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Kantnerová K, Kuhlbusch N, Juchelka D, Hilkert A, Kopf S, Neubauer C. A guide to precise measurements of isotope abundance by ESI-Orbitrap MS. Nat Protoc 2024:10.1038/s41596-024-00981-5. [PMID: 38654136 DOI: 10.1038/s41596-024-00981-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 02/08/2024] [Indexed: 04/25/2024]
Abstract
Stable isotopes of carbon, hydrogen, nitrogen, oxygen and sulfur are widespread in nature. Nevertheless, their relative abundance is not the same everywhere. This is due to kinetic isotope effects in enzymes and other physical principles such as equilibrium thermodynamics. Variations in isotope ratios offer unique insights into environmental pollution, trophic relationships in ecology, metabolic disorders and Earth history including climate history. Although classical isotope ratio mass spectrometry (IRMS) techniques still struggle to access intramolecular information like site-specific isotope abundance, electrospray ionization-Orbitrap mass spectrometry can be used to achieve precise and accurate intramolecular quantification of isotopically substituted molecules ('isotopocules'). This protocol describes two procedures. In the first one, we provide a step-by-step beginner's guide for performing multi-elemental, intramolecular and site-specific stable isotope analysis in unlabeled polar solutes by direct infusion. Using a widely available calibration solution, isotopocules of trifluoroacetic acid and immonium ions from the model peptide MRFA are quantified. In the second approach, nitrate is used as a simple model for a flow injection routine that enables access to a diverse range of naturally occurring isotopic signatures in inorganic oxyanions. Each procedure takes 2-3 h to complete and requires expertise only in general mass spectrometry. The workflows use optimized Orbitrap IRMS data-extraction and -processing software and are transferable to various analytes amenable to soft ionization, including metabolites, peptides, drugs and environmental pollutants. Optimized mass spectrometry systems will enable intramolecular isotope research in many areas of biology.
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Affiliation(s)
- Kristýna Kantnerová
- University of Colorado Boulder & Institute for Arctic and Alpine Research (INSTAAR), Boulder, CO, USA
| | - Nils Kuhlbusch
- Thermo Fisher Scientific GmbH, Bremen, Germany
- University of Münster, Münster, Germany
| | | | | | - Sebastian Kopf
- University of Colorado Boulder & Institute for Arctic and Alpine Research (INSTAAR), Boulder, CO, USA
| | - Cajetan Neubauer
- University of Colorado Boulder & Institute for Arctic and Alpine Research (INSTAAR), Boulder, CO, USA.
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2
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Agten A, Vilenne F, Prostko P, Valkenborg D. A compositional data model to predict the isotope distribution for average peptides using a compositional spline model. Proteomics 2024; 24:e2300154. [PMID: 38044297 DOI: 10.1002/pmic.202300154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023]
Abstract
We propose an updated approach for approximating the isotope distribution of average peptides given their monoisotopic mass. Our methodology involves in-silico cleavage of the entire UNIPROT database of human-reviewed proteins using Trypsin, generating a theoretical peptide dataset. The isotope distribution is computed using BRAIN. We apply a compositional data modelling strategy that utilizes an additive log-ratio transformation for the isotope probabilities followed by a penalized spline regression. Furthermore, due to the impact of the number of sulphur atoms on the course of the isotope distribution, we develop separate models for peptides containing zero up to five sulphur atoms. Additionally, we propose three methods to estimate the number of sulphur atoms based on an observed isotope distribution. The performance of the spline models and the sulphur prediction approaches is evaluated using a mean squared error and a modified Pearson's χ2 goodness-of-fit measure on an experimental UPS2 data set. Our analysis reveals that the variability in spectral accuracy, that is, the variability between MS1 scans, contributes more to the errors than the approximation of the theoretical isotope distribution by our proposed average peptide model. Moreover, we find that the accuracy of predicting the number of sulphur atoms based on the observed isotope distribution is limited by measurement accuracy.
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Affiliation(s)
- Annelies Agten
- Data Science Institute, Hasselt University, Diepenbeek, Belgium
| | - Frédérique Vilenne
- Data Science Institute, Hasselt University, Diepenbeek, Belgium
- Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Piotr Prostko
- Data Science Institute, Hasselt University, Diepenbeek, Belgium
| | - Dirk Valkenborg
- Data Science Institute, Hasselt University, Diepenbeek, Belgium
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3
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MacCoss MJ, Alfaro JA, Faivre DA, Wu CC, Wanunu M, Slavov N. Sampling the proteome by emerging single-molecule and mass spectrometry methods. Nat Methods 2023; 20:339-346. [PMID: 36899164 PMCID: PMC10044470 DOI: 10.1038/s41592-023-01802-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules, which has major implications in the development of proteomics technologies. We review strategies that have been helpful for counting billions of protein molecules by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and suggest that these strategies can benefit single-molecule methods, especially in mitigating the challenges of the wide dynamic range of the proteome.
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Affiliation(s)
- Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Javier Antonio Alfaro
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland.
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
- School of Informatics, University of Edinburgh, Edinburgh, UK.
| | - Danielle A Faivre
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christine C Wu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center and Barnett Institute, Northeastern University, Boston, MA, USA.
- Parallel Squared Technology Institute, Watertown, MA, USA.
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4
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Claesen J, Rockwood A, Gorshkov M, Valkenborg D. The isotope distribution: A rose with thorns. MASS SPECTROMETRY REVIEWS 2023. [PMID: 36744702 DOI: 10.1002/mas.21820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/03/2022] [Accepted: 10/21/2022] [Indexed: 06/18/2023]
Abstract
The isotope distribution, which reflects the number and probabilities of occurrence of different isotopologues of a molecule, can be theoretically calculated. With the current generation of (ultra)-high-resolution mass spectrometers, the isotope distribution of molecules can be measured with high sensitivity, resolution, and mass accuracy. However, the observed isotope distribution can differ substantially from the expected isotope distribution. Although differences between the observed and expected isotope distribution can complicate the analysis and interpretation of mass spectral data, they can be helpful in a number of specific applications. These applications include, yet are not limited to, the identification of peptides in proteomics, elucidation of the elemental composition of small organic molecules and metabolites, as well as wading through peaks in mass spectra of complex bioorganic mixtures such as petroleum and humus. In this review, we give a nonexhaustive overview of factors that have an impact on the observed isotope distribution, such as elemental isotope deviations, ion sampling, ion interactions, electronic noise and dephasing, centroiding, and apodization. These factors occur at different stages of obtaining the isotope distribution: during the collection of the sample, during the ionization and intake of a molecule in a mass spectrometer, during the mass separation and detection of ionized molecules, and during signal processing.
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Affiliation(s)
- Jürgen Claesen
- Department of Epidemiology and Data Science, Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, The Netherlands
- I-Biostat, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Alan Rockwood
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Mikhail Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Dirk Valkenborg
- I-Biostat, Data Science Institute, Hasselt University, Hasselt, Belgium
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5
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Heil LR, Remes PM, MacCoss MJ. Comparison of Unit Resolution Versus High-Resolution Accurate Mass for Parallel Reaction Monitoring. J Proteome Res 2021; 20:4435-4442. [PMID: 34319745 DOI: 10.1021/acs.jproteome.1c00377] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Parallel reaction monitoring (PRM) is an increasingly popular alternative to selected reaction monitoring (SRM) for targeted proteomics. PRM's strengths over SRM are that it monitors all product ions in a single spectrum, thus eliminating the need to select interference-free product ions prior to data acquisition, and that it is most frequently performed on high-resolution instruments, such as quadrupole-orbitrap and quadrupole-time-of-flight instruments. Here, we show that the primary advantage of PRM is the ability to monitor all transitions in parallel and that high-resolution data are not necessary to obtain high-quality quantitative data. We run the same scheduled PRM assay, measuring 432 peptides from 126 plasma proteins, multiple times on an Orbitrap Eclipse Tribrid mass spectrometer, alternating separate liquid chromatography-tandem mass spectrometry runs between the high-resolution Orbitrap and the unit resolution linear ion trap for PRM. We find that both mass analyzers have similar technical precision and that the linear ion trap's superior sensitivity gives it better lower limits of quantitation for over 62% of peptides in the assay.
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Affiliation(s)
- Lilian R Heil
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Philip M Remes
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
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6
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Remes PM, Yip P, MacCoss MJ. Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment. Anal Chem 2020; 92:11809-11817. [PMID: 32867497 DOI: 10.1021/acs.analchem.0c02075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Targeted mass spectrometry methods produce high-quality quantitative data in terms of limits of detection and dynamic range, at the cost of a substantial compromise in throughput compared to methods such as data independent and data dependent acquisition. The logistical and experimental issues inherent to maintaining assays of even several hundred targets are significant. Prominent among these issues is the drift in analyte retention time as liquid chromatography (LC) columns wear, forcing targeted scheduling windows to be much larger than LC peak widths. If these problems could be solved, proteomics assays would be capable of targeting thousands of peptides in an hour-long experiment, enabling large cohort studies to be performed without sacrificing sensitivity and specificity. We describe a solution in the form of a new method for real-time chromatographic alignment and demonstrate its application to a 56 min LC-gradient HeLa digest assay with 1489 targets. The method is based on the periodic acquisition of untargeted survey scans in a reference experiment and alignment to those scans during subsequent experiments. We describe how the method enables narrower scheduled retention time windows to be used. The narrower scheduling windows enables more targets to be included in the assay or proportionally more time to be allocated to each target, improving the sensitivity. Finally, we point out how the procedure could be improved and how much additional target multiplexing could be gained in the future.
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Affiliation(s)
- Philip M Remes
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Ping Yip
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
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7
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Kamischke C, Fan J, Bergeron J, Kulasekara HD, Dalebroux ZD, Burrell A, Kollman JM, Miller SI. The Acinetobacter baumannii Mla system and glycerophospholipid transport to the outer membrane. eLife 2019; 8:e40171. [PMID: 30638443 PMCID: PMC6365058 DOI: 10.7554/elife.40171] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/11/2019] [Indexed: 01/14/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria serves as a selective permeability barrier that allows entry of essential nutrients while excluding toxic compounds, including antibiotics. The OM is asymmetric and contains an outer leaflet of lipopolysaccharides (LPS) or lipooligosaccharides (LOS) and an inner leaflet of glycerophospholipids (GPL). We screened Acinetobacter baumannii transposon mutants and identified a number of mutants with OM defects, including an ABC transporter system homologous to the Mla system in E. coli. We further show that this opportunistic, antibiotic-resistant pathogen uses this multicomponent protein complex and ATP hydrolysis at the inner membrane to promote GPL export to the OM. The broad conservation of the Mla system in Gram-negative bacteria suggests the system may play a conserved role in OM biogenesis. The importance of the Mla system to Acinetobacter baumannii OM integrity and antibiotic sensitivity suggests that its components may serve as new antimicrobial therapeutic targets.
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Affiliation(s)
- Cassandra Kamischke
- Department of Microbiology, University of Washington, Seattle, United States
| | - Junping Fan
- Department of Microbiology, University of Washington, Seattle, United States
| | - Julien Bergeron
- Department of Biochemistry, University of Washington, Seattle, United States
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | | | - Zachary D Dalebroux
- Department of Microbiology, University of Washington, Seattle, United States
| | - Anika Burrell
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Samuel I Miller
- Department of Microbiology, University of Washington, Seattle, United States
- Department of Genome Sciences, University of Washington, Seattle, United States
- Department of Medicine, University of Washington, Seattle, United States
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8
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El Kennani S, Adrait A, Permiakova O, Hesse AM, Ialy-Radio C, Ferro M, Brun V, Cocquet J, Govin J, Pflieger D. Systematic quantitative analysis of H2A and H2B variants by targeted proteomics. Epigenetics Chromatin 2018; 11:2. [PMID: 29329550 PMCID: PMC5767011 DOI: 10.1186/s13072-017-0172-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/20/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Histones organize DNA into chromatin through a variety of processes. Among them, a vast diversity of histone variants can be incorporated into chromatin and finely modulate its organization and functionality. Classically, the study of histone variants has largely relied on antibody-based assays. However, antibodies have a limited efficiency to discriminate between highly similar histone variants. RESULTS In this study, we established a mass spectrometry-based analysis to address this challenge. We developed a targeted proteomics method, using selected reaction monitoring or parallel reaction monitoring, to quantify a maximum number of histone variants in a single multiplexed assay, even when histones are present in a crude extract. This strategy was developed on H2A and H2B variants, using 55 peptides corresponding to 25 different histone sequences, among which a few differ by a single amino acid. The methodology was then applied to mouse testis extracts in which almost all histone variants are expressed. It confirmed the abundance profiles of several testis-specific histones during successive stages of spermatogenesis and the existence of predicted H2A.L.1 isoforms. This methodology was also used to explore the over-expression pattern of H2A.L.1 isoforms in a mouse model of male infertility. CONCLUSIONS Our results demonstrate that targeted proteomics is a powerful method to quantify highly similar histone variants and isoforms. The developed method can be easily transposed to the study of human histone variants, whose abundance can be deregulated in various diseases.
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Affiliation(s)
- Sara El Kennani
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Annie Adrait
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Olga Permiakova
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Anne-Marie Hesse
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Côme Ialy-Radio
- INSERM U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Myriam Ferro
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Virginie Brun
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Julie Cocquet
- INSERM U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jérôme Govin
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France.
| | - Delphine Pflieger
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France. .,CNRS, FR CNRS 3425, Biosciences and Biotechnology Institute of Grenoble, Grenoble, France.
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9
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Trötzmüller M, Triebl A, Ajsic A, Hartler J, Köfeler H, Regittnig W. Determination of the Isotopic Enrichment of 13C- and 2H-Labeled Tracers of Glucose Using High-Resolution Mass Spectrometry: Application to Dual- and Triple-Tracer Studies. Anal Chem 2017; 89:12252-12260. [DOI: 10.1021/acs.analchem.7b03134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Martin Trötzmüller
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse
24, 8010 Graz, Austria
| | | | | | - Jürgen Hartler
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse
24, 8010 Graz, Austria
- Institute of Computational
Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Harald Köfeler
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse
24, 8010 Graz, Austria
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10
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Previs SF, Herath K, Castro-Perez J, Mahsut A, Zhou H, McLaren DG, Shah V, Rohm RJ, Stout SJ, Zhong W, Wang SP, Johns DG, Hubbard BK, Cleary MA, Roddy TP. Effect of Error Propagation in Stable Isotope Tracer Studies: An Approach for Estimating Impact on Apparent Biochemical Flux. Methods Enzymol 2015; 561:331-58. [PMID: 26358910 DOI: 10.1016/bs.mie.2015.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Stable isotope tracers are widely used to quantify metabolic rates, and yet a limited number of studies have considered the impact of analytical error on estimates of flux. For example, when estimating the contribution of de novo lipogenesis, one typically measures a minimum of four isotope ratios, i.e., the precursor and product labeling pre- and posttracer administration. This seemingly simple problem has 1 correct solution and 80 erroneous outcomes. In this report, we outline a methodology for evaluating the effect of error propagation on apparent physiological endpoints. We demonstrate examples of how to evaluate the influence of analytical error in case studies concerning lipid and protein synthesis; we have focused on (2)H2O as a tracer and contrast different mass spectrometry platforms including GC-quadrupole-MS, GC-pyrolysis-IRMS, LC-quadrupole-MS, and high-resolution FT-ICR-MS. The method outlined herein can be used to determine how to minimize variations in the apparent biology by altering the dose and/or the type of tracer. Likewise, one can facilitate biological studies by estimating the reduction in the noise of an outcome that is expected for a given increase in the number of replicate injections.
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Affiliation(s)
| | | | | | - Ablatt Mahsut
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Haihong Zhou
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | | | - Vinit Shah
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Rory J Rohm
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Steven J Stout
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Wendy Zhong
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | | | | | | | | | - Thomas P Roddy
- Merck Research Laboratories, Kenilworth, New Jersey, USA
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11
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Nasso S, Goetze S, Martens L. Ariadne’s Thread: A Robust Software Solution Leading to Automated Absolute and Relative Quantification of SRM Data. J Proteome Res 2015; 14:3779-92. [DOI: 10.1021/pr500996s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sara Nasso
- Department
of Biology, Institute of Molecular Systems Biology, ETH, Auguste-Piccard-Hof
1, ETH Hönggerberg, CH-8093 Zürich, Switzerland
- Institute
of Molecular Life Sciences, University of Zurich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
| | - Sandra Goetze
- Department
of Biology, Institute of Molecular Systems Biology, ETH, Auguste-Piccard-Hof
1, ETH Hönggerberg, CH-8093 Zürich, Switzerland
- Institute
of Molecular Life Sciences, University of Zurich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
| | - Lennart Martens
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, Ghent 9000, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, Ghent 9000, Belgium
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12
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Canterbury JD, Merrihew GE, Goodlett DR, MacCoss MJ, Shaffer SA. Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2048-59. [PMID: 25261218 PMCID: PMC4417682 DOI: 10.1007/s13361-014-0981-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 07/26/2014] [Accepted: 07/28/2014] [Indexed: 05/21/2023]
Abstract
The most common data collection in shotgun proteomics is via data-dependent acquisition (DDA), a process driven by an automated instrument control routine that directs MS/MS acquisition from the highest abundant signals to the lowest. An alternative to DDA is data-independent acquisition (DIA), a process in which a specified range in m/z is fragmented without regard to prioritization of a precursor ion or its relative abundance in the mass spectrum, thus potentially offering a more comprehensive analysis of peptides than DDA. In this work, we evaluate both DDA and DIA on three different linear ion trap instruments: an LTQ, an LTQ modified with an electrodynamic ion funnel, and an LTQ Velos. These instruments represent both older (LTQ) and newer (LTQ Velos) ion trap designs (i.e., linear versus dual ion traps, respectively), and allow direct comparison of peptide identifications using both DDA and DIA analysis. Further, as the LTQ Velos has an enhanced "S-lens" ion guide to improve ion flux, we found it logical to determine if the former LTQ model could be leveraged by improving sensitivity by modifying with an electrodynamic ion guide of significantly different design to the S-lens. We find that the ion funnel enabled LTQ identifies more proteins in the insoluble fraction of a yeast lysate than the other two instruments in DIA mode, whereas the faster scanning LTQ Velos performs better in DDA mode. We explore reasons for these results, including differences in scan speed, source ion optics, and linear ion trap design.
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Affiliation(s)
| | | | - David R. Goodlett
- Department of Medicinal Chemistry, University of Washington, Seattle
| | | | - Scott A. Shaffer
- Department of Medicinal Chemistry, University of Washington, Seattle
- Author to whom correspondence should be addressed: Scott A. Shaffer. Voice: 508-856-8917;
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13
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Gallien S, Duriez E, Domon B. Selected reaction monitoring applied to proteomics. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:298-312. [PMID: 21394846 DOI: 10.1002/jms.1895] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Selected reaction monitoring (SRM) performed on triple quadrupole mass spectrometers has been the reference quantitative technique to analyze small molecules for several decades. It is now emerging in proteomics as the ideal tool to complement shotgun qualitative studies; targeted SRM quantitative analysis offers high selectivity, sensitivity and a wide dynamic range. However, SRM applied to proteomics presents singularities that distinguish it from small molecules analysis. This review is an overview of SRM technology and describes the specificities and the technical aspects of proteomics experiments. Ongoing developments aiming at increasing multiplexing capabilities of SRM are discussed; they dramatically improve its throughput and extend its field of application to directed or supervised discovery experiments.
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Affiliation(s)
- Sebastien Gallien
- Luxembourg Clinical Proteomics center (LCP), Centre de Recherche Public de la Santé, 1 B rue Thomas Edison, L-1445 Strassen, Luxembourg
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14
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Maclean B, Tomazela DM, Abbatiello SE, Zhang S, Whiteaker JR, Paulovich AG, Carr SA, Maccoss MJ. Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry. Anal Chem 2010; 82:10116-24. [PMID: 21090646 DOI: 10.1021/ac102179j] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteomics experiments based on Selected Reaction Monitoring (SRM, also referred to as Multiple Reaction Monitoring or MRM) are being used to target large numbers of protein candidates in complex mixtures. At present, instrument parameters are often optimized for each peptide, a time and resource intensive process. Large SRM experiments are greatly facilitated by having the ability to predict MS instrument parameters that work well with the broad diversity of peptides they target. For this reason, we investigated the impact of using simple linear equations to predict the collision energy (CE) on peptide signal intensity and compared it with the empirical optimization of the CE for each peptide and transition individually. Using optimized linear equations, the difference between predicted and empirically derived CE values was found to be an average gain of only 7.8% of total peak area. We also found that existing commonly used linear equations fall short of their potential, and should be recalculated for each charge state and when introducing new instrument platforms. We provide a fully automated pipeline for calculating these equations and individually optimizing CE of each transition on SRM instruments from Agilent, Applied Biosystems, Thermo-Scientific and Waters in the open source Skyline software tool ( http://proteome.gs.washington.edu/software/skyline ).
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Affiliation(s)
- Brendan Maclean
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States
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15
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Tomazela DM, Patterson BW, Hanson E, Spence KL, Kanion TB, Salinger DH, Vicini P, Barret H, Heins HB, Cole FS, Hamvas A, MacCoss MJ. Measurement of human surfactant protein-B turnover in vivo from tracheal aspirates using targeted proteomics. Anal Chem 2010; 82:2561-7. [PMID: 20178338 DOI: 10.1021/ac1001433] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a method to measure protein synthesis and catabolism in humans without prior purification and use the method to measure the turnover of surfactant protein-B (SP-B). SP-B, a lung-specific, hydrophobic protein essential for fetal-neonatal respiratory transition, is present in only picomolar quantities in tracheal aspirate samples and difficult to isolate for dynamic turnover studies using traditional in vivo tracer techniques. Using infusion of [5,5,5-(2)H(3)] leucine and a targeted proteomics method, we measured both the quantity and kinetics of SP-B tryptic peptides in tracheal aspirate samples of symptomatic newborn infants. The fractional synthetic rate (FSR) of SP-B measured using the most abundant proteolytic fragment, a 10 amino acid peptide from the carboxy-terminus of proSP-B (SPTGEWLPR), from the circulating leucine pool was 0.035 +/- 0.005 h(-1), and the fractional catabolic rate was 0.044 +/- 0.003 h(-1). This technique permits high-throughput and sensitive measurement of turnover of low abundance proteins with minimal sample preparation.
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Affiliation(s)
- Daniela M Tomazela
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-5065, USA
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Du P, Stolovitzky G, Horvatovich P, Bischoff R, Lim J, Suits F. A noise model for mass spectrometry based proteomics. Bioinformatics 2008; 24:1070-7. [PMID: 18353791 DOI: 10.1093/bioinformatics/btn078] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Peicheng Du
- IBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598, USA.
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MacCoss MJ, Wu CC. Computational analysis of quantitative proteomics data using stable isotope labeling. Methods Mol Biol 2007; 359:177-89. [PMID: 17484118 DOI: 10.1007/978-1-59745-255-7_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Over the last few years, new proteomics methods have been developed for making quantitative comparisons using stable isotope labeling. Although these methods have paved the way for quantitative proteomics, the analysis of these data is often the rate-limiting step. In fact, many analyzes are still carried out manually, which adds a level of subjectivity to the data that will vary between laboratories and even analysts. In this chapter, we have attempted to summarize several of the key steps necessary for an individual to automate the analysis of quantitative proteomics data. The approach is straightfoward to implement for an individual with moderate programming experience and used to process proteomics data in an objective manner.
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Affiliation(s)
- Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, USA
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Lin WT, Hung WN, Yian YH, Wu KP, Han CL, Chen YR, Chen YJ, Sung TY, Hsu WL. Multi-Q: a fully automated tool for multiplexed protein quantitation. J Proteome Res 2006; 5:2328-38. [PMID: 16944945 DOI: 10.1021/pr060132c] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The iTRAQ labeling method combined with shotgun proteomic techniques represents a new dimension in multiplexed quantitation for relative protein expression measurement in different cell states. To expedite the analysis of vast amounts of spectral data, we present a fully automated software package, called Multi-Q, for multiplexed iTRAQ-based quantitation in protein profiling. Multi-Q is designed as a generic platform that can accommodate various input data formats from search engines and mass spectrometer manufacturers. To calculate peptide ratios, the software automatically processes iTRAQ's signature peaks, including peak detection, background subtraction, isotope correction, and normalization to remove systematic errors. Furthermore, Multi-Q allows users to define their own data-filtering thresholds based on semiempirical values or statistical models so that the computed results of fold changes in peptide ratios are statistically significant. This feature facilitates the use of Multi-Q with various instrument types with different dynamic ranges, which is an important aspect of iTRAQ analysis. The performance of Multi-Q is evaluated with a mixture of 10 standard proteins and human Jurkat T cells. The results are consistent with expected protein ratios and thus demonstrate the high accuracy, full automation, and high-throughput capability of Multi-Q as a large-scale quantitation proteomics tool. These features allow rapid interpretation of output from large proteomic datasets without the need for manual validation. Executable Multi-Q files are available on Windows platform at http://ms.iis.sinica.edu.tw/Multi-Q/.
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Affiliation(s)
- Wen-Ting Lin
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
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Blackler AR, Klammer AA, MacCoss MJ, Wu CC. Quantitative Comparison of Proteomic Data Quality between a 2D and 3D Quadrupole Ion Trap. Anal Chem 2006; 78:1337-44. [PMID: 16478131 DOI: 10.1021/ac051486a] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A 2D ion trap has a greater ion trapping efficiency, greater ion capacity before observing space-charging effects, and a faster ion ejection rate than a traditional 3D ion trap mass spectrometer. These hardware improvements should result in a significant increase in protein identifications from complex mixtures analyzed using shotgun proteomics. In this study, we compare the quality and quantity of peptide identifications using data-dependent acquisition of tandem mass spectra of peptides between two commercially available ion trap mass spectrometers (an LTQ and an LCQ XP Max). We demonstrate that the increased trapping efficiency, increased ion capacity, and faster ion ejection rate of the LTQ results in greater than 5-fold more protein identifications, better identification of low-abundance proteins, and higher confidence protein identifications when compared with a LCQ XP Max.
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Affiliation(s)
- Adele R Blackler
- Department of Pharmacology, University of Colorado Health Sciences Center, Aurora, CO 80045, USA
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MacCoss MJ, Wu CC, Matthews DE, Yates JR. Measurement of the Isotope Enrichment of Stable Isotope-Labeled Proteins Using High-Resolution Mass Spectra of Peptides. Anal Chem 2005; 77:7646-53. [PMID: 16316172 DOI: 10.1021/ac0508393] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stable isotope-enriched molecules are used as internal standards and as tracers of in vivo substrate metabolism. The accurate conversion of measured ratios in the mass spectrometer to mole ratios is complicated because a polyatomic molecule containing enriched atoms will result in a combinatorial distribution of isotopomers depending on the enrichment and number of "labeled" atoms. This effect could potentially cause a large error in the mole ratio measurement depending on which isotope peak or peaks were used to determine the ratio. We report a computational method that predicts isotope distributions over a range of enrichments and compares the predicted distributions to experimental peptide isotope distributions obtained by Fourier transform ion cyclotron resonance mass spectrometry. Our approach is accurate with measured enrichments within 1.5% of expected isotope distributions. The method is also precise with 4.9, 2.0, and 0.8% relative standard deviations for peptides containing 59, 79, and 99 atom % excess (15)N, respectively. The approach is automated making isotope enrichment calculations possible for thousands of peptides in a single muLC-FTICR-MS experiment.
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Affiliation(s)
- Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, 98195, USA.
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MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR. A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem 2004; 75:6912-21. [PMID: 14670053 DOI: 10.1021/ac034790h] [Citation(s) in RCA: 235] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitative shotgun proteomic analyses are facilitated using chemical tags such as ICAT and metabolic labeling strategies with stable isotopes. The rapid high-throughput production of quantitative "shotgun" proteomic data necessitates the development of software to automatically convert mass spectrometry-derived data of peptides into relative protein abundances. We describe a computer program called RelEx, which uses a least-squares regression for the calculation of the peptide ion current ratios from the mass spectrometry-derived ion chromatograms. RelEx is tolerant of poor signal-to-noise data and can automatically discard nonusable chromatograms and outlier ratios. We apply a simple correction for systematic errors that improves the accuracy of the quantitative measurement by 32 +/- 4%. Our automated approach was validated using labeled mixtures composed of known molar ratios and demonstrated in a real sample by measuring the effect of osmotic stress on protein expression in Saccharomyces cerevisiae.
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Affiliation(s)
- Michael J MacCoss
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Wu CC, MacCoss MJ, Howell KE, Matthews DE, Yates JR. Metabolic Labeling of Mammalian Organisms with Stable Isotopes for Quantitative Proteomic Analysis. Anal Chem 2004; 76:4951-9. [PMID: 15373428 DOI: 10.1021/ac049208j] [Citation(s) in RCA: 308] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To quantify proteins on a global level from mammalian tissue, a method was developed to metabolically introduce 15N stable isotopes into the proteins of Rattus norvegicus for use as internal standards. The long-term metabolic labeling of rats with a diet enriched in 15N did not result in adverse health consequences. The average 15N amino acid enrichments reflected the relative turnover rates in the different tissues and ranged from 74.3 mpe in brain to 92.2 mpe in plasma. Using the 15N-enriched liver as a quantitative internal standard, changes in individual protein levels in response to cycloheximide treatment were measured for 310 proteins. These measurements revealed 127 proteins with altered protein level (p < 0.05). Most proteins with altered level have previously reported functions involving xenobiotic metabolism and protein-folding machinery of the endoplasmic reticulum. This approach is a powerful tool for the global quantitation of proteins, is capable of measuring proteome-wide changes in response to a drug, and will be useful for studying animal models of disease.
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Affiliation(s)
- Christine C Wu
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Bibliography. Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:1164-1171. [PMID: 11747111 DOI: 10.1002/jms.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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