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The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics

Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF...

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Autores principales: Beck, Scarlet, Michalski, Annette, Raether, Oliver, Lubeck, Markus, Kaspar, Stephanie, Goedecke, Niels, Baessmann, Carsten, Hornburg, Daniel, Meier, Florian, Paron, Igor, Kulak, Nils A., Cox, Juergen, Mann, Matthias
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The American Society for Biochemistry and Molecular Biology 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587313/
https://www.ncbi.nlm.nih.gov/pubmed/25991688
http://dx.doi.org/10.1074/mcp.M114.047407
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author Beck, Scarlet
Michalski, Annette
Raether, Oliver
Lubeck, Markus
Kaspar, Stephanie
Goedecke, Niels
Baessmann, Carsten
Hornburg, Daniel
Meier, Florian
Paron, Igor
Kulak, Nils A.
Cox, Juergen
Mann, Matthias
author_facet Beck, Scarlet
Michalski, Annette
Raether, Oliver
Lubeck, Markus
Kaspar, Stephanie
Goedecke, Niels
Baessmann, Carsten
Hornburg, Daniel
Meier, Florian
Paron, Igor
Kulak, Nils A.
Cox, Juergen
Mann, Matthias
author_sort Beck, Scarlet
collection PubMed
description Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated liquid chromatography system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high tandem MS frequencies. The new reflectron and detector improve resolving power compared with the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) and accurate fold change determination in spike-in experiments in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originating from different tissues. Finally, after high pH reversed-phase fractionation we identified 9515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in single measurements of cerebellum—the highest proteome coverage reported with a QTOF instrument so far.
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spelling pubmed-45873132015-09-29 The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics Beck, Scarlet Michalski, Annette Raether, Oliver Lubeck, Markus Kaspar, Stephanie Goedecke, Niels Baessmann, Carsten Hornburg, Daniel Meier, Florian Paron, Igor Kulak, Nils A. Cox, Juergen Mann, Matthias Mol Cell Proteomics Research Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated liquid chromatography system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high tandem MS frequencies. The new reflectron and detector improve resolving power compared with the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) and accurate fold change determination in spike-in experiments in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originating from different tissues. Finally, after high pH reversed-phase fractionation we identified 9515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in single measurements of cerebellum—the highest proteome coverage reported with a QTOF instrument so far. The American Society for Biochemistry and Molecular Biology 2015-07 2015-05-19 /pmc/articles/PMC4587313/ /pubmed/25991688 http://dx.doi.org/10.1074/mcp.M114.047407 Text en © 2015 by The American Society for Biochemistry and Molecular Biology, Inc. Author's Choice—Final version free via Creative Commons CC-BY license (http://creativecommons.org/licenses/by/3.0) .
spellingShingle Research
Beck, Scarlet
Michalski, Annette
Raether, Oliver
Lubeck, Markus
Kaspar, Stephanie
Goedecke, Niels
Baessmann, Carsten
Hornburg, Daniel
Meier, Florian
Paron, Igor
Kulak, Nils A.
Cox, Juergen
Mann, Matthias
The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics
title The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics
title_full The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics
title_fullStr The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics
title_full_unstemmed The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics
title_short The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics
title_sort impact ii, a very high-resolution quadrupole time-of-flight instrument (qtof) for deep shotgun proteomics
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587313/
https://www.ncbi.nlm.nih.gov/pubmed/25991688
http://dx.doi.org/10.1074/mcp.M114.047407
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