with the regulation of chromatin structure during the cell cycle as well as transcriptional activation, DNA damage response, and cellular differentiation. Additionally, PTMs in histone H1 that have been linked to diseases such as cancer, autoimmune disorders, and viral infection are examined. Future perspectives and challenges in the profiling of histone H1 PTMs are also discussed.
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18
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Polasky DA, Dixit SM, Keating MF, Gadkari VV, Andrews PC, Ruotolo BT. Pervasive Charge Solvation Permeates Native-like Protein Ions and Dramatically Influences Top-down Sequencing Data. J Am Chem Soc 2020; 142:6750-6760. [DOI: 10.1021/jacs.0c01076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sugyan M. Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Michael F. Keating
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Varun V. Gadkari
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Philip C. Andrews
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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19
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Intact cell MALDI-TOF mass spectrometry, a promising proteomic profiling method in farm animal clinical and reproduction research. Theriogenology 2020; 150:113-121. [PMID: 32284210 DOI: 10.1016/j.theriogenology.2020.02.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 12/20/2022]
Abstract
The objective of this review is to provide new insights into the possible use of a proteomic method known as Intact Cell Matrix-Assisted Laser Desorption-ionization Time-Of-Flight Mass Spectrometry (ICM-MS) in animal clinical research. Here, we give an overview of the basics of this technique, its advantages and disadvantages compared with other proteomic approaches, past applications and future perspectives. A special emphasis on its implementation in animal reproduction science is given, including examples of the reliable use of ICM-MS on fertility screening. In mammals, the ICM-MS profiles from pig epididymal spermatozoa reflect the proteome changes that they undergo during epididymal maturation and could be associated with the acquisition of fertilizing ability. In chicken, using adequate pre-processing and bioinformatics analysis tools, sperm ICM-MS profiles showed characteristic spectral features that allowed their classification according to their actual fertilizing ability. The association of ICM-MS and Top-down proteomic strategies allowed the identification of chicken fertility biomarkers candidates such as protein vitelline membrane outer layer protein 1 (VMO-1) and avian beta-defensin 10 (AvBD10). In female reproduction, a similar approach on ovarian follicular cells allowed the identification of specific markers of oocyte maturation in the oocyte and surrounding cumulus cells. Altogether, these results indicate that ICM-MS profiling could be a suitable approach for molecular phenotyping of male and female gametes.
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20
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He L, Rockwood AL, Agarwal AM, Anderson LC, Weisbrod CR, Hendrickson CL, Marshall AG. Top-down proteomics-a near-future technique for clinical diagnosis? ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:136. [PMID: 32175429 DOI: 10.21037/atm.2019.12.67] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Lidong He
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Alan L Rockwood
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA.,Rockwood Scientific Consulting, Salt Lake City, UT, USA.,University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Archana M Agarwal
- University of Utah School of Medicine, Salt Lake City, UT, USA.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
| | - Christopher L Hendrickson
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
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21
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Timp W, Timp G. Beyond mass spectrometry, the next step in proteomics. SCIENCE ADVANCES 2020; 6:eaax8978. [PMID: 31950079 PMCID: PMC6954058 DOI: 10.1126/sciadv.aax8978] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
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Affiliation(s)
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory Timp
- Departments of Electrical Engineering and Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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22
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Kim SW, Choi JW, Yun JW, Chung IS, Cho HC, Song SE, Im SS, Song DK. Proteomics approach to identify serum biomarkers associated with the progression of diabetes in Korean patients with abdominal obesity. PLoS One 2019; 14:e0222032. [PMID: 31504048 PMCID: PMC6736247 DOI: 10.1371/journal.pone.0222032] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/20/2019] [Indexed: 12/25/2022] Open
Abstract
Type 2 diabetes is a metabolic disease with a group of metabolic derangements and inflammatory reactants in the serum. Despite the substantial public health implications, markers of diabetes progression with abdominal obesity are still needed to facilitate early detection and treatment. In this study, we performed a proteomic approach to identify differential target proteins underlying diabetes progression in patients with abdominal obesity. Proteomic differences were investigated in the serum of controls and patients with prediabetes or diabetes with or without abdominal obesity by 2-DE combined with MALDI-TOF-MS. Proteomics data were validated by western blot analyses and major protein-protein interactions were assessed using a network analysis with String database. Among 245 matched protein spots, 36 exhibited marked differences in normal patients with abdominal obesity, prediabetes, and diabetes compared to levels in normal patients without abdominal obesity. Seven (Alpha-1-antichymotrypsin, Alpha-1-antitrypsin, Apolipoprotein A-I, haptoglobin, retinol-binding protein 4, transthyretin, and zinc-alpha2-glycoprotein) of these spots exhibited significant differences between normal and prediabetes/diabetes patients. After a network analysis, functional annotation using Gene Ontology indicated that most of the identified proteins were involved in lipid transport, lipid localization, and the regulation of serum lipoprotein particle levels. Our results indicated that variation in the levels of these identified protein biomarkers has been reported in normal, prediabetes and diabetic Assessment of the levels of these biomarkers may contribute to the development of biomarkers for not only early diagnosis but also in prognosis of diabetes mellitus type 2.
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Affiliation(s)
- Sang Woo Kim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, South Korea
- Catholic Kwandong University, International St. Mary’s Hospital, Incheon Metropolitan City, South Korea
| | - Jung-Won Choi
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, South Korea
- Catholic Kwandong University, International St. Mary’s Hospital, Incheon Metropolitan City, South Korea
| | - Jong Won Yun
- Department of Biotechnology, Daegu University, Kyungsan, Kyungbuk, South Korea
| | - In-Sung Chung
- Division of Occupational and Environmental Medicine and Department of Preventive Medicine, Keimyung, University School of Medicine, Daegu, South Korea
| | - Ho Chan Cho
- Department of Internal Medicine, Keimyung, University School of Medicine, Daegu, South Korea
| | - Seung-Eun Song
- Department of Physiology and Obesity-mediated Disease Research Center, Keimyung, University School of Medicine, Daegu, South Korea
| | - Seung-Soon Im
- Department of Physiology and Obesity-mediated Disease Research Center, Keimyung, University School of Medicine, Daegu, South Korea
- * E-mail: (SSI); (DKS)
| | - Dae-Kyu Song
- Department of Physiology and Obesity-mediated Disease Research Center, Keimyung, University School of Medicine, Daegu, South Korea
- * E-mail: (SSI); (DKS)
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23
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Basharat AR, Iman K, Khalid MF, Anwar Z, Hussain R, Kabir HG, Tahreem M, Shahid A, Humayun M, Hayat HA, Mustafa M, Shoaib MA, Ullah Z, Zarina S, Ahmed S, Uddin E, Hamera S, Ahmad F, Chaudhary SU. SPECTRUM - A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data. Sci Rep 2019; 9:11267. [PMID: 31375721 PMCID: PMC6677810 DOI: 10.1038/s41598-019-47724-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 06/10/2019] [Indexed: 01/07/2023] Open
Abstract
Top-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry. TDP has an edge over other proteomics protocols in that it allows for: (i) accurate measurement of intact protein mass, (ii) high sequence coverage, and (iii) enhanced identification of post-translational modifications (PTMs). However, the complexity of TDP spectra poses a significant impediment to protein search and PTM characterization. Furthermore, limited software support is currently available in the form of search algorithms and pipelines. To address this need, we propose 'SPECTRUM', an open-architecture and open-source toolbox for TDP data analysis. Its salient features include: (i) MS2-based intact protein mass tuning, (ii) de novo peptide sequence tag analysis, (iii) propensity-driven PTM characterization, (iv) blind PTM search, (v) spectral comparison, (vi) identification of truncated proteins, (vii) multifactorial coefficient-weighted scoring, and (viii) intuitive graphical user interfaces to access the aforementioned functionalities and visualization of results. We have validated SPECTRUM using published datasets and benchmarked it against salient TDP tools. SPECTRUM provides significantly enhanced protein identification rates (91% to 177%) over its contemporaries. SPECTRUM has been implemented in MATLAB, and is freely available along with its source code and documentation at https://github.com/BIRL/SPECTRUM/.
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Affiliation(s)
- Abdul Rehman Basharat
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Zohra Anwar
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Rashid Hussain
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Humnah Gohar Kabir
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Maria Tahreem
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Anam Shahid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Maheen Humayun
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Hira Azmat Hayat
- Department of Computer Science, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Mustafa
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Ali Shoaib
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Zakir Ullah
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Lahore University of Management Sciences, Lahore, Pakistan
| | - Shamshad Zarina
- National Center for Proteomics, University of Karachi, Karachi, Pakistan
| | - Sameer Ahmed
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Emad Uddin
- Department of Mechanical Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Sadia Hamera
- Institute of Life Sciences, University of Rostock, Rostock, Germany
- Lahore University of Management Sciences, Lahore, Pakistan
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.
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24
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Khanal DD, Baghdady YZ, Figard BJ, Schug KA. Supercharging and multiple reaction monitoring of high-molecular-weight intact proteins using triple quadrupole mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:821-830. [PMID: 30791152 DOI: 10.1002/rcm.8418] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Different supercharging agents were tested to study their effect on the intensity and charge state distributions of high-molecular-weight intact proteins. The goal of this work was to increase chargeability and ionization efficiency for proteins ranging from 66 to 150 kDa, to enable subsequent optimization of multiple reaction monitoring (MRM) mode transitions with a triple quadrupole mass spectrometer for potential top-down quantitative analysis. METHODS Supercharging agents, such as meta-nitrobenzyl alcohol (m-NBA), dimethylsulfoxide, trifluoroethanol (TFE), and sulfolane were tested in different concentrations in 50/50 acetonitrile/water with 0.5% formic acid to examine the electrospray ionization response for three model proteins: bovine serum albumin (66 kDa), holo-transferrin (78 kDa), and immunoglobulin G (150 kDa). The settings of ionization source temperature and mobile phase flow rate were also examined. MRM transitions were developed for a wide range of precursor ions for each protein, and limits of detection were determined for the proteins in the presence of favorable additive combinations. RESULTS For most of the proteins, m-NBA (1%) and TFE (5%) worked most effectively, both to shift the charge state and increase intensity. This is the first report of the use of TFE as an effective agent for both increasing protein chargeability and ionization response. TFE increased ionization efficiency between 3- and 14-fold for the model proteins studied. Increases in both source temperature and flow rate reduced the magnitude of the average charge state observed. The MRM transitions of six to eight different precursor ions of the proteins were optimized and limits of detection in the nanogram quantity on column were determined. CONCLUSIONS The feasibility for top-down quantitative analysis of high-molecular-weight proteins with a triple quadrupole mass spectrometer was demonstrated. Further, additives such as TFE can be highly beneficial for increased chargeability and response of the proteins.
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Affiliation(s)
- Durga D Khanal
- Department of Chemistry and Biochemistry, The University of Texas Arlington, Arlington, TX, USA
| | - Yehia Z Baghdady
- Department of Chemistry and Biochemistry, The University of Texas Arlington, Arlington, TX, USA
| | - Benjamin J Figard
- Shimadzu Scientific Instruments, Inc., South Central Region (SCN), Houston, TX, USA
| | - Kevin A Schug
- Department of Chemistry and Biochemistry, The University of Texas Arlington, Arlington, TX, USA
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25
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Abstract
Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype.
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26
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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: 59] [Impact Index Per Article: 11.8] [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.
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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.
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27
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Inventory of proteoforms as a current challenge of proteomics: Some technical aspects. J Proteomics 2019; 191:22-28. [DOI: 10.1016/j.jprot.2018.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 02/08/2023]
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28
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Mass Spectrometry-Based Biomarkers in Drug Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:435-449. [PMID: 31347063 DOI: 10.1007/978-3-030-15950-4_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Advances in mass spectrometry, proteomics, protein bioanalytical approaches, and biochemistry have led to a rapid evolution and expansion in the area of mass spectrometry-based biomarker discovery and development. The last decade has also seen significant progress in establishing accepted definitions, guidelines, and criteria for the analytical validation, acceptance and qualification of biomarkers. These advances have coincided with a decreased return on investment for pharmaceutical research and development and an increasing need for better early decision making tools. Empowering development teams with tools to measure a therapeutic interventions impact on disease state and progression, measure target engagement and to confirm predicted pharmacodynamic effects is critical to efficient data-driven decision making. Appropriate implementation of a biomarker or a combination of biomarkers can enhance understanding of a drugs mechanism, facilitate effective translation from the preclinical to clinical space, enable early proof of concept and dose selection, and increases the efficiency of drug development. Here we will provide descriptions of the different classes of biomarkers that have utility in the drug development process as well as review specific, protein-centric, mass spectrometry-based approaches for the discovery of biomarkers and development of targeted assays to measure these markers in a selective and analytically precise manner.
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Abstract
The mechanism underlying many biological phenotypes remains unknown despite the increasing availability of whole genome and transcriptome sequencing. Direct measurement of changes in protein expression is an attractive alternative and has the potential to reveal novel processes. Mass spectrometry has become the standard method for proteomics, allowing both the confident identification and quantification of thousands of proteins from biological samples. In this review, mass spectrometry-based proteomic methods and their applications are described.
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Affiliation(s)
- J Robert O'Neill
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK. Robert.o'.,Department of Clinical Surgery, Royal Infirmary of Edinburgh, Edinburgh, UK. Robert.o'
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Calderón-Celis F, Sugiyama N, Yamanaka M, Sakai T, Diez-Fernández S, Calvete JJ, Sanz-Medel A, Encinar JR. Enhanced Universal Quantification of Biomolecules Using Element MS and Generic Standards: Application to Intact Protein and Phosphoprotein Determination. Anal Chem 2018; 91:1105-1112. [DOI: 10.1021/acs.analchem.8b04731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Naoki Sugiyama
- Agilent Technologies International Japan, Ltd., 9-1 Takakura-cho, Hachioji-shi, Tokyo 192-0033, Japan
| | - Michiko Yamanaka
- Agilent Technologies International Japan, Ltd., 9-1 Takakura-cho, Hachioji-shi, Tokyo 192-0033, Japan
| | - Tetsushi Sakai
- Agilent Technologies International Japan, Ltd., 9-1 Takakura-cho, Hachioji-shi, Tokyo 192-0033, Japan
| | - Silvia Diez-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Juan J. Calvete
- Instituto de Biomedicina de Valencia, IBV-CSIC, Jaume Roig 11, 46010 Valencia, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
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Mehaffey MR, Sanders JD, Holden DD, Nilsson CL, Brodbelt JS. Multistage Ultraviolet Photodissociation Mass Spectrometry To Characterize Single Amino Acid Variants of Human Mitochondrial BCAT2. Anal Chem 2018; 90:9904-9911. [PMID: 30016590 PMCID: PMC6323636 DOI: 10.1021/acs.analchem.8b02099] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Unraveling disease mechanisms requires a comprehensive understanding of how the interplay between higher-order structure and protein-ligand interactions impacts the function of a given protein. Recent advances in native mass spectrometry (MS) involving multimodal or higher-energy activation methods have allowed direct interrogation of intact protein complexes in the gas phase, allowing analysis of both composition and subunit connectivity. We report a multistage approach combining collisional activation and 193 nm ultraviolet photodissociation (UVPD) to characterize single amino acid variants of the human mitochondrial enzyme branched-chain amino acid transferase 2 (BCAT2), a protein implicated in chemotherapeutic resistance in glioblastoma tumors. Native electrospray ionization confirms that both proteins exist as homodimers. Front-end collisional activation disassembles the dimers into monomeric subunits that are further interrogated using UVPD to yield high sequence coverage of the mutated region. Additionally, holo (ligand-bound) fragment ions resulting from photodissociation reveal that the mutation causes destabilization of the interactions with a bound cofactor. This study demonstrates the unique advantages of implementing UVPD in a multistage MS approach for analyzing intact protein assemblies.
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Affiliation(s)
- M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Dustin D. Holden
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Carol L. Nilsson
- Institute of Experimental Medical Sciences, Lund University, SE-221, Lund Sweden
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Cai W, Hite ZL, Lyu B, Wu Z, Lin Z, Gregorich ZR, Messer AE, McIlwain SJ, Marston SB, Kohmoto T, Ge Y. Temperature-sensitive sarcomeric protein post-translational modifications revealed by top-down proteomics. J Mol Cell Cardiol 2018; 122:11-22. [PMID: 30048711 DOI: 10.1016/j.yjmcc.2018.07.247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/11/2018] [Accepted: 07/21/2018] [Indexed: 10/28/2022]
Abstract
Despite advancements in symptom management for heart failure (HF), this devastating clinical syndrome remains the leading cause of death in the developed world. Studies using animal models have greatly advanced our understanding of the molecular mechanisms underlying HF; however, differences in cardiac physiology and the manifestation of HF between animals, particularly rodents, and humans necessitates the direct interrogation of human heart tissue samples. Nevertheless, an ever-present concern when examining human heart tissue samples is the potential for artefactual changes related to temperature changes during tissue shipment or sample processing. Herein, we examined the effects of temperature on the post-translational modifications (PTMs) of sarcomeric proteins, the proteins responsible for muscle contraction, under conditions mimicking those that might occur during tissue shipment or sample processing. Using a powerful top-down proteomics method, we found that sarcomeric protein PTMs were differentially affected by temperature. Specifically, cardiac troponin I and enigma homolog isoform 2 showed robust increases in phosphorylation when tissue was incubated at either 4 °C or 22 °C. The observed increase is likely due to increased cyclic AMP levels and activation of protein kinase A in the tissue. On the contrary, cardiac troponin T and myosin regulatory light chain phosphorylation decreased when tissue was incubated at 4 °C or 22 °C. Furthermore, significant protein degradation was also observed after incubation at 4 °C or 22 °C. Overall, these results indicate that temperature exerts various effects on sarcomeric protein PTMs and careful tissue handling is critical for studies involving human heart samples. Moreover, these findings highlight the power of top-down proteomics for examining the integrity of cardiac tissue samples.
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Affiliation(s)
- Wenxuan Cai
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachary L Hite
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Beini Lyu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Andrew E Messer
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Steve B Marston
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Takushi Kohmoto
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ying Ge
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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Proteoform Analysis to Fulfill Unmet Clinical Needs and Reach Global Standardization of Protein Measurands in Clinical Chemistry Proteomics. Clin Lab Med 2018; 38:487-497. [PMID: 30115393 DOI: 10.1016/j.cll.2018.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In clinical testing of protein markers, structure variants of the measurand are often not taken into account. This heterogeneous character of protein measurands in immunoassays often renders test standardization impossible. Consequently, test results from different methods can lead to underdiagnosis or overdiagnosis and, thus, undertreatment or overtreatment of patients. The systematic structural analysis of protein isoforms has been coined proteoform profiling and is performed through mass spectrometry-based proteomics strategies. Knowledge on proteoforms allows refining existing uni-marker tests and moreover has great potential to contribute to the urgent need for new tests to predict prognosis and severity of diseases.
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Kennedy E, Hokmabadi M, Dong Z, McKelvey K, Nelson EM, Timp G. Method for Dynamically Detecting Secretions from Single Cells Using a Nanopore. NANO LETTERS 2018; 18:4263-4272. [PMID: 29870666 DOI: 10.1021/acs.nanolett.8b01257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Secreted proteins mediate cell-to-cell communications. Thus, eavesdropping on the secretome could reveal the cellular phenotype, but it is challenging to detect the proteins because they are secreted only in minute amounts and then diluted in blood plasma or contaminated by cell culture medium or the lysate. In this pilot study, it is demonstrated that secretions from single cancer cells can be detected and dynamically analyzed through measurements of blockades in the electrolytic current due to single molecules translocating through a nanopore in a thin inorganic membrane. It is established that the distribution of blockades can be used to differentiate three different cancer cell lines (U937, MDA-MB-231, and MCF-7) in real time and quickly (<20 s). Importantly, the distinctive blockades associated with the chemokine CCL5, a prognostic factor for disease progression in breast cancer, along with other low-mass biomarkers of breast cancer (PI3, TIMP1, and MMP1) were identified in the context of the secretome of these three cell types, tracked with time, and used to provide information on the cellular phenotype.
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35
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Khowal S, Naqvi SH, Monga S, Jain SK, Wajid S. Assessment of cellular and serum proteome from tongue squamous cell carcinoma patient lacking addictive proclivities for tobacco, betel nut, and alcohol: Case study. J Cell Biochem 2018; 119:5186-5221. [PMID: 29236289 DOI: 10.1002/jcb.26554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/30/2017] [Indexed: 02/06/2023]
Abstract
The intriguing molecular pathways involved in oral carcinogenesis are still ambiguous. The oral squamous cell carcinoma (OSCC) ranks as the most common type constituting more than 90% of the globally diagnosed oral cancers cases. The elevation in the OSCC incidence rate during past 10 years has an alarming impression on human healthcare. The major challenges associated with OSCC include delayed diagnosis, high metastatic rates, and low 5-year survival rates. The present work foundations on reverse genetic strategy and involves the identification of genes showing expressional variability in an OSCC case lacking addictive proclivities for tobacco, betel nut, and/or alcohol, major etiologies. The expression modulations in the identified genes were analyzed in 16 patients comprising oral pre-cancer and cancer histo-pathologies. The genes SCCA1 and KRT1 were found to down regulate while DNAJC13, GIPC2, MRPL17, IG-Vreg, SSFA2, and UPF0415 upregulated in the oral pre-cancer and cancer pathologies, implicating the genes as crucial players in oral carcinogenesis.
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Affiliation(s)
- Sapna Khowal
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Samar H Naqvi
- Molecular Diagnostics, Genetix Biotech Asia (P) Ltd., New Delhi, India
| | - Seema Monga
- Department of ENT, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard, New Delhi, India
| | - Swatantra K Jain
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
- Department of Biochemistry, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard, New Delhi, India
| | - Saima Wajid
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
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36
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Ntai I, Fornelli L, DeHart CJ, Hutton JE, Doubleday PF, LeDuc RD, van Nispen AJ, Fellers RT, Whiteley G, Boja ES, Rodriguez H, Kelleher NL. Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk. Proc Natl Acad Sci U S A 2018; 115:4140-4145. [PMID: 29610327 PMCID: PMC5910823 DOI: 10.1073/pnas.1716122115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mutations of the KRAS gene are found in human cancers with high frequency and result in the constitutive activation of its protein products. This leads to aberrant regulation of downstream pathways, promoting cell survival, proliferation, and tumorigenesis that drive cancer progression and negatively affect treatment outcomes. Here, we describe a workflow that can detect and quantify mutation-specific consequences of KRAS biochemistry, namely linked changes in posttranslational modifications (PTMs). We combined immunoaffinity enrichment with detection by top-down mass spectrometry to discover and quantify proteoforms with or without the Gly13Asp mutation (G13D) specifically in the KRAS4b isoform. The workflow was applied first to isogenic KRAS colorectal cancer (CRC) cell lines and then to patient CRC tumors with matching KRAS genotypes. In two cellular models, a direct link between the knockout of the mutant G13D allele and the complete nitrosylation of cysteine 118 of the remaining WT KRAS4b was observed. Analysis of tumor samples quantified the percentage of mutant KRAS4b actually present in cancer tissue and identified major differences in the levels of C-terminal carboxymethylation, a modification critical for membrane association. These data from CRC cells and human tumors suggest mechanisms of posttranslational regulation that are highly context-dependent and which lead to preferential production of specific KRAS4b proteoforms.
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Affiliation(s)
- Ioanna Ntai
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Luca Fornelli
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Caroline J DeHart
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Josiah E Hutton
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Peter F Doubleday
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Richard D LeDuc
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Alexandra J van Nispen
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Ryan T Fellers
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Gordon Whiteley
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892
| | - Neil L Kelleher
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208;
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
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Schmit PO, Vialaret J, Wessels HJ, van Gool AJ, Lehmann S, Gabelle A, Wood J, Bern M, Paape R, Suckau D, Kruppa G, Hirtz C. Towards a routine application of Top-Down approaches for label-free discovery workflows. J Proteomics 2018; 175:12-26. [DOI: 10.1016/j.jprot.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 07/14/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022]
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Polasky DA, Lermyte F, Nshanian M, Sobott F, Andrews PC, Loo JA, Ruotolo BT. Fixed-Charge Trimethyl Pyrilium Modification for Enabling Enhanced Top-Down Mass Spectrometry Sequencing of Intact Protein Complexes. Anal Chem 2018; 90:2756-2764. [PMID: 29360341 PMCID: PMC6340295 DOI: 10.1021/acs.analchem.7b04806] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mass spectrometry of intact proteins and protein complexes has the potential to provide a transformative level of information on biological systems, ranging from sequence and post-translational modification analysis to the structures of whole protein assemblies. This ambitious goal requires the efficient fragmentation of both intact proteins and the macromolecular, multicomponent machines they collaborate to create through noncovalent interactions. Improving technologies in an effort to achieve such fragmentation remains perhaps the greatest challenge facing current efforts to comprehensively analyze cellular protein composition and is essential to realizing the full potential of proteomics. In this work, we describe the use of a trimethyl pyrylium (TMP) fixed-charge covalent labeling strategy aimed at enhancing fragmentation for challenging intact proteins and intact protein complexes. Combining analysis of TMP-modified and unmodified protein complexes results in a greater diversity of regions within the protein that give rise to fragments, and results in an up to 2.5-fold increase in sequence coverage when compared to unmodified protein alone, for protein complexes up to 148 kDa. TMP modification offers a simple and powerful platform to expand the capabilities of existing mass spectrometric instrumentation for the complete characterization of intact protein assemblies.
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Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109
| | - Frederik Lermyte
- ♯ Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Michael Nshanian
- ‡ Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
| | - Frank Sobott
- ♯ Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- ° The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- + School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Phillip C. Andrews
- ‖ Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor MI, 48109
| | - Joseph A. Loo
- ‡ Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
- § Department of Biological Chemistry, David Geffen School of Medicine, and UCLA/DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109
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Avtonomov DM, Polasky DA, Ruotolo BT, Nesvizhskii AI. IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry. Anal Chem 2018; 90:2369-2375. [PMID: 29278491 PMCID: PMC5826643 DOI: 10.1021/acs.analchem.7b04999] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Top-down proteomics has emerged as a transformative method for the analysis of protein sequence and post-translational modifications (PTMs). Top-down experiments have historically been performed primarily on ultrahigh resolution mass spectrometers due to the complexity of spectra resulting from fragmentation of intact proteins, but recent advances in coupling ion mobility separations to faster, lower resolution mass analyzers now offer a viable alternative. However, software capable of interpreting the highly complex two-dimensional spectra that result from coupling ion mobility separation to top-down experiments is currently lacking. In this manuscript we present a software suite consisting of two programs, IMTBX ("IM Toolbox") and Grppr ("Grouper"), that enable fully automated processing of such data. We demonstrate the capabilities of this software suite by examining a series of intact proteins on a Waters Synapt G2 ion-mobility equipped mass spectrometer and compare the results to the manual and semiautomated data analysis procedures we have used previously.
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Affiliation(s)
- Dmitry M Avtonomov
- Department of Pathology, ‡Department of Chemistry, and §Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan United States
| | - Daniel A Polasky
- Department of Pathology, ‡Department of Chemistry, and §Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan United States
| | - Brandon T Ruotolo
- Department of Pathology, ‡Department of Chemistry, and §Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan United States
| | - Alexey I Nesvizhskii
- Department of Pathology, ‡Department of Chemistry, and §Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan United States
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40
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Hibbert SA, Ozols M, Griffiths CEM, Watson REB, Bell M, Sherratt MJ. Defining tissue proteomes by systematic literature review. Sci Rep 2018; 8:546. [PMID: 29323144 PMCID: PMC5765030 DOI: 10.1038/s41598-017-18699-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/14/2017] [Indexed: 12/24/2022] Open
Abstract
Defining protein composition is a key step in understanding the function of both healthy and diseased biological systems. There is currently little consensus between existing published proteomes in tissues such as the aorta, cartilage and organs such as skin. Lack of agreement as to both the number and identity of proteins may be due to issues in protein extraction, sensitivity/specificity of detection and the use of disparate tissue/cell sources. Here, we developed a method combining bioinformatics and systematic review to screen >32M articles from the Web of Science for evidence of proteins in healthy human skin. The resulting Manchester Proteome (www.manchesterproteome.manchester.ac.uk) collates existing evidence which characterises 2,948 skin proteins, 437 unique to our database and 2011 evidenced by both mass spectrometry and immune-based techniques. This approach circumvents the limitations of individual proteomics studies and can be applied to other species, organs, cells or disease-states. Accurate tissue proteomes will aid development of engineered constructs and offer insight into disease treatments by highlighting differences in proteomic composition.
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Affiliation(s)
- Sarah A Hibbert
- Division of Cell Matrix Biology & Regenerative Medicine, The University of Manchester, Manchester, UK.
| | - Matiss Ozols
- Division of Cell Matrix Biology & Regenerative Medicine, The University of Manchester, Manchester, UK
| | - Christopher E M Griffiths
- Centre for Dermatology Research, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachel E B Watson
- Centre for Dermatology Research, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Mike Bell
- Walgreens Boots Alliance, Thane Road, Nottingham, UK
| | - Michael J Sherratt
- Division of Cell Matrix Biology & Regenerative Medicine, The University of Manchester, Manchester, UK.
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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
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42
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Li H, Nguyen HH, Ogorzalek Loo RR, Campuzano IDG, Loo JA. An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes. Nat Chem 2018; 10:139-148. [PMID: 29359744 PMCID: PMC5784781 DOI: 10.1038/nchem.2908] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/06/2017] [Indexed: 12/23/2022]
Abstract
Mass spectrometry (MS) has become a crucial technique for the analysis of protein complexes. Native MS has traditionally examined protein subunit arrangements, while proteomics MS has focused on sequence identification. These two techniques are usually performed separately without taking advantage of the synergies between them. Here we describe the development of an integrated native MS and top-down proteomics method using Fourier-transform ion cyclotron resonance (FTICR) to analyse macromolecular protein complexes in a single experiment. We address previous concerns of employing FTICR MS to measure large macromolecular complexes by demonstrating the detection of complexes up to 1.8 MDa, and we demonstrate the efficacy of this technique for direct acquirement of sequence to higher-order structural information with several large complexes. We then summarize the unique functionalities of different activation/dissociation techniques. The platform expands the ability of MS to integrate proteomics and structural biology to provide insights into protein structure, function and regulation.
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Affiliation(s)
- Huilin Li
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Hong Hanh Nguyen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Rachel R Ogorzalek Loo
- Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
| | - Iain D G Campuzano
- Discovery Analytical Sciences, Amgen, Thousand Oaks, California 91320, USA
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA.,Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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43
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Calderón-Celis F, Sanz-Medel A, Encinar JR. Universal absolute quantification of biomolecules using element mass spectrometry and generic standards. Chem Commun (Camb) 2018; 54:904-907. [DOI: 10.1039/c7cc09059e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Standardless highly sensitive ICP-MS approach for the absolute and simultaneous quantification of important target biomolecules in life sciences.
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Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry
- University of Oviedo
- Julián Clavería 8
- 33006 Oviedo
- Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry
- University of Oviedo
- Julián Clavería 8
- 33006 Oviedo
- Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry
- University of Oviedo
- Julián Clavería 8
- 33006 Oviedo
- Spain
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44
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Chang HY, Chen CT, Ko CL, Chen YJ, Chen YJ, Hsu WL, Juo CG, Sung TY. iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm. Anal Chem 2017; 89:13128-13136. [DOI: 10.1021/acs.analchem.7b02343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Hui-Yin Chang
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Ching-Tai Chen
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chu-Ling Ko
- Department
of Computer Science, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yi-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Lian Hsu
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chiun-Gung Juo
- Molecular
Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
- PharmaEssentia Corp., Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
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45
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Toby TK, Abecassis M, Kim K, Thomas PM, Fellers RT, LeDuc RD, Kelleher NL, Demetris J, Levitsky J. Proteoforms in Peripheral Blood Mononuclear Cells as Novel Rejection Biomarkers in Liver Transplant Recipients. Am J Transplant 2017; 17:2458-2467. [PMID: 28510335 PMCID: PMC5612406 DOI: 10.1111/ajt.14359] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/20/2017] [Accepted: 05/06/2017] [Indexed: 01/25/2023]
Abstract
Biomarker profiles of acute rejection in liver transplant recipients could enhance the diagnosis and management of recipients. Our aim was to identify diagnostic proteoform signatures of acute rejection in circulating immune cells, using an emergent "top-down" proteomics methodology. We prepared differentially processed and cryopreserved cell lysates from 26 nonviral liver transplant recipients by molecular weight-based fractionation and analyzed them by mass spectrometry of whole proteins in three steps: (i) Nanocapillary liquid chromatography coupled with high-resolution tandem mass spectrometry; (ii) database searching to identify and characterize intact proteoforms; (iii) data processing through a hierarchical linear model matching the study design to quantify proteoform fold changes in patients with rejection versus normal liver function versus acute dysfunction without rejection. Differentially expressed proteoforms were seen in patients with rejection versus normal and nonspecific controls, most evidently in the cell preparations stored in traditional serum-rich media. Mapping analysis of these proteins back to genes through gene ontology and pathway analysis tools revealed multiple signaling pathways, including inflammation mediated by cytokines and chemokines. Larger studies are needed to validate these novel rejection signatures and test their predictive value for use in clinical management.
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Affiliation(s)
- T. K. Toby
- Department of Molecular Biosciences and Chemistry, Northwestern University, Chicago, IL
| | - M. Abecassis
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - K. Kim
- Department of Molecular Biosciences and Chemistry, Northwestern University, Chicago, IL
| | - P. M. Thomas
- Department of Molecular Biosciences and Chemistry, Northwestern University, Chicago, IL,National Resource for Translational & Developmental Proteomics, Northwestern University, Chicago, IL
| | - R. T. Fellers
- National Resource for Translational & Developmental Proteomics, Northwestern University, Chicago, IL
| | - R. D. LeDuc
- National Resource for Translational & Developmental Proteomics, Northwestern University, Chicago, IL
| | - N. L. Kelleher
- Department of Molecular Biosciences and Chemistry, Northwestern University, Chicago, IL,National Resource for Translational & Developmental Proteomics, Northwestern University, Chicago, IL
| | - J. Demetris
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - J. Levitsky
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL,Division of Gastroenterology and Hepatology, Northwestern University Feinberg School of Medicine, Chicago, IL,Corresponding author: Josh Levitsky,
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46
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A Routine 'Top-Down' Approach to Analysis of the Human Serum Proteome. Proteomes 2017; 5:proteomes5020013. [PMID: 28587287 PMCID: PMC5489773 DOI: 10.3390/proteomes5020013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 12/21/2022] Open
Abstract
Serum provides a rich source of potential biomarker proteoforms. One of the major obstacles in analysing serum proteomes is detecting lower abundance proteins owing to the presence of hyper-abundant species (e.g., serum albumin and immunoglobulins). Although depletion methods have been used to address this, these can lead to the concomitant removal of non-targeted protein species, and thus raise issues of specificity, reproducibility, and the capacity for meaningful quantitative analyses. Altering the native stoichiometry of the proteome components may thus yield a more complex series of issues than dealing directly with the inherent complexity of the sample. Hence, here we targeted method refinements so as to ensure optimum resolution of serum proteomes via a top down two-dimensional gel electrophoresis (2DE) approach that enables the routine assessment of proteoforms and is fully compatible with subsequent mass spectrometric analyses. Testing included various fractionation and non-fractionation approaches. The data show that resolving 500 µg protein on 17 cm 3–10 non-linear immobilised pH gradient strips in the first dimension followed by second dimension resolution on 7–20% gradient gels with a combination of lithium dodecyl sulfate (LDS) and sodium dodecyl sulfate (SDS) detergents markedly improves the resolution and detection of proteoforms in serum. In addition, well established third dimension electrophoretic separations in combination with deep imaging further contributed to the best available resolution, detection, and thus quantitative top-down analysis of serum proteomes.
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47
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Bengtson P, Valtonen-André C, Jonsson M. Phenotyping of α-1-Antitrypsin by liquid chromatography-high resolution mass spectrometry. CLINICAL MASS SPECTROMETRY (DEL MAR, CALIF.) 2016; 2:34-40. [PMID: 39192843 PMCID: PMC11324609 DOI: 10.1016/j.clinms.2017.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 11/19/2022]
Abstract
More than seventy-five isotypes of α-1-antitrypsin (AAT) have been described. To assess risks associated with AAT deficiency, isotype identification is necessary. Isoelectric focusing (IEF) is traditionally used for isotype differentiation, however, IEF has limited scope since it is a manual procedure that is not suitable for automation, and antitrypsin variants must differ in net charge in order to be resolved. In comparison, mass spectrometric assays are easily automated and offer a more complete solution for characterization of proteins. To capitalize on these advantages, we have developed a qualitative top-down liquid chromatography-mass spectrometry (LC-MS) method for selective phenotyping of AAT. This technique requires no sample pretreatment, and has the potential for use in routine clinical diagnostics. We have validated our LC-MS results against both DNA sequencing and IEF. Thus far, this method has identified the AAT variants PLowell, S and Z, as well as unique fragments shared by different M alleles. Its high selectivity is indirectly illustrated by the detection of a variant carrying the amino acid substitution p.Ala308Ser, which cannot be visualized by IEF.
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Affiliation(s)
- Per Bengtson
- Department of Clinical Chemistry, University Health Care in Region Skåne, Lund, Sweden
| | | | - Magnus Jonsson
- Department of Clinical Chemistry, University Health Care in Region Skåne, Malmö, Sweden
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48
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Vehus T, Roberg-Larsen H, Waaler J, Aslaksen S, Krauss S, Wilson SR, Lundanes E. Versatile, sensitive liquid chromatography mass spectrometry - Implementation of 10 μm OT columns suitable for small molecules, peptides and proteins. Sci Rep 2016; 6:37507. [PMID: 27897190 PMCID: PMC5126632 DOI: 10.1038/srep37507] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/28/2016] [Indexed: 12/14/2022] Open
Abstract
We have designed a versatile and sensitive liquid chromatographic (LC) system, featuring a monolithic trap column and a very narrow (10 μm ID) fused silica open tubular liquid chromatography (OTLC) separation column functionalized with C18-groups, for separating a wide range of molecules (from small metabolites to intact proteins). Compared to today's capillary/nanoLC approaches, our system provides significantly enhanced sensitivity (up to several orders) with matching or improved separation efficiency, and highly repeatable chromatographic performance. The chemical properties of the trap column and the analytical column were fine-tuned to obtain practical sample loading capacities (above 2 μg), an earlier bottleneck of OTLC. Using the OTLC system (combined with Orbitrap mass spectrometry), we could perform targeted metabolomics of sub-μg amounts of exosomes with 25 attogram detection limit of a breast cancer-related hydroxylated cholesterol. With the same set-up, sensitive bottom-up proteomics (targeted and untargeted) was possible, and high-resolving intact protein analysis. In contrast to state-of-the-art packed columns, our platform performs chromatography with very little dilution and is "fit-for-all", well suited for comprehensive analysis of limited samples, and has potential as a tool for challenges in diagnostics.
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Affiliation(s)
- T. Vehus
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
- Department of Engineering Sciences, University of Agder, Jon Lilletunsvei 9, NO-4891 Grimstad, Norway
| | - H. Roberg-Larsen
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - J. Waaler
- Unit for Cell Signaling, SFI-CAST Biomedical Innovation Center, Oslo University Hospital, Rikshospitalet, NO-0027 Oslo, Norway
| | - S. Aslaksen
- Unit for Cell Signaling, SFI-CAST Biomedical Innovation Center, Oslo University Hospital, Rikshospitalet, NO-0027 Oslo, Norway
| | - S. Krauss
- Unit for Cell Signaling, SFI-CAST Biomedical Innovation Center, Oslo University Hospital, Rikshospitalet, NO-0027 Oslo, Norway
| | - S. R. Wilson
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - E. Lundanes
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
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49
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Grebe SK, Singh RJ. Clinical peptide and protein quantification by mass spectrometry (MS). Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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50
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Toby TK, Fornelli L, Kelleher NL. Progress in Top-Down Proteomics and the Analysis of Proteoforms. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:499-519. [PMID: 27306313 PMCID: PMC5373801 DOI: 10.1146/annurev-anchem-071015-041550] [Citation(s) in RCA: 382] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a powerful method for the analysis of proteomes. Prevailing bottom-up proteomics operates at the level of the peptide, leading to issues with protein inference, connectivity, and incomplete sequence/modification information. Top-down proteomics (TDP), alternatively, applies MS at the proteoform level to analyze intact proteins with diverse sources of intramolecular complexity preserved during analysis. Fortunately, advances in prefractionation workflows, MS instrumentation, and dissociation methods for whole-protein ions have helped TDP emerge as an accessible and potentially disruptive modality with increasingly translational value. In this review, we discuss technical and conceptual advances in TDP, along with the growing power of proteoform-resolved measurements in clinical and translational research.
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Affiliation(s)
- Timothy K Toby
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208;
| | - Luca Fornelli
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Neil L Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208;
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
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