51
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Kelly RT, Tolmachev AV, Page JS, Tang K, Smith RD. The ion funnel: theory, implementations, and applications. MASS SPECTROMETRY REVIEWS 2010; 29:294-312. [PMID: 19391099 PMCID: PMC2824015 DOI: 10.1002/mas.20232] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The electrodynamic ion funnel has enabled the manipulation and focusing of ions in a pressure regime (0.1-30 Torr) that has challenged traditional approaches, and provided the basis for much greater mass spectrometer ion transmission efficiencies. The initial ion funnel implementations aimed to efficiently capture ions in the expanding gas jet of an electrospray ionization interface and radially focus them for efficient transfer through a conductance limiting orifice. We review the improvements in fundamental understanding of ion motion in ion funnels, the evolution in its implementations that have brought the ion funnel to its current state of refinement, as well as applications of the ion funnel for purposes such as ion trapping, ion cooling, low pressure electrospray, and ion mobility spectrometry.
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52
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Wenger CD, McAlister GC, Xia Q, Coon JJ. Sub-part-per-million precursor and product mass accuracy for high-throughput proteomics on an electron transfer dissociation-enabled orbitrap mass spectrometer. Mol Cell Proteomics 2010; 9:754-63. [PMID: 20124352 DOI: 10.1074/mcp.m900541-mcp200] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We demonstrate a new approach for internal mass calibration on an electron transfer dissociation-enabled linear ion trap-orbitrap hybrid mass spectrometer. Fluoranthene cations, a byproduct of the reaction used for generation of electron transfer dissociation reagent anions, are co-injected with the analyte cations in all orbitrap mass analysis events. The fluoranthene cations serve as a robust internal calibrant with minimal impact on scan time (<20 ms) or spectral quality. Following external mass calibration, 60 replicate LC-MS/MS runs of a complex peptide mixture were collected over the course of approximately 136 h (almost 6 days). Using only standard external mass calibration, the mass accuracy for a typical analysis was -3.31 +/- 0.93 ppm (sigma) for precursors and -2.32 +/- 0.89 ppm for products. After application of internal recalibration, mass accuracy improved to +0.77 +/- 0.71 ppm for precursors and +0.17 +/- 0.67 ppm for products. When all 60 replicate runs were analyzed together without internal mass recalibration, the mass accuracy was -1.23 +/- 1.54 ppm for precursors and -0.18 +/- 1.42 ppm for products, nearly a 2-fold drop in precision relative to an individual run. After internal mass recalibration, this improved to +0.80 +/- 0.70 ppm for precursors and +0.16 +/- 0.67 ppm for products, roughly equivalent to that obtained in a single run, demonstrating a near complete elimination of mass calibration drift.
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Affiliation(s)
- Craig D Wenger
- Department Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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53
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Brenton AG, Godfrey AR, Alamri M, Stein BK, Williams CM, Hunter AP, Wyatt MF. Analysis of large historical accurate mass data sets on sector mass spectrometers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3484-3487. [PMID: 19813284 DOI: 10.1002/rcm.4269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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54
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Reinsberg KG, Effelsberg U, Tallarek U. Microchip electrospray performance during gradient elution with bulk conductivity changes. LAB ON A CHIP 2009; 9:2914-2923. [PMID: 19789744 DOI: 10.1039/b905052c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This work identifies dynamic changes in bulk conductivity during reversed-phase HPLC gradient elution as a major source for spray mode changes and instabilities observed in ESI-MS. A commercial microchip-HPLC/ESI-MS configuration was modified to enable electrospray diagnostics based on frequency analysis of the microchip emitter current combined with spray imaging. This approach facilitated detection of different spray modes together with their onset potentials. Water/acetonitrile mixtures containing formic acid were selected as the electrosprayed solutions to represent typical conditions in reversed-phase HPLC. Experimental data are complemented by computational fluid dynamics simulations, treating the electrosprayed solution as leaky dielectric fluid, to address the influence of bulk conductivity and applied potential difference on the developing cone-jet morphology and stability.
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Affiliation(s)
- Klaus-Georg Reinsberg
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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55
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Jing L, Amster IJ. RAPID AND AUTOMATED PROCESSING OF MALDI-FTICR/MS DATA FOR N-METABOLIC LABELING IN A SHOTGUN PROTEOMICS ANALYSIS. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2009; 287:27-31. [PMID: 20160905 PMCID: PMC2769025 DOI: 10.1016/j.ijms.2009.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Offline high performance liquid chromatography combined with matrix assisted laser desorption and Fourier transform ion cyclotron resonance mass spectrometry (HPLC-MALDI-FTICR/MS) provides the means to rapidly analyze complex mixtures of peptides, such as those produced by proteolytic digestion of a proteome. This method is particularly useful for making quantitative measurements of changes in protein expression by using (15)N-metabolic labeling. Proteolytic digestion of combined labeled and unlabeled proteomes produces complex mixtures that with many mass overlaps when analyzed by HPLC-MALDI-FTICR/MS. A significant challenge to data analysis is the matching of pairs of peaks which represent an unlabeled peptide and its labeled counterpart. We have developed an algorithm and incorporated it into a compute program which significantly accelerates the interpretation of (15)N metabolic labeling data by automating the process of identifying unlabeled/labeled peak pairs. The algorithm takes advantage of the high resolution and mass accuracy of FTICR mass spectrometry. The algorithm is shown to be able to successfully identify the (15)N/(14)N peptide pairs and calculate peptide relative abundance ratios in highly complex mixtures from the proteolytic digest of a whole organism protein extract.
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Affiliation(s)
- Li Jing
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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56
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Rietschel B, Baeumlisberger D, Arrey TN, Bornemann S, Rohmer M, Schuerken M, Karas M, Meyer B. The Benefit of Combining nLC-MALDI-Orbitrap MS Data with nLC-MALDI-TOF/TOF Data for Proteomic Analyses Employing Elastase. J Proteome Res 2009; 8:5317-24. [DOI: 10.1021/pr900557k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin Rietschel
- Cluster of Excellence “Macromolecular Complexes”, Institute for Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Dominic Baeumlisberger
- Cluster of Excellence “Macromolecular Complexes”, Institute for Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Tabiwang N. Arrey
- Cluster of Excellence “Macromolecular Complexes”, Institute for Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Sandra Bornemann
- Cluster of Excellence “Macromolecular Complexes”, Institute for Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Marion Rohmer
- Cluster of Excellence “Macromolecular Complexes”, Institute for Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Malte Schuerken
- Cluster of Excellence “Macromolecular Complexes”, Institute for Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Michael Karas
- Cluster of Excellence “Macromolecular Complexes”, Institute for Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Bjoern Meyer
- Cluster of Excellence “Macromolecular Complexes”, Institute for Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
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57
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Köcher T, Pichler P, Schutzbier M, Stingl C, Kaul A, Teucher N, Hasenfuss G, Penninger JM, Mechtler K. High Precision Quantitative Proteomics Using iTRAQ on an LTQ Orbitrap: A New Mass Spectrometric Method Combining the Benefits of All. J Proteome Res 2009; 8:4743-52. [DOI: 10.1021/pr900451u] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Thomas Köcher
- Research Institute of Molecular Pathology (IMP), Vienna, Austria, Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria, University Medical Center Göttingen (UMG), Georg-August-Universität, Germany, and Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Peter Pichler
- Research Institute of Molecular Pathology (IMP), Vienna, Austria, Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria, University Medical Center Göttingen (UMG), Georg-August-Universität, Germany, and Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Michael Schutzbier
- Research Institute of Molecular Pathology (IMP), Vienna, Austria, Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria, University Medical Center Göttingen (UMG), Georg-August-Universität, Germany, and Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Christoph Stingl
- Research Institute of Molecular Pathology (IMP), Vienna, Austria, Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria, University Medical Center Göttingen (UMG), Georg-August-Universität, Germany, and Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Axel Kaul
- Research Institute of Molecular Pathology (IMP), Vienna, Austria, Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria, University Medical Center Göttingen (UMG), Georg-August-Universität, Germany, and Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Nils Teucher
- Research Institute of Molecular Pathology (IMP), Vienna, Austria, Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria, University Medical Center Göttingen (UMG), Georg-August-Universität, Germany, and Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Gerd Hasenfuss
- Research Institute of Molecular Pathology (IMP), Vienna, Austria, Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria, University Medical Center Göttingen (UMG), Georg-August-Universität, Germany, and Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Josef M. Penninger
- Research Institute of Molecular Pathology (IMP), Vienna, Austria, Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria, University Medical Center Göttingen (UMG), Georg-August-Universität, Germany, and Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna, Austria, Christian Doppler Laboratory for Proteome Analysis, University of Vienna, Vienna, Austria, University Medical Center Göttingen (UMG), Georg-August-Universität, Germany, and Institute of Molecular Biotechnology (IMBA), Vienna, Austria
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58
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Petyuk VA, Qian WJ, Smith RD, Smith DJ. Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry. Methods 2009; 50:77-84. [PMID: 19654045 DOI: 10.1016/j.ymeth.2009.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 07/27/2009] [Accepted: 07/30/2009] [Indexed: 10/20/2022] Open
Abstract
Voxelation creates expression atlases by high-throughput analysis of spatially registered cubes or voxels harvested from the brain. The modality independence of voxelation allows a variety of bioanalytical techniques to be used to map abundance. Protein expression patterns in the brain can be obtained using liquid chromatography (LC) combined with mass spectrometry (MS). Here we describe the methodology of voxelation as it pertains particularly to LC-MS proteomic analysis: sample preparation, instrumental set up and analysis, peptide identification and protein relative abundance quantitation. We also briefly describe some of the advantages, limitations and insights into the brain that can be obtained using combined proteomic and transcriptomic maps.
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Affiliation(s)
- Vladislav A Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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59
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Yates JR, Ruse CI, Nakorchevsky A. Proteomics by Mass Spectrometry: Approaches, Advances, and Applications. Annu Rev Biomed Eng 2009; 11:49-79. [DOI: 10.1146/annurev-bioeng-061008-124934] [Citation(s) in RCA: 798] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- John R. Yates
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037;
| | - Cristian I. Ruse
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037;
| | - Aleksey Nakorchevsky
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037;
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60
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Use of 18O water and ESI-MS detection in subsite characterisation and investigation of the hydrolytic action of an endoglucanase. Anal Bioanal Chem 2009; 394:1977-84. [DOI: 10.1007/s00216-009-2891-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 06/01/2009] [Accepted: 06/04/2009] [Indexed: 10/20/2022]
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61
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Volchenboum SL, Kristjansdottir K, Wolfgeher D, Kron SJ. Rapid validation of Mascot search results via stable isotope labeling, pair picking, and deconvolution of fragmentation patterns. Mol Cell Proteomics 2009; 8:2011-22. [PMID: 19435713 DOI: 10.1074/mcp.m800472-mcp200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Conventional LC-MS/MS data analysis matches each precursor ion and fragmentation pattern to their best fit within databases of theoretical spectra, yielding a peptide identification. Confidence is estimated by a score but can be validated by statistics, false discovery rates, and/or manual validation. A weakness is that each ion is evaluated independently, discarding potentially useful cross-correlations. In a classical approach to de novo sequence analysis, mixtures of peptides differing only in a carboxyl-terminal isotopic label yield fragmentation spectra with single, unlabeled b-type ions but pairs of isotope-labeled y-type ions, facilitating confident assignments. To apply this principle to identification by fragmentation pattern matching, we developed Validator, software that recognizes isotopic peptide pairs and compares their identifications and fragmentation patterns. Testing Validator 1 on a Mascot results file from FT-ICR LC-MS/MS of (16)O/(18)O-labeled yeast cell lysate peptides yielded 2,775 peptide pairs sharing a common identification but differing in carboxyl-terminal label. Comparing observed b- and y-ions with the predicted fragmentation pattern improved the threshold Mascot score for 5% false discovery from 36 to 22, significantly increasing both sensitivity and specificity. Validator 2, which identifies pairs by precursor mass difference alone before comparing observed fragmentation with that predicted by Mascot, found 2,021 isotopic pairs, similarly achieving improved sensitivity and specificity. Finally Validator 3, which finds pairs based on mass difference alone and then deconvolutes fragmentation patterns independently of Mascot, found 964 predicted peptides. Validator 3 allowed raw mass spectrometry data to be mined not only to validate Mascot results but also to discover peptides missed by Mascot. Using standard desktop hardware, the Validator 1-3 software processed the 11,536 spectra in the 93-MB Mascot .DAT file in less than 6 min (32 spectra/s), revealing high confidence peptide identifications without regard to Mascot score, far faster than manual or other independent validation methods.
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Affiliation(s)
- Samuel L Volchenboum
- Department of Pediatrics, The University of Chicago, Chicago, Illinois 60637, USA.
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62
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Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD. Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics 2009; 10:87. [PMID: 19292916 PMCID: PMC2666663 DOI: 10.1186/1471-2105-10-87] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2008] [Accepted: 03/17/2009] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls. RESULTS With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC) elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample. CONCLUSION Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, Decon2LS is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs.Decon2LS source code, installer, and tutorials may be downloaded free of charge at http://http:/ncrr.pnl.gov/software/.
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Affiliation(s)
- Navdeep Jaitly
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Anoop Mayampurath
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kyle Littlefield
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joshua N Adkins
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Gordon A Anderson
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008; 26:1367-72. [PMID: 19029910 DOI: 10.1038/nbt.1511] [Citation(s) in RCA: 10526] [Impact Index Per Article: 657.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 10/31/2008] [Indexed: 01/18/2023]
Abstract
Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.
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64
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Shi Y, Bajrami B, Morton M, Yao X. Cyclophosphoramidate Ion as Mass Defect Marker for Efficient Detection of Protein Serine Phosphorylation. Anal Chem 2008; 80:7614-23. [DOI: 10.1021/ac801355u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Shi
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Bekim Bajrami
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Martha Morton
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
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65
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Yao X, Diego P, Ramos AA, Shi Y. Averagine-Scaling Analysis and Fragment Ion Mass Defect Labeling in Peptide Mass Spectrometry. Anal Chem 2008; 80:7383-91. [DOI: 10.1021/ac801096e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Pamela Diego
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Alexis A. Ramos
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Yu Shi
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
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67
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Kruse U, Bantscheff M, Drewes G, Hopf C. Chemical and pathway proteomics: powerful tools for oncology drug discovery and personalized health care. Mol Cell Proteomics 2008; 7:1887-901. [PMID: 18676365 DOI: 10.1074/mcp.r800006-mcp200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In recent years mass spectrometry-based proteomics has moved beyond a mere quantitative description of protein expression levels and their possible correlation with disease or drug action. Impressive progress in LC-MS instrumentation together with the availability of new enabling tools and methods for quantitative proteome analysis and for identification of posttranslational modifications has triggered a surge of chemical and functional proteomics studies dissecting mechanisms of action of cancer drugs and molecular mechanisms that modulate signal transduction pathways. Despite the tremendous progress that has been made in the field, major challenges, relating to sensitivity, dynamic range, and throughput of the described methods, remain. In this review we summarize recent advances in LC-MS-based approaches and their application to cancer drug discovery and to studies of cancer-related pathways in cell culture models with particular emphasis on mechanistic studies of drug action in these systems. Moreover we highlight the emerging utility of pathway and chemical proteomics techniques for translational research in patient tissue.
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Affiliation(s)
- Ulrich Kruse
- Deptartment of Discovery Technology, Cellzome AG, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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68
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Kalli A, Håkansson K. Comparison of the Electron Capture Dissociation Fragmentation Behavior of Doubly and Triply Protonated Peptides from Trypsin, Glu-C, and Chymotrypsin Digestion. J Proteome Res 2008; 7:2834-44. [DOI: 10.1021/pr800038y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Anastasia Kalli
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055
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69
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Cappadona S, Levander F, Jansson M, James P, Cerutti S, Pattini L. Wavelet-based method for noise characterization and rejection in high-performance liquid chromatography coupled to mass spectrometry. Anal Chem 2008; 80:4960-8. [PMID: 18510348 DOI: 10.1021/ac800166w] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a new method for rejecting noise from HPLC-MS data sets. The algorithm reveals peptides at low concentrations by minimizing both the chemical and the random noise. The goal is reached through a systematic approach to characterize and remove the background. The data are represented as two-dimensional maps, in order to optimally exploit the complementary dimensions of separation of the peptides offered by the LC-MS technique. The virtual chromatograms, reconstructed from the spectrographic data, have proved to be more suitable to characterize the noise than the raw mass spectra. By means of wavelet analysis, it was possible to access both the chemical and the random noise, at different scales of the decomposition. The novel approach has proved to efficiently distinguish signal from noise and to selectively reject the background while preserving low-abundance peptides.
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Affiliation(s)
- Salvatore Cappadona
- Department of Bioengineering, IIT Unit, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
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70
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Kelly RT, Tang K, Irimia D, Toner M, Smith RD. Elastomeric microchip electrospray emitter for stable cone-jet mode operation in the nanoflow regime. Anal Chem 2008; 80:3824-31. [PMID: 18419138 PMCID: PMC2692495 DOI: 10.1021/ac8000786] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite widespread interest in combining laboratory-on-a-chip technologies with mass spectrometry (MS)-based analyses, the coupling of microfluidics to electrospray ionization (ESI)-MS remains challenging. We report a robust, integrated poly(dimethylsiloxane) microchip interface for ESI-MS using simple and widely accessible microfabrication procedures. The interface uses an auxiliary channel to provide electrical contact for the stable cone-jet electrospray without sample loss or dilution. The electric field at the channel terminus is enhanced by two vertical cuts that cause the interface to taper to a line rather than to a point, and the formation of a small Taylor cone at the channel exit ensures subnanoliter postcolumn dead volumes. Cone-jet mode electrospray was demonstrated for up to 90% aqueous solutions and for extended durations. Comparable ESI-MS sensitivities were achieved using both microchip and conventional fused silica capillary emitters, but stable cone-jet mode electrosprays could be established over a far broader range of flow rates (from 50-1000 nL/min) and applied potentials using the microchip emitters. This attribute of the microchip emitter should simplify electrospray optimization and make the stable electrospray more resistant to external perturbations.
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Affiliation(s)
- Ryan T Kelly
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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71
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Abstract
Systematic searches for plasma proteins that are biological indicators, or biomarkers, for cancer are underway. The difficulties caused by the complexity of biological-fluid proteomes and tissue proteomes (which contribute proteins to plasma) and by the extensive heterogeneity among diseases, subjects and levels of sample procurement are gradually being overcome. This is being achieved through rigorous experimental design and in-depth quantitative studies. The expected outcome is the development of panels of biomarkers that will allow early detection of cancer and prediction of the probable response to therapy. Achieving these objectives requires high-quality specimens with well-matched controls, reagent resources, and an efficient process to confirm discoveries through independent validation studies.
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Affiliation(s)
- Samir M Hanash
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
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Manes NP, Estep RD, Mottaz HM, Moore RJ, Clauss TRW, Monroe ME, Du X, Adkins JN, Wong SW, Smith RD. Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions. J Proteome Res 2008; 7:960-8. [PMID: 18205298 DOI: 10.1021/pr070432+] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Orthopoxviruses are among the largest and most complex of the animal viruses. In response to the recent emergence of monkeypox in Africa and the threat of smallpox bioterrorism, two orthopoxviruses with different pathogenic potentials, human monkeypox virus and vaccinia virus, were proteomically compared with the goal of identifying proteins required for pathogenesis. Orthopoxviruses were grown in HeLa cells to two different viral forms (intracellular mature virus and extracellular enveloped virus), purified by sucrose gradient ultracentrifugation, denatured using RapiGest surfactant, and digested with trypsin. Unfractionated samples and strong cation exchange HPLC fractions were analyzed by high-resolution reversed-phase nano-LC-MS/MS, and analyses of the MS/MS spectra using SEQUEST and X! Tandem resulted in the confident identification of hundreds of monkeypox, vaccinia, and copurified host-cell proteins. The unfractionated samples were additionally analyzed by LC-MS using an LTQ-Orbitrap, and the accurate mass and elution time tag approach was used to perform quantitative comparisons. Possible pathophysiological roles of differentially abundant Orthopoxvirus proteins are discussed. Data, processed results, and protocols are available at http://www.proteomicsresource.org/.
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Affiliation(s)
- Nathan P Manes
- Fundamental Science Division and Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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Schaeffer-Reiss C. A brief summary of the different types of mass spectrometers used in proteomics. Methods Mol Biol 2008; 484:3-16. [PMID: 18592169 DOI: 10.1007/978-1-59745-398-1_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Recent technical innovations in mass spectrometry-based techniques have resulted in a range of highly sensitive and versatile instruments for high-throughput, high-sensitive, proteome-scale profiling. This wide diversity of instrumentation commercially available for mass spectrometry-based proteomics makes the choice of instrumentation sometimes difficult. The choice of instruments depends on the biological problem and the proteomic strategy chosen for protein identification. This chapter will give a short overview of the instruments routinely used in proteomic laboratories and the technical criteria that should be considered before instrument selection.
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Affiliation(s)
- Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse Bio-Organique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS/ Université Louis Pasteur, Strasbourg, France
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Jing L, Li C, Wong RL, Kaplan DA, Amster IJ. Improved mass accuracy for higher mass peptides by using SWIFT excitation for MALDI-FTICR mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:76-81. [PMID: 18061475 PMCID: PMC2242857 DOI: 10.1016/j.jasms.2007.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 10/18/2007] [Accepted: 10/22/2007] [Indexed: 05/25/2023]
Abstract
Stepwise-external calibration has previously been shown to produce sub part-per-million (ppm) mass accuracy for the MALDI-FTICR/MS analyses of peptides up to m/z 2500. The present work extends these results to ions up to m/z 4000. Mass measurement errors for ions of higher mass-to-charge are larger than for ions below m/z 2500 when using conventional chirp excitation to detect ions. Mass accuracy obtained by using stored waveform inverse Fourier transform (SWIFT) excitation was evaluated and compared with chirp excitation. Analysis of measurement errors reveals that SWIFT excitation provides smaller deviations from the calibration equation and better mass accuracy than chirp excitation for a wide mass range and for widely varying ion populations.
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Affiliation(s)
- Li Jing
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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