1
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Schachner LF, Mullen C, Phung W, Hinkle JD, Beardsley MI, Bentley T, Day P, Tsai C, Sukumaran S, Baginski T, DiCara D, Agard NJ, Masureel M, Gober J, ElSohly AM, Melani R, Syka JEP, Huguet R, Marty MT, Sandoval W. Exposing the molecular heterogeneity of glycosylated biotherapeutics. Nat Commun 2024; 15:3259. [PMID: 38627419 PMCID: PMC11021452 DOI: 10.1038/s41467-024-47693-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
The heterogeneity inherent in today's biotherapeutics, especially as a result of heavy glycosylation, can affect a molecule's safety and efficacy. Characterizing this heterogeneity is crucial for drug development and quality assessment, but existing methods are limited in their ability to analyze intact glycoproteins or other heterogeneous biotherapeutics. Here, we present an approach to the molecular assessment of biotherapeutics that uses proton-transfer charge-reduction with gas-phase fractionation to analyze intact heterogeneous and/or glycosylated proteins by mass spectrometry. The method provides a detailed landscape of the intact molecular weights present in biotherapeutic protein preparations in a single experiment. For glycoproteins in particular, the method may offer insights into glycan composition when coupled with a suitable bioinformatic strategy. We tested the approach on various biotherapeutic molecules, including Fc-fusion, VHH-fusion, and peptide-bound MHC class II complexes to demonstrate efficacy in measuring the proteoform-level diversity of biotherapeutics. Notably, we inferred the glycoform distribution for hundreds of molecular weights for the eight-times glycosylated fusion drug IL22-Fc, enabling correlations between glycoform sub-populations and the drug's pharmacological properties. Our method is broadly applicable and provides a powerful tool to assess the molecular heterogeneity of emerging biotherapeutics.
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Affiliation(s)
- Luis F Schachner
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Christopher Mullen
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Wilson Phung
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Joshua D Hinkle
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | | | - Tracy Bentley
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Peter Day
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Christina Tsai
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
- Protein Analytical Development, Ascendis Pharma, Palo Alto, CA, USA
| | - Siddharth Sukumaran
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
- Translational Pharmacometrics, Janssen, Horsham, PA, USA
| | - Tomasz Baginski
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Danielle DiCara
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Nicholas J Agard
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Matthieu Masureel
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Joshua Gober
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Adel M ElSohly
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Rafael Melani
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - John E P Syka
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Romain Huguet
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA.
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2
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Kline JT, Belford MW, Boeser CL, Huguet R, Fellers RT, Greer JB, Greer SM, Horn DM, Durbin KR, Dunyach JJ, Ahsan N, Fornelli L. Orbitrap Mass Spectrometry and High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Enable the in-Depth Analysis of Human Serum Proteoforms. J Proteome Res 2023; 22:3418-3426. [PMID: 37774690 PMCID: PMC10629265 DOI: 10.1021/acs.jproteome.3c00488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Indexed: 10/01/2023]
Abstract
Blood serum and plasma are arguably the most commonly analyzed clinical samples, with dozens of proteins serving as validated biomarkers for various human diseases. Top-down proteomics may provide additional insights into disease etiopathogenesis since this approach focuses on protein forms, or proteoforms, originally circulating in blood, potentially providing access to information about relevant post-translational modifications, truncations, single amino acid substitutions, and many other sources of protein variation. However, the vast majority of proteomic studies on serum and plasma are carried out using peptide-centric, bottom-up approaches that cannot recapitulate the original proteoform content of samples. Clinical laboratories have been slow to adopt top-down analysis, also due to higher sample handling requirements. In this study, we describe a straightforward protocol for intact proteoform sample preparation based on the depletion of albumin and immunoglobulins, followed by simplified protein fractionation via polyacrylamide gel electrophoresis. After molecular weight-based fractionation, we supplemented the traditional liquid chromatography-tandem mass spectrometry (LC-MS2) data acquisition with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to further simplify serum proteoform mixtures. This LC-FAIMS-MS2 method led to the identification of over 1000 serum proteoforms < 30 kDa, outperforming traditional LC-MS2 data acquisition and more than doubling the number of proteoforms identified in previous studies.
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Affiliation(s)
- Jake T. Kline
- Department
of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | | | | | - Romain Huguet
- Thermo
Scientific, San Jose, California 95134, United States
| | - Ryan T. Fellers
- Proteinaceous,
Inc., Evanston, Illinois 60204, United
States
| | - Joseph B. Greer
- Proteinaceous,
Inc., Evanston, Illinois 60204, United
States
| | | | - David M. Horn
- Thermo
Scientific, San Jose, California 95134, United States
| | | | | | - Nagib Ahsan
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
- Mass
Spectrometry, Proteomics and Metabolomics Core Facility, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Luca Fornelli
- Department
of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
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3
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Shuken SR, McAlister GC, Barshop WD, Canterbury JD, Bergen D, Huang J, Huguet R, Paulo JA, Zabrouskov V, Gygi SP, Yu Q. Deep Proteomic Compound Profiling with the Orbitrap Ascend Tribrid Mass Spectrometer Using Tandem Mass Tags and Real-Time Search. Anal Chem 2023; 95:15180-15188. [PMID: 37811788 PMCID: PMC10785648 DOI: 10.1021/acs.analchem.3c01701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Tandem mass tags (TMT) and tribrid mass spectrometers are a powerful combination for high-throughput proteomics with high quantitative accuracy. Increasingly, this technology is being used to map the effects of drugs on the proteome. However, the depth of proteomic profiling is still limited by sensitivity and speed. The new Orbitrap Ascend mass spectrometer was designed to address these limitations with a combination of hardware and software improvements. We evaluated the performance of the Ascend in multiple contexts including deep proteomic profiling. We found that the Ascend exhibited increased sensitivity, yielding higher signal-to-noise ratios than the Orbitrap Eclipse with shorter injection times. As a result, higher numbers of peptides and proteins were identified and quantified, especially with low sample input. TMT measurements had significantly improved signal-to-noise ratios, improving quantitative precision. In a fractionated 16plex sample that profiled proteomic differences across four human cell lines, the Ascend was able to quantify hundreds more proteins than the Eclipse, many of them low-abundant proteins, and the Ascend was able to quantify >8000 proteins in 30% less instrument time. We used the Ascend to analyze 8881 proteins in HCT116 cancer cells treated with covalent sulfolane/sulfolene inhibitors of peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1), a phosphorylation-specific peptidyl-prolyl cis-trans isomerase implicated in several cancers. We characterized these PIN1 inhibitors' effects on the proteome and identified discrepancies among the different compounds, which will facilitate a better understanding of the structure-activity relationship of this class of compounds. The Ascend was able to quantify statistically significant, potentially therapeutically relevant changes in proteins that the Eclipse could not detect.
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Affiliation(s)
- Steven R Shuken
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Graeme C McAlister
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - William D Barshop
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Jesse D Canterbury
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - David Bergen
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Jingjing Huang
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - João A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
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4
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He Y, Shishkova E, Peters-Clarke TM, Brademan DR, Westphall MS, Bergen D, Huang J, Huguet R, Senko MW, Zabrouskov V, McAlister GC, Coon JJ. Evaluation of the Orbitrap Ascend Tribrid Mass Spectrometer for Shotgun Proteomics. Anal Chem 2023; 95:10655-10663. [PMID: 37389810 PMCID: PMC10528367 DOI: 10.1021/acs.analchem.3c01155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Mass spectrometry (MS)-based proteomics is a powerful technology to globally profile protein abundances, activities, interactions, and modifications. The extreme complexity of proteomics samples, which often contain hundreds of thousands of analytes, necessitates continuous development of MS techniques and instrumentation to improve speed, sensitivity, precision, and accuracy, among other analytical characteristics. Here, we systematically evaluated the Orbitrap Ascend Tribrid mass spectrometer in the context of shotgun proteomics, and we compared its performance to that of the previous generation of Tribrid instruments─the Orbitrap Eclipse. The updated architecture of the Orbitrap Ascend includes a second ion-routing multipole (IRM) in front of the redesigned C-trap/Orbitrap and a new ion funnel that allows gentler ion introduction, among other changes. These modifications in Ascend hardware configuration enabled an increase in parallelizable ion injection time during higher-energy collisional dissociation (HCD) Orbitrap tandem MS (FTMS2) analysis of ∼5 ms. This enhancement was particularly valuable in the analyses of limited sample amounts, where improvements in sensitivity resulted in up to 140% increase in the number of identified tryptic peptides. Further, analysis of phosphorylated peptides enriched from the K562 human cell line yielded up to ∼50% increase in the number of unique phosphopeptides and localized phosphosites. Strikingly, we also observed a ∼2-fold boost in the number of detected N-glycopeptides, likely owing to the improvements in ion transmission and sensitivity. In addition, we performed the multiplexed quantitative proteomics analyses of TMT11-plex labeled HEK293T tryptic peptides and observed 9-14% increase in the number of quantified peptides. In conclusion, the Orbitrap Ascend consistently outperformed its predecessor the Orbitrap Eclipse in various bottom-up proteomic analyses, and we anticipate that it will generate reproducible and in-depth datasets for numerous proteomic applications.
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Affiliation(s)
- Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | | | | | - Michael S. Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - David Bergen
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | | | | | | | | | | | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
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5
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Kline JT, Belford MW, Huang J, Greer JB, Bergen D, Fellers RT, Greer SM, Horn DM, Zabrouskov V, Huguet R, Boeser CL, Durbin KR, Fornelli L. Improved Label-Free Quantification of Intact Proteoforms Using Field Asymmetric Ion Mobility Spectrometry. Anal Chem 2023. [PMID: 37252723 DOI: 10.1021/acs.analchem.3c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The high-throughput quantification of intact proteoforms using a label-free approach is typically performed on proteins in the 0-30 kDa mass range extracted from whole cell or tissue lysates. Unfortunately, even when high-resolution separation of proteoforms is achieved by either high-performance liquid chromatography or capillary electrophoresis, the number of proteoforms that can be identified and quantified is inevitably limited by the inherent sample complexity. Here, we benchmark label-free quantification of proteoforms of Escherichia coli by applying gas-phase fractionation (GPF) via field asymmetric ion mobility spectrometry (FAIMS). Recent advances in Orbitrap instrumentation have enabled the acquisition of high-quality intact and fragmentation mass spectra without the need for averaging time-domain transients prior to Fourier transform. The resulting speed improvements allowed for the application of multiple FAIMS compensation voltages in the same liquid chromatography-tandem mass spectrometry experiment without increasing the overall data acquisition cycle. As a result, the application of FAIMS to label-free quantification based on intact mass spectra substantially increases the number of both identified and quantified proteoforms without penalizing quantification accuracy in comparison to traditional label-free experiments that do not adopt GPF.
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Affiliation(s)
- Jake T Kline
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | | | - Jingjing Huang
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Joseph B Greer
- Proteinaceous, Inc., Evanston, Illinois 60208, United States
| | - David Bergen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Ryan T Fellers
- Proteinaceous, Inc., Evanston, Illinois 60208, United States
| | | | - David M Horn
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | | | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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6
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Ruwolt M, He Y, Borges Lima D, Barshop W, Broichhagen J, Huguet R, Viner R, Liu F. Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity. Anal Chem 2023; 95:5248-5255. [PMID: 36926872 PMCID: PMC10061366 DOI: 10.1021/acs.analchem.2c05141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is a universal tool for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental advances improved cross-link identification by enriching the cross-linker-modified peptides chemically with the use of enrichable cross-linkers. However, mono-links (i.e., peptides modified with a hydrolyzed cross-linker) still hinder efficient cross-link identification since a large proportion of measurement time is spent on their MS2 acquisition. Currently, cross-links and mono-links cannot be separated by sample preparation techniques or chromatography because they are chemically almost identical. Here, we found that based on the intensity ratios of four diagnostic peaks when using PhoX/tBu-PhoX cross-linkers, cross-links and mono-links can be partially distinguished. Harnessing their characteristic intensity ratios for real-time library search (RTLS)-based triggering of high-resolution MS2 scans increased the number of cross-link identifications from both single protein samples and intact E. coli cells. Specifically, RTLS improves cross-link identification from unenriched samples and short gradients, emphasizing its advantages in high-throughput approaches and when instrument time or sample amount is limited.
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Affiliation(s)
- Max Ruwolt
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - Yi He
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Diogo Borges Lima
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - William Barshop
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Johannes Broichhagen
- Department of Chemical Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Fan Liu
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany.,Charité─Universitätsmedizin Berlin, Charitépl. 1, Berlin 10117, Germany
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7
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Schachner LF, Phung W, Han G, Darwish M, Bell A, Mellors JS, Srzentic K, Huguet R, Blanchette C, Sandoval W. High-Throughput, Quantitative Analysis of Peptide-Exchanged MHCI Complexes by Native Mass Spectrometry. Anal Chem 2022; 94:14593-14602. [PMID: 36179215 PMCID: PMC9607865 DOI: 10.1021/acs.analchem.2c02423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022]
Abstract
Immune monitoring in cancer immunotherapy involves screening CD8+ T-cell responses against neoantigens, the tumor-specific peptides presented by Major histocompatibility complex Class I (MHCI) on the cell surface. High-throughput immune monitoring requires methods to produce and characterize small quantities of thousands of MHCI-peptide complexes that may be tested for a patient's T-cell response. MHCI synthesis has been achieved using a photocleavable peptide that is exchanged by the neoantigen; however, assays that measure peptide exchange currently disassemble the complex prior to analysis─precluding direct molecular characterization. Here, we use native mass spectrometry (MS) to profile intact recombinant MHCI complexes and directly measure peptide exchange. Coupled with size-exclusion chromatography or capillary-zone electrophoresis, the assay identified all tested human leukocyte antigen (HLA)/peptide combinations in the nanomole to picomole range with minimal run time, reconciling the synthetic and analytical requirements of MHCI-peptide screening with the downstream T-cell assays. We further show that the assay can be "multiplexed" by measuring exchange of multiple peptides simultaneously and also enables calculation of Vc50, a measure of gas-phase stability. Additionally, MHCI complexes were fragmented by top-down sequencing, demonstrating that the intact complex, peptide sequence, and their binding affinity can be determined in a single analysis. This screening tool for MHCI-neoantigen complexes represents a step toward the application of state-of-the-art MS technology in translational settings. Not only is this assay already informing on the viability of immunotherapy in practice, the platform also holds promise to inspire novel MS readouts for increasingly complex biomolecules used in the diagnosis and treatment of disease.
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Affiliation(s)
- Luis F. Schachner
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South
San Francisco, California 94080, United States
| | - Wilson Phung
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South
San Francisco, California 94080, United States
| | - Guanghui Han
- BGI
Americas, San Jose, California 95134, United States
| | - Martine Darwish
- Department
of Protein Chemistry, Genentech Inc., South San Francisco, California 94080, United States
| | - Ashley Bell
- 908
Devices, Carrboro, North Carolina 27510, United States
| | | | | | - Romain Huguet
- Thermo
Fisher Scientific, San Jose, California 95134, United States
| | - Craig Blanchette
- Department
of Protein Chemistry, Genentech Inc., South San Francisco, California 94080, United States
| | - Wendy Sandoval
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South
San Francisco, California 94080, United States
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8
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Nitika, Zheng B, Ruan L, Kline JT, Omkar S, Sikora J, Texeira Torres M, Wang Y, Takakuwa JE, Huguet R, Klemm C, Segarra VA, Winters MJ, Pryciak PM, Thorpe PH, Tatebayashi K, Li R, Fornelli L, Truman AW. Comprehensive characterization of the Hsp70 interactome reveals novel client proteins and interactions mediated by posttranslational modifications. PLoS Biol 2022; 20:e3001839. [PMID: 36269765 PMCID: PMC9629621 DOI: 10.1371/journal.pbio.3001839] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/02/2022] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
Hsp70 interactions are critical for cellular viability and the response to stress. Previous attempts to characterize Hsp70 interactions have been limited by their transient nature and the inability of current technologies to distinguish direct versus bridged interactions. We report the novel use of cross-linking mass spectrometry (XL-MS) to comprehensively characterize the Saccharomyces cerevisiae (budding yeast) Hsp70 protein interactome. Using this approach, we have gained fundamental new insights into Hsp70 function, including definitive evidence of Hsp70 self-association as well as multipoint interaction with its client proteins. In addition to identifying a novel set of direct Hsp70 interactors that can be used to probe chaperone function in cells, we have also identified a suite of posttranslational modification (PTM)-associated Hsp70 interactions. The majority of these PTMs have not been previously reported and appear to be critical in the regulation of client protein function. These data indicate that one of the mechanisms by which PTMs contribute to protein function is by facilitating interaction with chaperones. Taken together, we propose that XL-MS analysis of chaperone complexes may be used as a unique way to identify biologically important PTMs on client proteins.
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Affiliation(s)
- Nitika
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Bo Zheng
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
| | - Jake T. Kline
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States America
| | - Siddhi Omkar
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Jacek Sikora
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois, United States America
| | - Mara Texeira Torres
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
| | - Jade E. Takakuwa
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Romain Huguet
- Thermo Scientific, San Jose, California, United States America
| | - Cinzia Klemm
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Verónica A. Segarra
- Departments of Biological Sciences and Chemistry, Goucher College, Baltimore, Maryland, United States America
| | - Matthew J. Winters
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States America
| | - Peter M. Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States America
| | - Peter H. Thorpe
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Kazuo Tatebayashi
- Laboratory of Molecular Genetics, Frontier Research Unit, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States America
| | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States America
| | - Andrew W. Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
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9
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Furtwängler B, Üresin N, Motamedchaboki K, Huguet R, Lopez-Ferrer D, Zabrouskov V, Porse BT, Schoof EM. Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics. Mol Cell Proteomics 2022; 21:100219. [PMID: 35219906 PMCID: PMC8961214 DOI: 10.1016/j.mcpro.2022.100219] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/24/2022] [Accepted: 02/23/2022] [Indexed: 10/26/2022] Open
Abstract
In the young field of single-cell proteomics (scMS), there is a great need for improved global proteome characterization, both in terms of proteins quantified per cell and quantitative performance thereof. The recently introduced real-time search (RTS) on the Orbitrap Eclipse Tribrid mass spectrometer in combination with SPS-MS3 acquisition has been shown to be beneficial for the measurement of samples that are multiplexed using isobaric tags. Multiplexed scMS requires high ion injection times and high-resolution spectra to quantify the single-cell signal; however, the carrier channel facilitates peptide identification and thus offers the opportunity for fast on-the-fly precursor filtering before committing to the time-intensive quantification scan. Here, we compared classical MS2 acquisition against RTS-SPS-MS3, both using the Orbitrap Eclipse Tribrid MS with the FAIMS Pro ion mobility interface and present a new acquisition strategy termed RETICLE (RTS enhanced quant of single cell spectra) that makes use of fast real-time searched linear ion trap scans to preselect MS1 peptide precursors for quantitative MS2 Orbitrap acquisition. We show that classical MS2 acquisition is outperformed by both RTS-SPS-MS3 through increased quantitative accuracy at similar proteome coverage, and RETICLE through higher proteome coverage, with the latter enabling the quantification of over 1000 proteins per cell at an MS2 injection time of 750 ms using a 2 h gradient.
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Affiliation(s)
- Benjamin Furtwängler
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Nil Üresin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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10
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Bailey AO, Huguet R, Mullen C, Syka JEP, Russell WK. Ion-Ion Charge Reduction Addresses Multiple Challenges Common to Denaturing Intact Mass Analysis. Anal Chem 2022; 94:3930-3938. [PMID: 35189062 DOI: 10.1021/acs.analchem.1c04973] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Complete LC-MS-based protein primary sequence characterization requires measurement of intact protein profiles under denaturing and/or reducing conditions. To address issues of protein overcharging of unstructured proteins under acidic, denaturing conditions and sample heterogeneity (macro- and micro-scales) which often confound denaturing intact mass analysis of a wide variety of protein samples, we propose the use of broadband isolation of entire charge state distributions of intact proteins followed by ion-ion proton transfer charge reduction, which we have termed "full scan PTCR" (fsPTCR). Using rapid denaturing size exclusion chromatography coupled to fsPTCR-Orbitrap MS and time-resolved deconvolution data analysis, we demonstrate a strategy for method optimization, leading to significant analytical advantages over conventional MS1. Denaturing analysis of the flexible bacterial translation initiation factor 2 (91 kDa) using fsPTCR reduced overcharging and showed an 11-fold gain in S/N compared to conventional MS1. Analysis by fsPTCR-MS of the microheterogeneous glycoprotein fetuin revealed twice as many proteoforms as MS1 (112 vs 56). In a macroheterogeneous mixture of proteins ranging from 14 to 148 kDa, fsPTCR provided more than 10-fold increased sensitivity and quantitative accuracy for diluted bovine serum albumin (66 kDa). Finally, our analysis shows that collisional gas pressure is a key parameter which can be utilized during fsPTCR to retain or remove larger proteins from acquired spectra.
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Affiliation(s)
- Aaron O Bailey
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Christopher Mullen
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - John E P Syka
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - William K Russell
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
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11
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Kline JT, Mullen C, Durbin KR, Oates RN, Huguet R, Syka JEP, Fornelli L. Sequential Ion-Ion Reactions for Enhanced Gas-Phase Sequencing of Large Intact Proteins in a Tribrid Orbitrap Mass Spectrometer. J Am Soc Mass Spectrom 2021; 32:2334-2345. [PMID: 33900069 DOI: 10.1021/jasms.1c00062] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Obtaining extensive sequencing of an intact protein is essential in order to simultaneously determine both the nature and exact localization of chemical and genetic modifications which distinguish different proteoforms arising from the same gene. To effectively achieve such characterization, it is necessary to take advantage of the analytical potential offered by the top-down mass spectrometry approach to protein sequence analysis. However, as a protein increases in size, its gas-phase dissociation produces overlapping, low signal-to-noise fragments. The application of advanced ion dissociation techniques such as electron transfer dissociation (ETD) and ultraviolet photodissociation (UVPD) can improve the sequencing results compared to slow-heating techniques such as collisional dissociation; nonetheless, even ETD- and UVPD-based approaches have thus far fallen short in their capacity to reliably enable extensive sequencing of proteoforms ≥30 kDa. To overcome this issue, we have applied proton transfer charge reduction (PTCR) to limit signal overlap in tandem mass spectra (MS2) produced by ETD (alone or with supplemental ion activation, EThcD). Compared to conventional MS2 experiments, following ETD/EThcD MS2 with PTCR MS3 prior to m/z analysis of deprotonated product ions in the Orbitrap mass analyzer proved beneficial for the identification of additional large protein fragments (≥10 kDa), thus improving the overall sequencing and in particular the coverage of the central portion of all four analyzed proteins spanning from 29 to 56 kDa. Specifically, PTCR-based data acquisition led to 39% sequence coverage for the 56 kDa glutamate dehydrogenase, which was further increased to 44% by combining fragments obtained via HCD followed by PTCR MS3.
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Affiliation(s)
- Jake T Kline
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019, United States
| | - Christopher Mullen
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | | | - Ryan N Oates
- Department of Chemistry and Biochemistry, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019, United States
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - John E P Syka
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Luca Fornelli
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019, United States
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12
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Siméon S, Galy A, Woerther P, Fihman V, Gallien S, Deux J, Gomart C, Huguet R, Lim P, Lepeule R. Existe-t-il encore des endocardites infectieuses non documentées microbiologiquement ? Infect Dis Now 2021. [DOI: 10.1016/j.idnow.2021.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Cohn W, Huguet R, Zabrouskov V, Whitelegge J. Dissociation Strategies to Maximize Coverage of α-Helical Domains in Top-Down Mass Spectrometry of Integral Membrane Proteins. J Am Soc Mass Spectrom 2021; 32:1380-1387. [PMID: 33956438 DOI: 10.1021/jasms.1c00031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Transmembrane α-helical domains of membrane proteins tend to remain structured in the gas phase, presenting a challenge for efficient electron capture/transfer dissociation during top-down dissociation mass spectrometry (MS) experiments. In this study, we compare results from different dissociation modes on a modern Orbitrap platform applied to a model integral membrane protein containing two transmembrane helices, the c-subunit of the Fo domain of the chloroplast ATP synthase. Using commercially available options, we compare collisionally activated dissociation (CAD) with the related variant higher-energy collisional dissociation (HCD) and with electron transfer dissociation (ETD). HCD performed better than CAD and ETD. A combined method utilizing both ETD and HCD (EThcD) demonstrates significant synergy over HCD or ETD alone, representing a robust option analogous to activated ion electron capture dissociation, whereby an infrared laser was used to heat the protein ion alongside electron bombardment. Ultraviolet photodissociation at 213 nm displays at least three backbone dissociation mechanisms and covered nearly 100% of backbone bonds, suggesting significant potential for this technique.
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Affiliation(s)
- Whitaker Cohn
- The Pasarow Mass Spectrometry Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90024, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95054, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95054, United States
| | - Julian Whitelegge
- The Pasarow Mass Spectrometry Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90024, United States
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14
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Gerbasi VR, Melani RD, Abbatiello SE, Belford MW, Huguet R, McGee JP, Dayhoff D, Thomas PM, Kelleher NL. Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics. Anal Chem 2021; 93:6323-6328. [PMID: 33844503 DOI: 10.1021/acs.analchem.1c00402] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Field asymmetric ion mobility spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity and enables more proteins to be identified by providing additional gas-phase separation. Here, we tested the performance of cylindrical FAIMS for the identification and characterization of proteoforms by top-down mass spectrometry of heterogeneous protein mixtures. Combining FAIMS with chromatographic separation resulted in a 62% increase in protein identifications, an 8% increase in proteoform identifications, and an improvement in proteoform identification compared to samples analyzed without FAIMS. In addition, utilization of FAIMS resulted in the identification of proteins encoded by lower-abundance mRNA transcripts. These improvements were attributable, in part, to improved signal-to-noise for proteoforms with similar retention times. Additionally, our results show that the optimal compensation voltage of any given proteoform was correlated with the molecular weight of the analyte. Collectively these results suggest that the addition of FAIMS can enhance top-down proteomics in both discovery and targeted applications.
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Affiliation(s)
- Vincent R Gerbasi
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States.,Pacific Northwest National Laboratories, Richland, Washington 99352, United States
| | - Rafael D Melani
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Susan E Abbatiello
- Northeastern University, Boston, Massachusetts 02115, United States.,Thermo Fisher Scientific, San Jose, California 98665, United States
| | | | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 98665, United States
| | - John P McGee
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Dawson Dayhoff
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
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15
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Gaun A, Lewis Hardell KN, Olsson N, O'Brien JJ, Gollapudi S, Smith M, McAlister G, Huguet R, Keyser R, Buffenstein R, McAllister FE. Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice. J Proteome Res 2021; 20:1280-1295. [PMID: 33499602 DOI: 10.1021/acs.jproteome.0c00681] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Performing large-scale plasma proteome profiling is challenging due to limitations imposed by lengthy preparation and instrument time. We present a fully automated multiplexed proteome profiling platform (AutoMP3) using the Hamilton Vantage liquid handling robot capable of preparing hundreds to thousands of samples. To maximize protein depth in single-shot runs, we combined 16-plex Tandem Mass Tags (TMTpro) with high-field asymmetric waveform ion mobility spectrometry (FAIMS Pro) and real-time search (RTS). We quantified over 40 proteins/min/sample, doubling the previously published rates. We applied AutoMP3 to investigate the naked mole-rat plasma proteome both as a function of the circadian cycle and in response to ultraviolet (UV) treatment. In keeping with the lack of synchronized circadian rhythms in naked mole-rats, we find few circadian patterns in plasma proteins over the course of 48 h. Furthermore, we quantify many disparate changes between mice and naked mole-rats at both 48 h and one week after UV exposure. These species differences in plasma protein temporal responses could contribute to the pronounced cancer resistance observed in naked mole-rats. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD022891.
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Affiliation(s)
- Aleksandr Gaun
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Kaitlyn N Lewis Hardell
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States.,Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892-7315, United States
| | - Niclas Olsson
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Jonathon J O'Brien
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Sudha Gollapudi
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Megan Smith
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Graeme McAlister
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Robert Keyser
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Rochelle Buffenstein
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
| | - Fiona E McAllister
- Calico Life Sciences LLC, South San Francisco, California 94080-7095, United States
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16
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Fard D, Huguet R, Koutsoukis A, Deguillard C, Tuffreau AS, Deux JF, Lim P, Teiger E. [SARS-COV-2 myocarditis. An update]. Ann Cardiol Angeiol (Paris) 2020; 69:349-354. [PMID: 33069383 PMCID: PMC7543970 DOI: 10.1016/j.ancard.2020.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/04/2020] [Indexed: 01/08/2023]
Abstract
The outbreak of the SARS-CoV-2 virus responsible for the COVID-19 disease has given rise to a new disease whose boundaries are still to be discovered. While the first data suggested a purely respiratory infection, the most recent publications highlight a large pleomorphism of the disease, responsible for multiple organ damage, of which cardiac injury seems to be the most represented. This cardiac injury can present as acute myocarditis. Our aim was to discuss the pathophysiological rationale underlying the existence of SARS-CoV-2 myocarditis and to analyze the literature data regarding the diagnosis and treatment of this particular entity.
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Affiliation(s)
- D Fard
- Inserm U955, Institut Mondor de recherche biomédicale, université Paris-Est Créteil, 94010 Créteil, France; Service de cardiologie, hôpital universitaire Henri-Mondor, AP-HP, 94010 Créteil, France.
| | - R Huguet
- Inserm U955, Institut Mondor de recherche biomédicale, université Paris-Est Créteil, 94010 Créteil, France; Service de cardiologie, hôpital universitaire Henri-Mondor, AP-HP, 94010 Créteil, France
| | - A Koutsoukis
- Inserm U955, Institut Mondor de recherche biomédicale, université Paris-Est Créteil, 94010 Créteil, France; Service de cardiologie, hôpital universitaire Henri-Mondor, AP-HP, 94010 Créteil, France
| | - C Deguillard
- Inserm U955, Institut Mondor de recherche biomédicale, université Paris-Est Créteil, 94010 Créteil, France; Service de cardiologie, hôpital universitaire Henri-Mondor, AP-HP, 94010 Créteil, France
| | - A-S Tuffreau
- Inserm U955, Institut Mondor de recherche biomédicale, université Paris-Est Créteil, 94010 Créteil, France; Service de cardiologie, hôpital universitaire Henri-Mondor, AP-HP, 94010 Créteil, France
| | - J-F Deux
- Inserm U955, Institut Mondor de recherche biomédicale, université Paris-Est Créteil, 94010 Créteil, France; Service d'imagerie médicale, hôpital universitaire Henri-Mondor, AP-HP, 94010 Créteil, France
| | - P Lim
- Inserm U955, Institut Mondor de recherche biomédicale, université Paris-Est Créteil, 94010 Créteil, France; Service de cardiologie, hôpital universitaire Henri-Mondor, AP-HP, 94010 Créteil, France
| | - E Teiger
- Inserm U955, Institut Mondor de recherche biomédicale, université Paris-Est Créteil, 94010 Créteil, France; Service de cardiologie, hôpital universitaire Henri-Mondor, AP-HP, 94010 Créteil, France
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17
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Cong Y, Motamedchaboki K, Misal SA, Liang Y, Guise AJ, Truong T, Huguet R, Plowey ED, Zhu Y, Lopez-Ferrer D, Kelly RT. Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell. Chem Sci 2020; 12:1001-1006. [PMID: 34163866 PMCID: PMC8178986 DOI: 10.1039/d0sc03636f] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/15/2020] [Indexed: 12/27/2022] Open
Abstract
We report on the combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer for greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions for more effective MS analysis of multiply charged peptides, resulting in an average of 1056 protein groups identified from single HeLa cells without MS1-level feature matching. This is 2.3 times more identifications than without FAIMS and a far greater level of proteome coverage for single mammalian cells than has been previously reported for a label-free study. Differential analysis of single microdissected motor neurons and interneurons from human spinal tissue indicated a similar level of proteome coverage, and the two subpopulations of cells were readily differentiated based on single-cell label-free quantification.
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Affiliation(s)
- Yongzheng Cong
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | | | - Santosh A Misal
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | | | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | | | | | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | | | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
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18
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Hugues B, Emsen B, Ternacle J, Huguet R, Fiore A, Lepeule R, Chevalier X, Abulizi M, Eymard F. FRI0439 PET-CT IN THE ASSESSMENT OF OSTEOARTICULAR INFECTIONS ASSOCIATED WITH INFECTIVE ENDOCARDITIS. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.6185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:Five to eleven percent of infective endocarditis (IE) are associated with a musculoskeletal infection. Thanks to its good sensitivity, the use of PET-CT in this pathology makes it possible to confirm the diagnosis by seeking valvular hypermetabolism but also by mapping distant septic foci.Objectives:The main objective of our study was to assess the prevalence of osteoarticular fixation (OAF) with PET-CT, symptomatic or not, in patients with IE. The secondary objectives were to determine predictive factors for osteoarticular infections such as the type of valve damage (native or prosthetic) and germ.Methods:This study was carried out on the basis of a prospective cohort of patients admitted in the department of cardiology in Henri Mondor Hospital for IE suspicion between August 2015 and July 2019. Demographic, clinical, bacteriological, imaging and therapeutic data have been collected. Patients matching Duke’s modified criteria according to ESC 2015 (Duke + IE) and / or a cardiac fixation according to standard whole-body PET-CT were included in the analysis. All of the PET-CT scans were reviewed by a nuclear medicine specialist to confirm whether or not there was a heart condition and to look for septic-looking OAF.Results:From this cohort, we included 90 IE Duke + patients and 42 patients with cardiac PET-CT fixation (including 31 IE Duke +). In the IE Duke + group, we found OAF in 18 patients (20%), 39% of whom were asymptomatic. There were 9 spondylodiscitis (4 on the cervical level, 7 on the thoracic level, and 2 on the lumbar level), 5 glenohumeral arthritis, 2 coxofemoral arthritis, 1 sternoclavicular arthritis and 1 sacroiliac arthritis. The IE affected the aortic valve in 50% of the cases and the mitral valve in 22%. In other cases, the infection involved the internal automatic defibrillator (ICD) or the pacemaker. The valves were prosthetic in 73% of the cases. The bacterial ecology was mainly represented by Enterococcus faecalis (39%) then staphylococcus aureus (17%) against 14% and 13% respectively in the entire IE Duke + group. In the group with cardiac PET-CT fixation, OAF was found in 10 patients (40%), 70% of whom were asymptomatic. Among them, there were 5 spondylodiscitis (2 cervico- thoracic and 3 exclusively thoracic), 2 glenohumeral arthritis (20%), 2 coxofemoral arthritis and 1 sternoclavicular arthritis. The IE affected the aortic valve in 60% of the cases, mitral in 30% of the cases and it was an infection on ICD in 10% of the cases. The main germs found were Enterococcus faecalis (30% of cases) and Staphylococcus epidermidis (20% of cases).Conclusion:In patients with IE, PET-CT seems to be interesting in detection of osteoarticular infections, and consequently, could impact the diagnosis and the treatment modalities. In our cohort, 1 patient in 5 had an OAF and nearly 40% of them were asymptomatic. The overrepresentation of enterococcus is consistent with recent data in the literatureReferences:[1]Dahl A, Iversen K, Tonder N, Hoest N, Arpi M, Dalsgaard M, et al. Prevalence of Infective Endocarditis in Enterococcus faecalis Bacteremia. J Am Coll Cardiol. 16 juill 2019;74(2):193‑201.Disclosure of Interests:Benjamin HUGUES: None declared, Bérivan EMSEN: None declared, Julien TERNACLE: None declared, Raphaëlle HUGUET: None declared, Antonio FIORE: None declared, Raphaëlle LEPEULE: None declared, Xavier Chevalier: None declared, Mukedaisi ABULIZI: None declared, Florent Eymard Consultant of: Regenlab
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19
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Gault J, Liko I, Landreh M, Shutin D, Bolla JR, Jefferies D, Agasid M, Yen HY, Ladds MJGW, Lane DP, Khalid S, Mullen C, Remes PM, Huguet R, McAlister G, Goodwin M, Viner R, Syka JEP, Robinson CV. Combining native and 'omics' mass spectrometry to identify endogenous ligands bound to membrane proteins. Nat Methods 2020; 17:505-508. [PMID: 32371966 PMCID: PMC7332344 DOI: 10.1038/s41592-020-0821-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/25/2020] [Indexed: 02/08/2023]
Abstract
Ligands bound to protein assemblies provide critical information for function, yet are often difficult to capture and define. Here we develop a top-down method, 'nativeomics', unifying 'omics' (lipidomics, proteomics, metabolomics) analysis with native mass spectrometry to identify ligands bound to membrane protein assemblies. By maintaining the link between proteins and ligands, we define the lipidome/metabolome in contact with membrane porins and a mitochondrial translocator to discover potential regulators of protein function.
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Affiliation(s)
- Joseph Gault
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Idlir Liko
- Department of Chemistry, University of Oxford, Oxford, UK
- OMass Therapeutics, Oxford, UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Denis Shutin
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | - Mark Agasid
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
| | | | | | | | | | | | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, USA
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20
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Yu Q, Paulo JA, Naverrete-Perea J, McAlister GC, Canterbury JD, Bailey DJ, Robitaille AM, Huguet R, Zabrouskov V, Gygi SP, Schweppe DK. Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics. Anal Chem 2020; 92:6478-6485. [PMID: 32250601 DOI: 10.1021/acs.analchem.9b05685] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The rise of sample multiplexing in quantitative proteomics for the dissection of complex phenotypic comparisons has been advanced by the development of ever more sensitive and robust instrumentation. Here, we evaluated the utility of the Orbitrap Eclipse Tribrid mass spectrometer (advanced quadrupole filter, optimized FTMS scan overhead) and new instrument control software features (Precursor Fit filtering, TurboTMT and Real-time Peptide Search filtering). Multidimensional comparisons of these novel features increased total peptide identifications by 20% for SPS-MS3 methods and 14% for HRMS2 methods. Importantly Real-time Peptide Search filtering enabled a ∼2× throughput improvement for quantification. Across the board, these sensitivity increases were attained without sacrificing quantitative accuracy. New hardware and software features enable more efficient characterization in pursuit of comparative whole proteome insights.
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Affiliation(s)
- Qing Yu
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | | | | | | | - Derek J Bailey
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Steven P Gygi
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Devin K Schweppe
- Harvard Medical School, Boston, Massachusetts 02115, United States
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21
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Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey DJ, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Wouters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP. Correction to Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry. Anal Chem 2020; 92:4690. [PMID: 32134636 PMCID: PMC10777686 DOI: 10.1021/acs.analchem.0c00888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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McGee JP, Melani RD, Goodwin M, McAlister G, Huguet R, Senko MW, Compton PD, Kelleher NL. Voltage Rollercoaster Filtering of Low-Mass Contaminants During Native Protein Analysis. J Am Soc Mass Spectrom 2020; 31:763-767. [PMID: 32126774 PMCID: PMC7274025 DOI: 10.1021/jasms.9b00037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Intact protein mass spectrometry (MS) via electrospray-based methods is often degraded by low-mass contaminants, which can suppress the spectral quality of the analyte of interest via space-charge effects. Consequently, selective removal of contaminants by their mobilities would benefit native MS if achieved without additional hardware and before the mass analyzer regions used for selection, analyte readout, or tandem MS. Here, we use the high-pressure multipole within the source of an Orbitrap Tribrid as the foundation for a coarse ion filter. Using this method, we show complete filtration of 2 mM polyethylene glycol (PEG-1000) during native MS of SILu mAb antibody present at a 200× lower concentration. We also show the generality of the process by rescuing 10 μM tetrameric pyruvate kinase from 2 mM PEG-1000, asserting this voltage rollercoaster filtering (VRF) method for use in native MS as an efficient alternative to conventional purification methods.
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Affiliation(s)
- John P McGee
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Michael Goodwin
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Graeme McAlister
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Philip D Compton
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
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23
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Courtenay LA, Huguet R, Yravedra J. Scratches and grazes: a detailed microscopic analysis of trampling phenomena. J Microsc 2020; 277:107-117. [PMID: 32017080 DOI: 10.1111/jmi.12873] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/10/2020] [Accepted: 02/02/2020] [Indexed: 11/28/2022]
Abstract
Sedimentary abrasion and postdepositional damage to fossil remains are of great interest if considering the possible distortion they could produce in the archaeological and paleontological record. Since their discovery, natural agents such as trampling phenomena have been a topic of great taphonomic interest. Nevertheless, the majority of investigation into these traces has focused almost exclusively on their differentiation from other anthropic agents such as cut marks. In recent years, advances into bone surface modification analysis via geometric morphometrics have proven useful for in-depth characterization of different taphonomic traces; including cut, tooth and percussion marks. Through this, a preliminary study of trampling marks using advanced 3D digital microscopy was able to detect differences between what have since been known as scratch and graze marks. The present study expands from this, developing a more detailed analysis of these traces. Here, we use advanced data science techniques to provide a means of understanding trampling mark variations, contributing to our knowledge of site formation processes. Our results show how scratch and graze marks are a product of progressional decay and changes in cortical hardness, providing a new means of understanding taphonomic processes. LAY DESCRIPTION: The study of microscopic bone surface modifications in archaeology and palaeontology is of great importance, allowing for a detailed reconstruction of the formation of a site and providing a means of interpreting the fossil register. The damage that sedimentary abrasion can produce, however, is likely to distort and influence these studies, thus requiring a detailed understanding of the different traces that can be found on different materials. Here, we use advanced 3D digital microscopy and pattern recognition algorithms to analyse the different marks produced in different sedimentological contexts, also controlling for other variables such as the state of the bone when buried, the type of bone and the time exposed to these types of damages. Through this detailed microscopic analysis of these types of damages, we are able to conclude that morphological variations in trampling marks are product of the state of decay when the bones are buried.
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Affiliation(s)
- L A Courtenay
- Department of Cartographic and Terrain Engineering, Higher Polytechnic School of Ávila, Higher Polytechnic School of Ávila, University of Salamanca, Hornos Caleros 50, 05003, Ávila, Spain.,Área de Prehistoria, Universitat de Rovir i Virgili (URV), Avignuda de Catalunya 35, 43002, Tarragona, Spain.,Institut de Paleoecologia Humana i Evolució Social (IPHES), C/Marcellí Domingo s/n, Campus Sescelades URV (Edifici W3) E3, 43002, Tarragona, Spain
| | - R Huguet
- Área de Prehistoria, Universitat de Rovir i Virgili (URV), Avignuda de Catalunya 35, 43002, Tarragona, Spain.,Institut de Paleoecologia Humana i Evolució Social (IPHES), C/Marcellí Domingo s/n, Campus Sescelades URV (Edifici W3) E3, 43002, Tarragona, Spain.,Unit Associated to CSIC, Departamento de Paleobiologia, Museo de Ciencias Naturales, calle José Gutiérrez Abascal, s/n, 28006, Madrid, Spain
| | - J Yravedra
- Department of Prehistory, Complutense University, Prof. Aranguren s/n, 28040, Madrid, Spain.,Director of the C. A. I. Archaeometry and Archaeological Analysis, Complutense University, Professor Aranguren s/n, 28040, Madrid, Spain
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24
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Fornelli L, Srzentić K, Toby TK, Doubleday PF, Huguet R, Mullen C, Melani RD, Dos Santos Seckler H, DeHart CJ, Weisbrod CR, Durbin KR, Greer JB, Early BP, Fellers RT, Zabrouskov V, Thomas PM, Compton PD, Kelleher NL. Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics. Mol Cell Proteomics 2020; 19:405-420. [PMID: 31888965 PMCID: PMC7000117 DOI: 10.1074/mcp.tir119.001638] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 11/29/2019] [Indexed: 11/06/2022] Open
Abstract
Top-down proteomics studies intact proteoform mixtures and offers important advantages over more common bottom-up proteomics technologies, as it avoids the protein inference problem. However, achieving complete molecular characterization of investigated proteoforms using existing technologies remains a fundamental challenge for top-down proteomics. Here, we benchmark the performance of ultraviolet photodissociation (UVPD) using 213 nm photons generated by a solid-state laser applied to the study of intact proteoforms from three organisms. Notably, the described UVPD setup applies multiple laser pulses to induce ion dissociation, and this feature can be used to optimize the fragmentation outcome based on the molecular weight of the analyzed biomolecule. When applied to complex proteoform mixtures in high-throughput top-down proteomics, 213 nm UVPD demonstrated a high degree of complementarity with the most employed fragmentation method in proteomics studies, higher-energy collisional dissociation (HCD). UVPD at 213 nm offered higher average proteoform sequence coverage and degree of proteoform characterization (including localization of post-translational modifications) than HCD. However, previous studies have shown limitations in applying database search strategies developed for HCD fragmentation to UVPD spectra which contains up to nine fragment ion types. We therefore performed an analysis of the different UVPD product ion type frequencies. From these data, we developed an ad hoc fragment matching strategy and determined the influence of each possible ion type on search outcomes. By paring down the number of ion types considered in high-throughput UVPD searches from all types down to the four most abundant, we were ultimately able to achieve deeper proteome characterization with UVPD. Lastly, our detailed product ion analysis also revealed UVPD cleavage propensities and determined the presence of a product ion produced specifically by 213 nm photons. All together, these observations could be used to better elucidate UVPD dissociation mechanisms and improve the utility of the technique for proteomic applications.
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Affiliation(s)
- Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Kristina Srzentić
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Timothy K Toby
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Peter F Doubleday
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134
| | | | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Henrique Dos Santos Seckler
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Caroline J DeHart
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | | | - Kenneth R Durbin
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208; Proteinaceous Inc., Evanston, Illinois 60201
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Bryan P Early
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | | | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208.
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25
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Cong Y, Liang Y, Motamedchaboki K, Huguet R, Truong T, Zhao R, Shen Y, Lopez-Ferrer D, Zhu Y, Kelly RT. Improved Single-Cell Proteome Coverage Using Narrow-Bore Packed NanoLC Columns and Ultrasensitive Mass Spectrometry. Anal Chem 2020; 92:2665-2671. [PMID: 31913019 DOI: 10.1021/acs.analchem.9b04631] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-cell proteomics can provide unique insights into biological processes by resolving heterogeneity that is obscured by bulk measurements. Gains in the overall sensitivity and proteome coverage through improvements in sample processing and analysis increase the information content obtained from each cell, particularly for less abundant proteins. Here we report on improved single-cell proteome coverage through the combination of the previously developed nanoPOTS platform with further miniaturization of liquid chromatography (LC) separations and implementation of an ultrasensitive latest generation mass spectrometer. Following nanoPOTS sample preparation, protein digests from single cells were separated using a 20 μm i.d. in-house-packed nanoLC column. Separated peptides were ionized using an etched fused-silica emitter capable of stable operation at the ∼20 nL/min flow rate provided by the LC separation. Ultrasensitive LC-MS analysis was achieved using the Orbitrap Eclipse Tribrid mass spectrometer. An average of 362 protein groups were identified by tandem mass spectrometry (MS/MS) from single HeLa cells, and 874 protein groups were identified using the Match Between Runs feature of MaxQuant. This represents an >70% increase in label-free proteome coverage for single cells relative to previous efforts using larger bore (30 μm i.d.) LC columns coupled to a previous-generation Orbitrap Fusion Lumos mass spectrometer.
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Affiliation(s)
- Yongzheng Cong
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Yiran Liang
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | | | - Romain Huguet
- Thermo Fisher Scientific , San Jose , California 95134 , United States
| | - Thy Truong
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yufeng Shen
- CoAnn Technologies, LLC , Richland , Washington 99354 , United States
| | | | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States.,Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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26
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Juguet W, Faivre L, Deguillard C, Fard D, Pelletier V, Oliver L, Damy T, Mongardon N, Mekontso-Dessap A, Dubois Randé J, Gallet R, Huguet R, Lim P. Levosimendan added to dobutamine in acute decompensated heart failure refractory to dobutamine. Archives of Cardiovascular Diseases Supplements 2020. [DOI: 10.1016/j.acvdsp.2019.09.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Huguet R, Mullen C, Srzentić K, Greer JB, Fellers RT, Zabrouskov V, Syka JEP, Kelleher NL, Fornelli L. Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms. Anal Chem 2019; 91:15732-15739. [PMID: 31714757 DOI: 10.1021/acs.analchem.9b03925] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the recent technological advances in Fourier transform mass spectrometry (FTMS) instrumentation, top-down proteomics (TDP) is currently mostly applied to the characterization of proteoforms <30 kDa due to the poor performance of high-resolution FTMS for the analysis of larger proteoforms and the high complexity of intact proteomes in the 30-60 kDa mass range. Here, we propose a novel data acquisition method based on ion-ion proton transfer, herein termed proton transfer charge reduction (PTCR), to investigate large proteoforms of Pseudomonas aeruginosa in a high-throughput fashion. We designed a targeted data acquisition strategy, named tPTCR, which applies two consecutive gas phase fractionation steps for obtaining intact precursor masses: first, a narrow (1.5 m/z-wide) quadrupole filter m/z transmission window is used to select a subset of charge states from all ionized proteoform cations; second, this aliquot of protein cations is subjected to PTCR in order to reduce their average charge state: upon m/z analysis in an Orbitrap, proteoform mass spectra with minimal m/z peak overlap and easy-to-interpret charge state distributions are obtained, simplifying the proteoform mass calculation. Subsequently, the same quadrupole-selected narrow m/z region of analytes is subjected to collisional dissociation to obtain proteoform sequence information, which used in combination with intact mass information leads to proteoform identification through an off-line database search. The newly proposed method was benchmarked against the previously developed "medium/high" data-dependent acquisition strategy and doubled the number of UniProt entries and proteoforms >30 kDa identified on the liquid chromatography time scale.
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Affiliation(s)
- Romain Huguet
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Christopher Mullen
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Kristina Srzentić
- Thermo Fisher Scientific , 790 Memorial Drive, Suite 2D , Cambridge , Massachusetts 02139 , United States
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - John E P Syka
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Luca Fornelli
- Department of Biology , University of Oklahoma , 730 Van Vleet Oval , Norman , Oklahoma 73071 , United States
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28
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Hernandez-Alba O, Houel S, Hessmann S, Erb S, Rabuka D, Huguet R, Josephs J, Beck A, Drake PM, Cianférani S. A Case Study to Identify the Drug Conjugation Site of a Site-Specific Antibody-Drug-Conjugate Using Middle-Down Mass Spectrometry. J Am Soc Mass Spectrom 2019; 30:2419-2429. [PMID: 31429052 DOI: 10.1007/s13361-019-02296-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
Middle-down mass spectrometry (MD MS) has emerged as a promising alternative to classical bottom-up approaches for protein characterization. Middle-level experiments after enzymatic digestion are routinely used for subunit analysis of monoclonal antibody (mAb)-related compounds, providing information on drug load distribution and average drug-to-antibody ratio (DAR). However, peptide mapping is still the gold standard for primary amino acid sequence assessment, post-translational modifications (PTM), and drug conjugation identification and localization. However, peptide mapping strategies can be challenging when dealing with more complex and heterogeneous mAb formats, like antibody-drug conjugates (ADCs). We report here, for the first time, MD MS analysis of a third-generation site-specific DAR4 ADC using different fragmentation techniques, including higher-energy collisional- (HCD), electron-transfer (ETD) dissociation and 213 nm ultraviolet photodissociation (UVPD). UVPD used as a standalone technique for ADC subunit analysis afforded, within the same liquid chromatography-MS/MS run, enhanced performance in terms of primary sequence coverage compared to HCD- or ETD-based MD approaches, and generated substantially more MS/MS fragments containing either drug conjugation or glycosylation site information, leading to confident drug/glycosylation site identification. In addition, our results highlight the complementarity of ETD and UVPD for both primary sequence validation and drug conjugation/glycosylation site assessment. Altogether, our results highlight the potential of UVPD for ADC MD MS analysis for drug conjugation/glycosylation site assessment, and indicate that MD MS strategies can improve structural characterization of empowered next-generation mAb-based formats, especially for PTMs and drug conjugation sites validation.
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Affiliation(s)
- Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS IPHC UMR 7178, Université de Strasbourg, ECPM R5-0 - 25 Rue Becquerel, Cedex 2, 67087, Strasbourg, France
| | - Stéphane Houel
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS IPHC UMR 7178, Université de Strasbourg, ECPM R5-0 - 25 Rue Becquerel, Cedex 2, 67087, Strasbourg, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS IPHC UMR 7178, Université de Strasbourg, ECPM R5-0 - 25 Rue Becquerel, Cedex 2, 67087, Strasbourg, France
| | - David Rabuka
- Catalent Biologics West, 5703 Hollis Street, Emeryville, CA, 94530, USA
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - Jonathan Josephs
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - Alain Beck
- IRPF, Centre d'Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois, France
| | - Penelope M Drake
- Catalent Biologics West, 5703 Hollis Street, Emeryville, CA, 94530, USA
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS IPHC UMR 7178, Université de Strasbourg, ECPM R5-0 - 25 Rue Becquerel, Cedex 2, 67087, Strasbourg, France.
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29
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Melani RD, Srzentić K, Gerbasi VR, McGee JP, Huguet R, Fornelli L, Kelleher NL. Direct measurement of light and heavy antibody chains using ion mobility and middle-down mass spectrometry. MAbs 2019; 11:1351-1357. [PMID: 31607219 PMCID: PMC6816405 DOI: 10.1080/19420862.2019.1668226] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The analysis of monoclonal antibodies (mAbs) by a middle-down mass spectrometry (MS) approach is a growing field that attracts the attention of many researchers and biopharmaceutical companies. Usually, liquid fractionation techniques are used to separate mAbs polypeptides chains before MS analysis. Gas-phase fractionation techniques such as high-field asymmetric waveform ion mobility spectrometry (FAIMS) can replace liquid-based separations and reduce both analysis time and cost. Here, we present a rapid FAIMS tandem MS method capable of characterizing the polypeptide sequence of mAbs light and heavy chains in an unprecedented, easy, and fast fashion. This new method uses commercially available instruments and takes ~24 min, which is 40-60% faster than regular liquid chromatography-MS/MS analysis, to acquire fragmentation data using different dissociation methods.
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Affiliation(s)
- Rafael D Melani
- Departments of Chemistry, Molecular Biosciences, and Chemical and Biological Engineering; the Chemistry of Life Processes Institute; and the Proteomics Center of Excellence, Northwestern University , Evanston , IL , USA
| | | | - Vincent R Gerbasi
- Departments of Chemistry, Molecular Biosciences, and Chemical and Biological Engineering; the Chemistry of Life Processes Institute; and the Proteomics Center of Excellence, Northwestern University , Evanston , IL , USA
| | - John P McGee
- Departments of Chemistry, Molecular Biosciences, and Chemical and Biological Engineering; the Chemistry of Life Processes Institute; and the Proteomics Center of Excellence, Northwestern University , Evanston , IL , USA
| | | | - Luca Fornelli
- Department of Biology, University of Oklahoma , Norman , OK , USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences, and Chemical and Biological Engineering; the Chemistry of Life Processes Institute; and the Proteomics Center of Excellence, Northwestern University , Evanston , IL , USA
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30
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Mukherjee S, Fang M, Kok WM, Kapp EA, Thombare VJ, Huguet R, Hutton CA, Reid GE, Roberts BR. Establishing Signature Fragments for Identification and Sequencing of Dityrosine Cross-Linked Peptides Using Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2019; 91:12129-12133. [DOI: 10.1021/acs.analchem.9b02986] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Soumya Mukherjee
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Mengxuan Fang
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - W. Mei Kok
- University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
| | - Eugene A. Kapp
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Varsha J. Thombare
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Craig A. Hutton
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Gavin E. Reid
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Blaine R. Roberts
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
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31
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Huguet R, Fard D, D’humières T, Brault-Meslin O, Nahory L, Faivre L, Dubois-Randé J, Ternacle J, Oliver L, Lim P. Three-Dimensional inferior vena cava for assessing central venous pressure in patients with cardiogenic shock. Archives of Cardiovascular Diseases Supplements 2019. [DOI: 10.1016/j.acvdsp.2019.01.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey DJ, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Woulters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP. Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry. Anal Chem 2019; 91:4010-4016. [PMID: 30672687 DOI: 10.1021/acs.analchem.8b05399] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multiplexed, isobaric tagging methods are powerful techniques to increase throughput, precision, and accuracy in quantitative proteomics. The dynamic range and accuracy of quantitation, however, can be limited by coisolation of tag-containing peptides that release reporter ions and conflate quantitative measurements across precursors. Methods to alleviate these effects often lead to the loss of protein and peptide identifications through online or offline filtering of interference containing spectra. To alleviate this effect, high-Field Asymmetric-waveform Ion Mobility Spectroscopy (FAIMS) has been proposed as a method to reduce precursor coisolation and improve the accuracy and dynamic range of multiplex quantitation. Here we tested the use of FAIMS to improve quantitative accuracy using previously established TMT-based interference standards (triple-knockout [TKO] and Human-Yeast Proteomics Resource [HYPER]). We observed that FAIMS robustly improved the quantitative accuracy of both high-resolution MS2 (HRMS2) and synchronous precursor selection MS3 (SPS-MS3)-based methods without sacrificing protein identifications. We further optimized and characterized the main factors that enable robust use of FAIMS for multiplexed quantitation. We highlight these factors and provide method recommendations to take advantage of FAIMS technology to improve isobaric-tag-quantification moving forward.
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Affiliation(s)
- Devin K Schweppe
- Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States
| | - Satendra Prasad
- Thermo Scientific LSMS, San Jose , California 95134 , United States
| | | | - José Navarrete-Perea
- Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States
| | - Derek J Bailey
- Thermo Scientific LSMS, San Jose , California 95134 , United States
| | - Romain Huguet
- Thermo Scientific LSMS, San Jose , California 95134 , United States
| | - Mark P Jedrychowski
- Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States
| | - Ramin Rad
- Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States
| | - Graeme McAlister
- Thermo Scientific LSMS, San Jose , California 95134 , United States
| | | | - Eloy R Woulters
- Thermo Scientific LSMS, San Jose , California 95134 , United States
| | - Vlad Zabrouskov
- Thermo Scientific LSMS, San Jose , California 95134 , United States
| | | | - João A Paulo
- Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States
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33
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Ríos L, Kivell TL, Lalueza-Fox C, Estalrrich A, García-Tabernero A, Huguet R, Quintino Y, de la Rasilla M, Rosas A. Skeletal Anomalies in The Neandertal Family of El Sidrón (Spain) Support A Role of Inbreeding in Neandertal Extinction. Sci Rep 2019; 9:1697. [PMID: 30737446 PMCID: PMC6368597 DOI: 10.1038/s41598-019-38571-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/31/2018] [Indexed: 12/12/2022] Open
Abstract
Neandertals disappeared from the fossil record around 40,000 bp, after a demographic history of small and isolated groups with high but variable levels of inbreeding, and episodes of interbreeding with other Paleolithic hominins. It is reasonable to expect that high levels of endogamy could be expressed in the skeleton of at least some Neandertal groups. Genetic studies indicate that the 13 individuals from the site of El Sidrón, Spain, dated around 49,000 bp, constituted a closely related kin group, making these Neandertals an appropriate case study for the observation of skeletal signs of inbreeding. We present the complete study of the 1674 identified skeletal specimens from El Sidrón. Altogether, 17 congenital anomalies were observed (narrowing of the internal nasal fossa, retained deciduous canine, clefts of the first cervical vertebra, unilateral hypoplasia of the second cervical vertebra, clefting of the twelfth thoracic vertebra, diminutive thoracic or lumbar rib, os centrale carpi and bipartite scaphoid, tripartite patella, left foot anomaly and cuboid-navicular coalition), with at least four individuals presenting congenital conditions (clefts of the first cervical vertebra). At 49,000 years ago, the Neandertals from El Sidrón, with genetic and skeletal evidence of inbreeding, could be representative of the beginning of the demographic collapse of this hominin phenotype.
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Affiliation(s)
- L Ríos
- Department of Physical Anthropology, Aranzadi Zientzia Elkartea, Zorroagagaina 11, 20014, Donostia, Gipuzkoa, Basque Country, Spain.
| | - T L Kivell
- Skeletal Biology Research Centre, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, CT2 7NR, UK.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - C Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
| | - A Estalrrich
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria IIIPC (Universidad de Cantabria, Santander, Gobierno de Cantabria), Avda. de los Castros 52, 39005, Santander, Cantabria, Spain
| | - A García-Tabernero
- Paleoanthropology Group, Department of Paleobiology. Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - R Huguet
- IPHES, Institut Catala de Paleoecologia Humana i Evolució Social, Campus Sescelades URV (Edifici W3), 43007, Tarragona, Spain.,Area de Prehistoria, Universitat Rovira i Virgili, Avda. Catalunya 35, 43002, Tarragona, Spain.,Unidad asociada al CSIC, Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Calle José Gutierrez Abascal 2, 28006, Madrid, Spain
| | - Y Quintino
- Laboratorio de Evolución Humana, Dpto. de Ciencias Históricas y Geografía, Universidad de Burgos, Edificio I+D+i, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain
| | - M de la Rasilla
- Área de Prehistoria Departamento de Historia, Universidad de Oviedo, Calle Teniente Alfonso Martínez s/n, 33011, Oviedo, Spain
| | - A Rosas
- Paleoanthropology Group, Department of Paleobiology. Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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34
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Fard D, Huguet R, Doan H, San S, Faivre L, D’humières T, Dubois-Randé J, Oliver L, Ternacle J, Lim P. Is functional tricuspid regurgitation decrease under diuretic correlated with outcome? Archives of Cardiovascular Diseases Supplements 2019. [DOI: 10.1016/j.acvdsp.2018.10.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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Hebert AS, Prasad S, Belford MW, Bailey DJ, McAlister GC, Abbatiello SE, Huguet R, Wouters ER, Dunyach JJ, Brademan DR, Westphall MS, Coon JJ. Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer. Anal Chem 2018; 90:9529-9537. [PMID: 29969236 PMCID: PMC6145172 DOI: 10.1021/acs.analchem.8b02233] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Liquid chromatography (LC) prefractionation is often implemented to increase proteomic coverage; however, while effective, this approach is laborious, requires considerable sample amount, and can be cumbersome. We describe how interfacing a recently described high-field asymmetric waveform ion mobility spectrometry (FAIMS) device between a nanoelectrospray ionization (nanoESI) emitter and an Orbitrap hybrid mass spectrometer (MS) enables the collection of single-shot proteomic data with comparable depth to that of conventional two-dimensional LC approaches. This next generation FAIMS device incorporates improved ion sampling at the ESI-FAIMS interface, increased electric field strength, and a helium-free ion transport gas. With fast internal compensation voltage (CV) stepping (25 ms/transition), multiple unique gas-phase fractions may be analyzed simultaneously over the course of an MS analysis. We have comprehensively demonstrated how this device performs for bottom-up proteomics experiments as well as characterized the effects of peptide charge state, mass loading, analysis time, and additional variables. We also offer recommendations for the number of CVs and which CVs to use for different lengths of experiments. Internal CV stepping experiments increase protein identifications from a single-shot experiment to >8000, from over 100 000 peptide identifications in as little as 5 h. In single-shot 4 h label-free quantitation (LFQ) experiments of a human cell line, we quantified 7818 proteins with FAIMS using intra-analysis CV switching compared to 6809 without FAIMS. Single-shot FAIMS results also compare favorably with LC fractionation experiments. A 6 h single-shot FAIMS experiment generates 8007 protein identifications, while four fractions analyzed for 1.5 h each produce 7776 protein identifications.
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Affiliation(s)
- Alexander S. Hebert
- Genome Center of Wisconsin, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Satendra Prasad
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Derek J. Bailey
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | | | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Eloy R. Wouters
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Dain R. Brademan
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Michael S. Westphall
- Genome Center of Wisconsin, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53706, United States
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36
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Ribeyrolles S, San R, Lepeule R, Moussafeur A, Faivre L, Nahory L, Huguet R, Gallien S, Decousser JW, Fihman V, Fiore A, Mongardon N, Lim P, Ternacle J, Oliver L. P4191Low-CRP infective endocarditis: description of a particular entity. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy563.p4191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- S Ribeyrolles
- University Hospital Henri Mondor, Department of Cardiovascular Medicine, SOS Endocardite Unit, Creteil, France
| | - R San
- University Hospital Henri Mondor, Department of Cardiovascular Medicine, SOS Endocardite Unit, Creteil, France
| | - R Lepeule
- University Hospital Henri Mondor, Antimicrobial stewardship team, SOS Endocardite Unit, Creteil, France
| | - A Moussafeur
- University Hospital Henri Mondor, Department of Cardiovascular Medicine, SOS Endocardite Unit, Creteil, France
| | - L Faivre
- University Hospital Henri Mondor, Department of Cardiovascular Medicine, SOS Endocardite Unit, Creteil, France
| | - L Nahory
- University Hospital Henri Mondor, Department of Cardiovascular Medicine, SOS Endocardite Unit, Creteil, France
| | - R Huguet
- University Hospital Henri Mondor, Department of Cardiovascular Medicine, SOS Endocardite Unit, Creteil, France
| | - S Gallien
- University Hospital Henri Mondor, Department of Infectious Diseases, SOS Endocardite Unit, Creteil, France
| | - J W Decousser
- University Hospital Henri Mondor, Department of Microbiology, SOS Endocardite Unit, Creteil, France
| | - V Fihman
- University Hospital Henri Mondor, Department of Microbiology, SOS Endocardite Unit, Creteil, France
| | - A Fiore
- University Hospital Henri Mondor, Department of Cardiac Surgery, SOS Endocardite Unit, Creteil, France
| | - N Mongardon
- University Hospital Henri Mondor, Department of Anesthesiology and Critical Care Medicine, SOS Endocardite Unit, Creteil, France
| | - P Lim
- University Hospital Henri Mondor, Department of Cardiovascular Medicine, SOS Endocardite Unit, Creteil, France
| | - J Ternacle
- University Hospital Henri Mondor, Department of Cardiovascular Medicine, SOS Endocardite Unit, Creteil, France
| | - L Oliver
- University Hospital Henri Mondor, Department of Cardiovascular Medicine, SOS Endocardite Unit, Creteil, France
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37
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Fornelli L, Srzentić K, Huguet R, Mullen C, Sharma S, Zabrouskov V, Fellers RT, Durbin KR, Compton PD, Kelleher NL. Accurate Sequence Analysis of a Monoclonal Antibody by Top-Down and Middle-Down Orbitrap Mass Spectrometry Applying Multiple Ion Activation Techniques. Anal Chem 2018; 90:8421-8429. [PMID: 29894161 DOI: 10.1021/acs.analchem.8b00984] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Targeted top-down (TD) and middle-down (MD) mass spectrometry (MS) offer reduced sample manipulation during protein analysis, limiting the risk of introducing artifactual modifications to better capture sequence information on the proteoforms present. This provides some advantages when characterizing biotherapeutic molecules such as monoclonal antibodies, particularly for the class of biosimilars. Here, we describe the results obtained analyzing a monoclonal IgG1, either in its ∼150 kDa intact form or after highly specific digestions yielding ∼25 and ∼50 kDa subunits, using an Orbitrap mass spectrometer on a liquid chromatography (LC) time scale with fragmentation from ion-photon, ion-ion, and ion-neutral interactions. Ultraviolet photodissociation (UVPD) used a new 213 nm solid-state laser. Alternatively, we applied high-capacity electron-transfer dissociation (ETD HD), alone or in combination with higher energy collisional dissociation (EThcD). Notably, we verify the degree of complementarity of these ion activation methods, with the combination of 213 nm UVPD and ETD HD producing a new record sequence coverage of ∼40% for TD MS experiments. The addition of EThcD for the >25 kDa products from MD strategies generated up to 90% of complete sequence information in six LC runs. Importantly, we determined an optimal signal-to-noise threshold for fragment ion deconvolution to suppress false positives yet maximize sequence coverage and implemented a systematic validation of this process using the new software TDValidator. This rigorous data analysis should elevate confidence for assignment of dense MS2 spectra and represents a purposeful step toward the application of TD and MD MS for deep sequencing of monoclonal antibodies.
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Affiliation(s)
- Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Kristina Srzentić
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Romain Huguet
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Christopher Mullen
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Seema Sharma
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Kenneth R Durbin
- Proteinaceous, Incorporated , Evanston , Illinois 60201 , United States
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
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38
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Brodie NI, Huguet R, Zhang T, Viner R, Zabrouskov V, Pan J, Petrotchenko EV, Borchers CH. Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation. Anal Chem 2018; 90:3079-3082. [PMID: 29336549 DOI: 10.1021/acs.analchem.7b03655] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Top-down hydrogen-deuterium exchange (HDX) analysis using electron capture or transfer dissociation Fourier transform mass spectrometry (FTMS) is a powerful method for the analysis of secondary structure of proteins in solution. The resolution of the method is a function of the degree of fragmentation of backbone bonds in the proteins. While fragmentation is usually extensive near the N- and C-termini, electron capture (ECD) or electron transfer dissociation (ETD) fragmentation methods sometimes lack good coverage of certain regions of the protein, most often in the middle of the sequence. Ultraviolet photodissociation (UVPD) is a recently developed fast-fragmentation technique, which provides extensive backbone fragmentation that can be complementary in sequence coverage to the aforementioned electron-based fragmentation techniques. Here, we explore the application of electrospray ionization (ESI)-UVPD FTMS on an Orbitrap Fusion Lumos Tribrid mass spectrometer to top-down HDX analysis of proteins. We have incorporated UVPD-specific fragment-ion types and fragment-ion mixtures into our isotopic envelope fitting software (HDX Match) for the top-down HDX analysis. We have shown that UVPD data is complementary to ETD, thus improving the overall resolution when used as a combined approach.
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Affiliation(s)
- Nicholas I Brodie
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Romain Huguet
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Terry Zhang
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Rosa Viner
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jingxi Pan
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Evgeniy V Petrotchenko
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Christoph H Borchers
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada.,Department of Biochemistry and Microbiology , University of Victoria , Petch Building, Room 270d, 3800 Finnerty Road , Victoria , British Columbia V8P 5C2 , Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montreal , Quebec H3T 1E2 , Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montreal , Quebec H3T 1E2 , Canada
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39
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Hebert AS, Thöing C, Riley NM, Kwiecien NW, Shiskova E, Huguet R, Cardasis HL, Kuehn A, Eliuk S, Zabrouskov V, Westphall MS, McAlister GC, Coon JJ. Improved Precursor Characterization for Data-Dependent Mass Spectrometry. Anal Chem 2018; 90:2333-2340. [PMID: 29272103 DOI: 10.1021/acs.analchem.7b04808] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Modern ion trap mass spectrometers are capable of collecting up to 60 tandem MS (MS/MS) scans per second, in theory providing acquisition speeds that can sample every eluting peptide precursor presented to the MS system. In practice, however, the precursor sampling capacity enabled by these ultrafast acquisition rates is often underutilized due to a host of reasons (e.g., long injection times and wide analyzer mass ranges). One often overlooked reason for this underutilization is that the instrument exhausts all the peptide features it identifies as suitable for MS/MS fragmentation. Highly abundant features can prevent annotation of lower abundance precursor ions that occupy similar mass-to-charge (m/z) space, which ultimately inhibits the acquisition of an MS/MS event. Here, we present an advanced peak determination (APD) algorithm that uses an iterative approach to annotate densely populated m/z regions to increase the number of peptides sampled during data-dependent LC-MS/MS analyses. The APD algorithm enables nearly full utilization of the sampling capacity of a quadrupole-Orbitrap-linear ion trap MS system, which yields up to a 40% increase in unique peptide identifications from whole cell HeLa lysates (approximately 53 000 in a 90 min LC-MS/MS analysis). The APD algorithm maintains improved peptide and protein identifications across several modes of proteomic data acquisition, including varying gradient lengths, different degrees of prefractionation, peptides derived from multiple proteases, and phosphoproteomic analyses. Additionally, the use of APD increases the number of peptides characterized per protein, providing improved protein quantification. In all, the APD algorithm increases the number of detectable peptide features, which maximizes utilization of the high MS/MS capacities and significantly improves sampling depth and identifications in proteomic experiments.
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Affiliation(s)
| | | | | | | | | | - Romain Huguet
- Thermo Fisher Scientific , San Jose, California 95134, United States
| | - Helene L Cardasis
- Thermo Fisher Scientific , San Jose, California 95134, United States
| | | | - Shannon Eliuk
- Thermo Fisher Scientific , San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , San Jose, California 95134, United States
| | | | | | - Joshua J Coon
- Morgridge Institute for Research , Madison, Wisconsin 53406 United States
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40
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Huguet R, Vandecasteele G, Fischmeister R, Algalarrondo V. Role of cAMP-phosphodiesterases in cardiac recovery after β–adrenergic stimulation: an in vivo preliminary study. Archives of Cardiovascular Diseases Supplements 2017. [DOI: 10.1016/s1878-6480(17)30289-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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41
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Le Page S, van Belkum A, Fulchiron C, Huguet R, Raoult D, Rolain JM. Evaluation of the PREVI® Isola automated seeder system compared to reference manual inoculation for antibiotic susceptibility testing by the disk diffusion method. Eur J Clin Microbiol Infect Dis 2015; 34:1859-69. [PMID: 26092031 DOI: 10.1007/s10096-015-2424-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
The disk diffusion (DD) method remains the most popular manual technique for antibiotic susceptibility testing (AST) in clinical microbiology laboratories. This is because of its simplicity, reproducibility, and limited cost compared to (automated) microdilution systems, which are usually less sensitive at detecting certain important mechanisms of resistance. Here, we evaluate the PREVI® Isola automated seeder system using a new protocol for spreading bacterial suspensions (eight deposits of calibrated inocula of bacteria, followed by two rounds of rotation) in comparison with manual DD reference testing on a large series of clinical and reference strains. The average time required for seeding one agar plate for DD with this new protocol was 51 s per plate, i.e., 70 agar plates/h. Reproducibility and repeatability was assessed on three reference and three randomly chosen clinical strains, as usually requested by the European Committee on Antimicrobial Susceptibility Testing (EUCAST), and was excellent compared to the manual method. The standard deviations of zones of growth inhibition showed no statistical discrimination. The correlation between the two methods, assessed using 294 clinical isolates and a panel of six antibiotics (n = 3,528 zones of growth inhibition measured), was excellent, with a correlation coefficient of 0.977. The new PREVI® Isola protocol adapted for DD had a sensitivity of 99 % and a specificity of 100 % compared to the manual technique for interpreting DD as recommended by the EUCAST.
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Affiliation(s)
- S Le Page
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
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42
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Brunner AM, Lössl P, Liu F, Huguet R, Mullen C, Yamashita M, Zabrouskov V, Makarov A, Altelaar AFM, Heck AJR. Benchmarking Multiple Fragmentation Methods on an Orbitrap Fusion for Top-down Phospho-Proteoform Characterization. Anal Chem 2015; 87:4152-8. [DOI: 10.1021/acs.analchem.5b00162] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Andrea M. Brunner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584CH Utrecht, The Netherlands
- Netherlands Proteomics
Center, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Philip Lössl
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584CH Utrecht, The Netherlands
- Netherlands Proteomics
Center, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Fan Liu
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584CH Utrecht, The Netherlands
- Netherlands Proteomics
Center, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Christopher Mullen
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Masami Yamashita
- Forschungsgruppe
Zelluläre Strukturbiologie, Max-Planck-Institut für
Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Alexander Makarov
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584CH Utrecht, The Netherlands
- Thermo Fisher
Scientific (Bremen) GmbH, Hanna-Kunath-Strasse
11, 28199 Bremen, Germany
| | - A. F. Maarten Altelaar
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584CH Utrecht, The Netherlands
- Netherlands Proteomics
Center, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584CH Utrecht, The Netherlands
- Netherlands Proteomics
Center, Padualaan 8, 3584CH Utrecht, The Netherlands
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Galland M, Huguet R, Arc E, Cueff G, Job D, Rajjou L. Dynamic proteomics emphasizes the importance of selective mRNA translation and protein turnover during Arabidopsis seed germination. Mol Cell Proteomics 2014; 13:252-68. [PMID: 24198433 PMCID: PMC3879618 DOI: 10.1074/mcp.m113.032227] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/23/2013] [Indexed: 01/02/2023] Open
Abstract
During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [(35)S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment.
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Affiliation(s)
- Marc Galland
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Romain Huguet
- ¶CNRS/Bayer CropScience Joint Laboratory (UMR5240), F-69263 Lyon, France
| | - Erwann Arc
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Gwendal Cueff
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Dominique Job
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
- ¶CNRS/Bayer CropScience Joint Laboratory (UMR5240), F-69263 Lyon, France
| | - Loïc Rajjou
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
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Dean MC, Rosas A, Estalrrich A, García-Tabernero A, Huguet R, Lalueza-Fox C, Bastir M, de la Rasilla M. Longstanding dental pathology in Neandertals from El Sidrón (Asturias, Spain) with a probable familial basis. J Hum Evol 2013; 64:678-86. [PMID: 23615378 DOI: 10.1016/j.jhevol.2013.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/15/2013] [Accepted: 03/18/2013] [Indexed: 10/26/2022]
Abstract
Two Neandertal specimens from El Sidrón, northern Spain, show evidence of retained left mandibular deciduous canines. These individuals share the same mitochondrial (mtDNA) haplotype, indicating they are maternally related and suggesting a potential heritable basis for these dental anomalies. Radiographs and medical CT scans provide evidence of further, more extensive dental pathology in one of these specimens. An anomalous deciduous canine crown morphology that developed before birth subsequently suffered a fracture of the crown exposing the pulp sometime after eruption into functional occlusion. This led to death of the tooth, periapical granuloma formation and arrested deciduous canine root growth at an estimated age of 2.5 years. At some point the underlying permanent canine tooth became horizontally displaced and came to lie low in the trabecular bone of the mandibular corpus. A dentigerous cyst then developed around the crown. Anterior growth displacement of the mandible continued around the stationary permanent canine, leaving it posteriorly positioned in the mandibular corpus by the end of the growth period beneath the third permanent molar roots, which, in turn, suggests a largely horizontal growth vector. Subsequent longstanding repeated infections of the expanding cyst cavity are evidenced by bouts of bone deposition and resorption of the boundary walls of the cyst cavity. This resulted in the establishment of two permanent bony drainage sinuses, one through the buccal plate of the alveolar bone anteriorly, immediately beneath the infected deciduous canine root, and the other through the buccal plate anterior to the mesial root of the first permanent molar. It is probable that this complicated temporal sequence of dental pathologies had an initial heritable trigger that progressed in an unusually complex way in one of these individuals. During life, this individual may have been largely unaware of this ongoing pathology.
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Affiliation(s)
- M C Dean
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
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Carbonell E, Cáceres I, Lozano M, Saladié P, Rosell J, Lorenzo C, Vallverdú J, Huguet R, Canals A, Bermúdez de Castro JM. A Reply to Otterbein. Current Anthropology 2011. [DOI: 10.1086/659747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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46
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Rispail N, Soanes DM, Ant C, Czajkowski R, Grünler A, Huguet R, Perez-Nadales E, Poli A, Sartorel E, Valiante V, Yang M, Beffa R, Brakhage AA, Gow NAR, Kahmann R, Lebrun MH, Lenasi H, Perez-Martin J, Talbot NJ, Wendland J, Di Pietro A. Comparative genomics of MAP kinase and calcium-calcineurin signalling components in plant and human pathogenic fungi. Fungal Genet Biol 2009; 46:287-98. [PMID: 19570501 DOI: 10.1016/j.fgb.2009.01.002] [Citation(s) in RCA: 230] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 01/16/2009] [Accepted: 01/17/2009] [Indexed: 01/22/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades and the calcium-calcineurin pathway control fundamental aspects of fungal growth, development and reproduction. Core elements of these signalling pathways are required for virulence in a wide array of fungal pathogens of plants and mammals. In this review, we have used the available genome databases to explore the structural conservation of three MAPK cascades and the calcium-calcineurin pathway in ten different fungal species, including model organisms, plant pathogens and human pathogens. While most known pathway components from the model yeast Saccharomyces cerevisiae appear to be widely conserved among taxonomically and biologically diverse fungi, some of them were found to be restricted to the Saccharomycotina. The presence of multiple paralogues in certain species such as the zygomycete Rhizopus oryzae and the incorporation of new functional domains that are lacking in S. cerevisiae signalling proteins, most likely reflect functional diversification or adaptation as filamentous fungi have evolved to occupy distinct ecological niches.
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Affiliation(s)
- Nicolas Rispail
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
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Rajjou L, Belghazi M, Huguet R, Robin C, Moreau A, Job C, Job D. Proteomic investigation of the effect of salicylic acid on Arabidopsis seed germination and establishment of early defense mechanisms. Plant Physiol 2006; 141:910-23. [PMID: 16679420 PMCID: PMC1489900 DOI: 10.1104/pp.106.082057] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The influence of salicylic acid (SA) on elicitation of defense mechanisms in Arabidopsis (Arabidopsis thaliana) seeds and seedlings was assessed by physiological measurements combined with global expression profiling (proteomics). Parallel experiments were carried out using the NahG transgenic plants expressing the bacterial gene encoding SA hydroxylase, which cannot accumulate the active form of this plant defense elicitor. SA markedly improved germination under salt stress. Proteomic analyses disclosed a specific accumulation of protein spots regulated by SA as inferred by silver-nitrate staining of two-dimensional gels, detection of carbonylated (oxidized) proteins, and neosynthesized proteins with [35S]-methionine. The combined results revealed several processes potentially affected by SA. This molecule enhanced the reinduction of the late maturation program during early stages of germination, thereby allowing the germinating seeds to reinforce their capacity to mount adaptive responses in environmental water stress. Other processes affected by SA concerned the quality of protein translation, the priming of seed metabolism, the synthesis of antioxidant enzymes, and the mobilization of seed storage proteins. All the observed effects are likely to improve seed vigor. Another aspect revealed by this study concerned the oxidative stress entailed by SA in germinating seeds, as inferred from a characterization of the carbonylated (oxidized) proteome. Finally, the proteomic data revealed a close interplay between abscisic signaling and SA elicitation of seed vigor.
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Affiliation(s)
- Loïc Rajjou
- Centre National de la Recherche Scientifique, Bayer CropScience Joint Laboratory, Unité Mixte de Recherche 2847, F-69263 Lyon cedex 09, France
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Parés JM, Pérez-González A, Rosas A, Benito A, Bermúdez de Castro JM, Carbonell E, Huguet R. Matuyama-age lithic tools from the Sima del Elefante site, Atapuerca (northern Spain). J Hum Evol 2006; 50:163-9. [PMID: 16249015 DOI: 10.1016/j.jhevol.2005.08.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Revised: 08/22/2005] [Accepted: 08/30/2005] [Indexed: 10/25/2022]
Abstract
Paleomagnetic results obtained from the sedimentary fill at the Sima del Elefante site in Atapuerca, Spain, reveal a geomagnetic reversal, interpreted as the Matuyama-Brunhes boundary (0.78 Ma). The uppermost lithostratigraphic units (E17 through E19), which contain Mode II and III archaeological assemblages, display normal polarity magnetization, whereas the six lowermost units (E9 through E16) yield negative latitudinal virtual geomagnetic pole positions. Units E9 through E13, all of which display reverse magnetic polarity, contain Mode I (Oldowan) lithic tools, testifying to the presence of humans in the early Pleistocene (0.78-1.77 Ma).
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Affiliation(s)
- Josep M Parés
- Department of Geological Sciences, University of Michigan, 2534 C.C. Little Building, Ann Arbor, MI 48109, USA.
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Vallverdú J, Allué E, Bischoff JL, Cáceres I, Carbonell E, Cebrià A, García-Antón D, Huguet R, Ibáñez N, Martínez K, Pastó I, Rosell J, Saladié P, Vaquero M. Short human occupations in the Middle Palaeolithic level I of the Abric Romani rock-shelter (Capellades, Barcelona, Spain). J Hum Evol 2005; 48:157-74. [PMID: 15701529 DOI: 10.1016/j.jhevol.2004.10.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Accepted: 10/06/2004] [Indexed: 10/25/2022]
Abstract
This paper presents a multidisciplinary study on the size of the occupied surfaces, provisioning strategies and behaviour planning at the Romani rock-shelter, using the Middle Palaeolithic record of the level i. This level is dated around 46.000 BP through U/Th ages. A behavioural interpretation is proposed, which emphasises the activities and the systemic value of the archaeological artefacts and structures. Occupation patterns are identified on the basis of the accumulations formed by human activities. These archaeological accumulations, consisting of artefacts and hearths, are easily defined visually as spatial units. The relationships between these accumulations, established by means of refitted remains, indicate that differences can be established between: 1) small and medium-sized occupation surfaces; 2) restricted and diversified provisioning strategies. This variability suggests that different modes of occupation are represented in the same archaeological level. The human activities reveal the generalization of fire technology. In almost all sizes of the occupation surfaces, the exploitation of vegetal resources near the Abric Romani marks the threshold of the restricted provisioning strategy. Limited use and fragmented knapping activities are recorded in the lithic assemblage. Faunal remains show differential transport. The exploitation of lithic, faunal and vegetal resources characterizes the diversified provisioning strategy. The small occupation surfaces and restricted provisioning strategies suggest short settlements in the Abric Romani. This shorter occupation model complements the longer diversified provisioning strategy recorded in both small and medium-sized occupied surfaces. The selection of precise elements for transport and the possible deferred consumption in the diversified provision strategy suggest an individual supply. In this respect, Neanderthal occupations in the Romani rock-shelter show a direct relation to: 1) hunting strategic resources; 2) high, linear mobility.
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Affiliation(s)
- J Vallverdú
- Area de Prehistòria, Departament d'Història i Geografia, Universitat Rovira i Virgili, Plaça Imperial Tàrraco, 1, 43.005 Tarragona, Spain.
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Marsol A, Huguet R, González-Pedrouzo E, Miranda-Sanromà E, Giné-Gomá J. Lesiones traumáticas cervicales tratadas con artrodesis anterior con placa. Rev Esp Cir Ortop Traumatol (Engl Ed) 2004. [DOI: 10.1016/s1888-4415(04)76194-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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