1
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Angel TE, Naylor BC, Price JC, Evans C, Szapacs M. Improved Sensitivity for Protein Turnover Quantification by Monitoring Immonium Ion Isotopologue Abundance. Anal Chem 2019; 91:9732-9740. [PMID: 31259532 DOI: 10.1021/acs.analchem.9b01329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe an analytical strategy allowing for the direct quantification of stable isotope label incorporation in newly synthesized proteins following administration of the stable isotope tracer deuterium oxide. We present a demonstration of coupling high-resolution mass spectrometry, metabolic stable isotope labeling, and MS/MS-based isotopologue quantification for the measurement of protein turnover. Stable isotope labeling with deuterium oxide, followed by immonium ion isotopologue quantification, is a more sensitive strategy for determining protein fractional synthesis rates compared to peptide centric mass isotopomer distribution analysis approaches when labeling time and/or stable isotope tracer exposure is limited and, as such, offers a great advantage for human studies.
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Affiliation(s)
- Thomas E Angel
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Bradley C Naylor
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - John C Price
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Christopher Evans
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Matthew Szapacs
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
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2
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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3
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Frost DC, Buchberger AR, Li L. Mass Defect-Based Dimethyl Pyrimidinyl Ornithine (DiPyrO) Tags for Multiplex Quantitative Proteomics. Anal Chem 2017; 89:10798-10805. [PMID: 28795795 PMCID: PMC7491675 DOI: 10.1021/acs.analchem.7b02098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have developed a novel amine-reactive mass defect-based chemical tag, dimethyl pyrimidinyl ornithine (DiPyrO), that is compact in size, is suitable for various biological samples, and enables highly multiplexed quantification of peptides at the MS1 level without increasing mass spectral complexity. The DiPyrO tag structure incorporates heavy isotopes in a variety of configurations to impart as much as 45.3 mDa or as little as 5.8 mDa per tag between labeled peptides. Notably, peptides containing lysine are labeled with two tags, doubling the imparted mass defect to up to 90.6 mDa for the duplex tags and effectively reducing the resolving power requirement compared to previously reported mass defect-based quantification approaches. This permits current and previous generation LTQ-Orbitrap platforms to perform confident quantitative analyses of two DiPyrO-labeled samples at 100K resolving power, whereas 3-plex and 6-plex quantifications are possible at 240K and 480K resolving powers, respectively. In this work, we discuss the design and synthesis of the DiPyrO tag, characterize its effect on labeled proteome analysis by nanoLC-MS2, and demonstrate proof-of-principle applications of the duplex and triplex tags for quantitative proteomics using high-resolution MS acquisition on the Orbitrap Elite and Orbitrap Fusion Lumos.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Amanda R Buchberger
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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4
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Di Y, Zhang Y, Zhang L, Tao T, Lu H. MdFDIA: A Mass Defect Based Four-Plex Data-Independent Acquisition Strategy for Proteome Quantification. Anal Chem 2017; 89:10248-10255. [PMID: 28872844 DOI: 10.1021/acs.analchem.7b01635] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Data-independent acquisition (DIA) has recently emerged as a powerful quantitative approach for large-scale proteome quantification, providing a sensitive and reproducible alternative to data-dependent acquisition (DDA). However, lack of compatible multiplexed quantification methods is a bottleneck of DIA. To alleviate this challenge, we present a mass defect based four-plex data-independent acquisition strategy, termed "MdFDIA", for parallel analysis of four different protein samples in a DIA experiment without the additional complexity of tandem mass spectrometry (MS2) spectra. MdFDIA is a hybrid approach that combines stable isotope labeling with amino acids in cell culture (SILAC) and dimethyl labeling. Briefly, the isotopes 13C615N2-lysine (+8.0142 Da, light) and D8-lysine (+8.0512 Da, heavy) were metabolically embedded in different proteome samples during cell culture. Then, two 13C615N2-lysine and D8-lysine labeled protein samples were digested with Lys-C, followed by in vitro labeling with light (213CD2H, +34.06312 Da) and heavy (2CD3, +34.06896 Da) dimethyl groups, respectively, producing four different pseudoisobaric labeled protein samples. The labeled samples were then equally mixed and analyzed by DIA. The subtle mass differences between the four labeled forms in MS2 scans can be resolved on an Orbitrap Fusion Lumos instrument to facilitate quantification without abundance information encoded in MS2 spectra. Additionally, a systematic investigation was carried out and revealed that MdFDIA enabled a significant decrease of the adverse impact on the accuracy of the quantitative assays arising from the chromatographic isotope effect, especially the deuterium effect, which typically occurs in a DDA experiment. Additionally, MdFDIA provided a method for validating the fragment type in the DIA spectra identification result. Furthermore, MdFDIA was applied to quantitative proteome analyses of four different breast cancer cell lines, demonstrating the feasibility of this strategy for biological applications.
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Affiliation(s)
| | | | | | | | - Haojie Lu
- Department of Chemistry, Fudan University , Shanghai, 200433, People's Republic of China
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5
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Diaz JE, Morgan CW, Minogue CE, Hebert AS, Coon JJ, Wells JA. A Split-Abl Kinase for Direct Activation in Cells. Cell Chem Biol 2017; 24:1250-1258.e4. [PMID: 28919041 DOI: 10.1016/j.chembiol.2017.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/15/2017] [Accepted: 08/02/2017] [Indexed: 12/18/2022]
Abstract
To dissect the cellular roles of individual kinases, it is useful to design tools for their selective activation. We describe the engineering of a split-cAbl kinase (sKin-Abl) that is rapidly activated in cells with rapamycin and allows temporal, dose, and compartmentalization control. Our design strategy involves an empirical screen in mammalian cells and identification of split site in the N lobe. This split site leads to complete loss of activity, which can be restored upon small-molecule-induced dimerization in cells. Remarkably, the split site is transportable to the related Src Tyr kinase and the distantly related Ser/Thr kinase, AKT, suggesting broader applications to kinases. To quantify the fold induction of phosphotyrosine (pTyr) modification, we employed quantitative proteomics, NeuCode SILAC. We identified a number of known Abl substrates, including autophosphorylation sites and novel pTyr targets, 432 pTyr sites in total. We believe that this split-kinase technology will be useful for direct activation of protein kinases in cells.
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Affiliation(s)
- Juan E Diaz
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Charles W Morgan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | | | | | - Joshua J Coon
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA; Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53706, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.
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6
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Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS. UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2016; 88:3990-7. [PMID: 26938041 PMCID: PMC4850734 DOI: 10.1021/acs.analchem.6b00261] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
De novo peptide sequencing by mass spectrometry represents an important strategy for characterizing novel peptides and proteins, in which a peptide's amino acid sequence is inferred directly from the precursor peptide mass and tandem mass spectrum (MS/MS or MS(3)) fragment ions, without comparison to a reference proteome. This method is ideal for organisms or samples lacking a complete or well-annotated reference sequence set. One of the major barriers to de novo spectral interpretation arises from confusion of N- and C-terminal ion series due to the symmetry between b and y ion pairs created by collisional activation methods (or c, z ions for electron-based activation methods). This is known as the "antisymmetric path problem" and leads to inverted amino acid subsequences within a de novo reconstruction. Here, we combine several key strategies for de novo peptide sequencing into a single high-throughput pipeline: high-efficiency carbamylation blocks lysine side chains, and subsequent tryptic digestion and N-terminal peptide derivatization with the ultraviolet chromophore AMCA yield peptides susceptible to 351 nm ultraviolet photodissociation (UVPD). UVPD-MS/MS of the AMCA-modified peptides then predominantly produces y ions in the MS/MS spectra, specifically addressing the antisymmetric path problem. Finally, the program UVnovo applies a random forest algorithm to automatically learn from and then interpret UVPD mass spectra, passing results to a hidden Markov model for de novo sequence prediction and scoring. We show this combined strategy provides high-performance de novo peptide sequencing, enabling the de novo sequencing of thousands of peptides from an Escherichia coli lysate at high confidence.
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Affiliation(s)
- Scott A Robotham
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Andrew P Horton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - Joe R Cannon
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Victoria C Cotham
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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7
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Potts GK, Voigt EA, Bailey DJ, Rose CM, Westphall MS, Hebert AS, Yin J, Coon JJ. Neucode Labels for Multiplexed, Absolute Protein Quantification. Anal Chem 2016; 88:3295-303. [PMID: 26882330 PMCID: PMC5141612 DOI: 10.1021/acs.analchem.5b04773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We describe a new method to accomplish multiplexed, absolute protein quantification in a targeted fashion. The approach draws upon the recently developed neutron encoding (NeuCode) metabolic labeling strategy and parallel reaction monitoring (PRM). Since PRM scanning relies upon high-resolution tandem mass spectra for targeted protein quantification, incorporation of multiple NeuCode labeled peptides permits high levels of multiplexing that can be accessed from high-resolution tandem mass spectra. Here we demonstrate this approach in cultured cells by monitoring a viral infection and the corresponding viral protein production over many infection time points in a single experiment. In this context the NeuCode PRM combination affords up to 30 channels of quantitative information in a single MS experiment.
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Affiliation(s)
- Gregory K Potts
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Emily A Voigt
- Department of Chemical and Biological Engineering, University of Wisconsin , Madison, Wisconsin 53706, United States
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Derek J Bailey
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Christopher M Rose
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Alexander S Hebert
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin , Madison, Wisconsin 53706, United States
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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8
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Devabhaktuni A, Elias JE. Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets. J Proteome Res 2016; 15:732-42. [PMID: 26743026 DOI: 10.1021/acs.jproteome.5b00861] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dependent on concise, predefined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference databases. However, such algorithms have been difficult to apply to complex protein mixtures, in part due to a lack of methods for automatically validating de novo sequencing results. Here, we present novel metrics for benchmarking de novo sequencing algorithm performance on large-scale proteomics data sets and present a method for accurately calibrating false discovery rates on de novo results. We also present a novel algorithm (LADS) that leverages experimentally disambiguated fragmentation spectra to boost sequencing accuracy and sensitivity. LADS improves sequencing accuracy on longer peptides relative to that of other algorithms and improves discriminability of correct and incorrect sequences. Using these advancements, we demonstrate accurate de novo identification of peptide sequences not identifiable using database search-based approaches.
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Affiliation(s)
- Arun Devabhaktuni
- Department of Chemical & Systems Biology, Stanford University , Stanford, California 94035, United States
| | - Joshua E Elias
- Department of Chemical & Systems Biology, Stanford University , Stanford, California 94035, United States
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9
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Affiliation(s)
- Nicholas M. Riley
- 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
| | - 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
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10
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Rose CM, Rush MJP, Riley NM, Merrill AE, Kwiecien NW, Holden DD, Mullen C, Westphall MS, Coon JJ. A calibration routine for efficient ETD in large-scale proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1848-57. [PMID: 26111518 PMCID: PMC5642106 DOI: 10.1007/s13361-015-1183-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 05/11/2023]
Abstract
Electron transfer dissociation (ETD) has been broadly adopted and is now available on a variety of commercial mass spectrometers. Unlike collisional activation techniques, optimal performance of ETD requires considerable user knowledge and input. ETD reaction duration is one key parameter that can greatly influence spectral quality and overall experiment outcome. We describe a calibration routine that determines the correct number of reagent anions necessary to reach a defined ETD reaction rate. Implementation of this automated calibration routine on two hybrid Orbitrap platforms illustrate considerable advantages, namely, increased product ion yield with concomitant reduction in scan rates netting up to 75% more unique peptide identifications in a shotgun experiment. Graphical Abstract ᅟ.
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Affiliation(s)
- Christopher M Rose
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
| | - Matthew J P Rush
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
| | - Nicholas M Riley
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
| | - Anna E Merrill
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
| | - Nicholas W Kwiecien
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
| | | | | | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA.
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, 53706, USA.
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA.
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11
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Rhoads TW, Prasad A, Kwiecien NW, Merrill AE, Zawack K, Westphall MS, Schroeder FC, Kimble J, Coon JJ. NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans. Mol Cell Proteomics 2015; 14:2922-35. [PMID: 26392051 DOI: 10.1074/mcp.m115.049684] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 01/05/2023] Open
Abstract
The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress.
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Affiliation(s)
| | - Aman Prasad
- ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | | | | | - Kelson Zawack
- ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853
| | | | - Frank C Schroeder
- ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853
| | - Judith Kimble
- ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Joshua J Coon
- From the Departments of ‡Chemistry, §Biomolecular Chemistry, ¶Genome Center,
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12
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Greer T, Hao L, Nechyporenko A, Lee S, Vezina CM, Ricke WA, Marker PC, Bjorling DE, Bushman W, Li L. Custom 4-Plex DiLeu Isobaric Labels Enable Relative Quantification of Urinary Proteins in Men with Lower Urinary Tract Symptoms (LUTS). PLoS One 2015; 10:e0135415. [PMID: 26267142 PMCID: PMC4534462 DOI: 10.1371/journal.pone.0135415] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 07/21/2015] [Indexed: 12/19/2022] Open
Abstract
The relative quantification of proteins using liquid chromatography mass spectrometry (LC-MS) has allowed researchers to compile lists of potential disease markers. These complex quantitative workflows often include isobaric labeling of enzymatically-produced peptides to analyze their relative abundances across multiple samples in a single LC-MS run. Recent efforts by our lab have provided scientists with cost-effective alternatives to expensive commercial labels. Although the quantitative performance of these dimethyl leucine (DiLeu) labels has been reported using known ratios of complex protein and peptide standards, their potential in large-scale proteomics studies using a clinically relevant system has never been investigated. Our work rectifies this oversight by implementing 4-plex DiLeu to quantify proteins in the urine of aging human males who suffer from lower urinary tract symptoms (LUTS). Protein abundances in 25 LUTS and 15 control patients were compared, revealing that of the 836 proteins quantified, 50 were found to be differentially expressed (>20% change) and statistically significant (p-value <0.05). Gene ontology (GO) analysis of the differentiated proteins showed that many were involved in inflammatory responses and implicated in fibrosis. While confirmation of individual protein abundance changes would be required to verify protein expression, this study represents the first report using the custom isobaric label, 4-plex DiLeu, to quantify protein abundances in a clinically relevant system.
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Affiliation(s)
- Tyler Greer
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ling Hao
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anatoliy Nechyporenko
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sanghee Lee
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chad M. Vezina
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Will A. Ricke
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Paul C. Marker
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dale E. Bjorling
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Wade Bushman
- Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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13
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Frost DC, Greer T, Xiang F, Liang Z, Li L. Development and characterization of novel 8-plex DiLeu isobaric labels for quantitative proteomics and peptidomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1115-24. [PMID: 25981542 PMCID: PMC4837894 DOI: 10.1002/rcm.7201] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/05/2015] [Accepted: 03/22/2015] [Indexed: 05/08/2023]
Abstract
RATIONALE Relative quantification of proteins via their enzymatically digested peptide products determines disease biomarker candidate lists in discovery studies. Isobaric label-based strategies using TMT and iTRAQ allow for up to 10 samples to be multiplexed in one experiment, but their expense limits their use. The demand for cost-effective tagging reagents capable of multiplexing many samples led us to develop an 8-plex version of our isobaric labeling reagent, DiLeu. METHODS The original 4-plex DiLeu reagent was extended to an 8-plex set by coupling isotopic variants of dimethylated leucine to an alanine balance group designed to offset the increasing mass of the label's reporter group. Tryptic peptides from a single protein digest, a protein mixture digest, and Saccharomyces cerevisiae lysate digest were labeled with 8-plex DiLeu and analyzed via nanospray liquid chromatography/tandem mass spectrometry (nanoLC/MS(2) ) on a Q-Exactive Orbitrap mass spectrometer. Characteristics of 8-plex DiLeu-labeled peptides, including quantitative accuracy and fragmentation, were examined. RESULTS An 8-plex set of DiLeu reagents with 1 Da spaced reporters was synthesized at a yield of 36%. The average cost to label eight 100 µg peptide samples was calculated to be approximately $15. Normalized collision energy tests on the Q-Exactive revealed that a higher-energy collisional dissociation value of 27 generated the optimum number of high-quality spectral matches. Relative quantification of DiLeu-labeled peptides yielded normalized median ratios accurate to within 12% of their expected values. CONCLUSIONS Cost-effective 8-plex DiLeu reagents can be synthesized and applied to relative peptide and protein quantification. These labels increase the multiplexing capacity of our previous 4-plex implementation without requiring high-resolution instrumentation to resolve reporter ion signals.
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Affiliation(s)
| | - Tyler Greer
- Department of Chemistry, University of Wisconsin–Madison
| | - Feng Xiang
- School of Pharmacy, University of Wisconsin–Madison
| | - Zhidan Liang
- School of Pharmacy, University of Wisconsin–Madison
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin–Madison
- Department of Chemistry, University of Wisconsin–Madison
- Address reprint requests to: Dr. Lingjun Li, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI 53705, USA. . Phone: (608) 265-8491, Fax: (608) 262-5345
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14
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Mondal A, Potts GK, Dawson AR, Coon JJ, Mehle A. Phosphorylation at the homotypic interface regulates nucleoprotein oligomerization and assembly of the influenza virus replication machinery. PLoS Pathog 2015; 11:e1004826. [PMID: 25867750 PMCID: PMC4395114 DOI: 10.1371/journal.ppat.1004826] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/21/2015] [Indexed: 11/22/2022] Open
Abstract
Negative-sense RNA viruses assemble large ribonucleoprotein (RNP) complexes that direct replication and transcription of the viral genome. Influenza virus RNPs contain the polymerase, genomic RNA and multiple copies of nucleoprotein (NP). During RNP assembly, monomeric NP oligomerizes along the length of the genomic RNA. Regulated assembly of the RNP is essential for virus replication, but how NP is maintained as a monomer that subsequently oligomerizes to form RNPs is poorly understood. Here we elucidate a mechanism whereby NP phosphorylation regulates oligomerization. We identified new evolutionarily conserved phosphorylation sites on NP and demonstrated that phosphorylation of NP decreased formation of higher-order complexes. Two phosphorylation sites were located on opposite sides of the NP:NP interface. In both influenza A and B virus, mutating or mimicking phosphorylation at these residues blocked homotypic interactions and drove NP towards a monomeric form. Highlighting the central role of this process during infection, these mutations impaired RNP formation, polymerase activity and virus replication. Thus, dynamic phosphorylation of NP regulates RNP assembly and modulates progression through the viral life cycle. Replication and transcription by negative-sense RNA viruses occurs in large macromolecular complexes. These complexes contain the viral polymerase, genomic RNA, and multiple copies of nucleoprotein that bind RNA and oligomerize to coat the genome. For influenza virus, nucleoprotein (NP) non-specifically binds nucleic acids and spontaneously oligomerizes. It is essential that a portion of NP be maintained as a monomer so that it can selectively oligomerize into replication complexes. Despite the fact that this process must be tightly regulated during the viral life cycle, how this regulation is achieved is largely unknown. Here we show that phosphorylation of NP negatively regulates assembly of the influenza virus replication machinery. We identified two phosphorylation sites on opposite sides of the NP:NP interface and showed that phosphorylation at either site blocks homotypic interactions, distorting the monomer:oligomer balance of NP in cells and severely impairing virus replication. Our findings show that the phospho-regulated conversion of NP between mono- and oligomeric states is important for RNP formation, gene expression and viral replication. Moreover, we showed that these critical phosphorylation sites play the same role in influenza B virus and are likely present in influenza C and D viruses, suggesting our results are broadly applicable across viral strains and genera and reveal a global regulatory strategy for Orthomyxoviridae.
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Affiliation(s)
- Arindam Mondal
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Gregory K. Potts
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Anthony R. Dawson
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
- Cellular and Molecular Biology Graduate Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Andrew Mehle
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
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15
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Minogue CE, Hebert AS, Rensvold JW, Westphall MS, Pagliarini DJ, Coon JJ. Multiplexed quantification for data-independent acquisition. Anal Chem 2015; 87:2570-5. [PMID: 25621425 DOI: 10.1021/ac503593d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Data-independent acquisition (DIA) strategies provide a sensitive and reproducible alternative to data-dependent acquisition (DDA) methods for large-scale quantitative proteomic analyses. Unfortunately, DIA methods suffer from incompatibility with common multiplexed quantification methods, specifically stable isotope labeling approaches such as isobaric tags and stable isotope labeling of amino acids in cell culture (SILAC). Here we expand the use of neutron-encoded (NeuCode) SILAC to DIA applications (NeuCoDIA), producing a strategy that enables multiplexing within DIA scans without further convoluting the already complex MS(2) spectra. We demonstrate duplex NeuCoDIA analysis of both mixed-ratio (1:1 and 10:1) yeast and mouse embryo myogenesis proteomes. Analysis of the mixed-ratio yeast samples revealed the strong accuracy and precision of our NeuCoDIA method, both of which were comparable to our established MS(1)-based quantification approach. NeuCoDIA also uncovered the dynamic protein changes that occur during myogenic differentiation, demonstrating the feasibility of this methodology for biological applications. We consequently establish DIA quantification of NeuCode SILAC as a useful and practical alternative to DDA-based approaches.
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Affiliation(s)
- Catherine E Minogue
- Department of Chemistry, ‡Genome Center of Wisconsin, §Department of Biomolecular Chemistry, and ∥Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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16
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Ulbrich A, Bailey DJ, Westphall MS, Coon JJ. Organic acid quantitation by NeuCode methylamidation. Anal Chem 2014; 86:4402-8. [PMID: 24684282 DOI: 10.1021/ac500270q] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have developed a multiplexed quantitative analysis method for carboxylic acids by liquid chromatography high resolution mass spectrometry. The method employs neutron encoded (NeuCode) methylamine labels ((13)C or (15)N enriched) that are affixed to carboxylic acid functional groups to enable duplex quantitation via mass defect measurement. This work presents the first application of NeuCode quantitation to small molecules. We have applied this technique to detect adulteration of olive oil by quantitative analysis of fatty acid methyl amide derivatives, and the quantitative accuracy of the NeuCode analysis was validated by GC/MS. Currently, the method enables duplex quantitation and is expandable to at least 6-plex analysis.
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Affiliation(s)
- Arne Ulbrich
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, Merrill AE, Smith LM, Hebert AS, Westphall MS, Pagliarini DJ, Garcia BA, Coon JJ. Neutron-encoded mass signatures for quantitative top-down proteomics. Anal Chem 2014; 86:2314-9. [PMID: 24475910 PMCID: PMC3983007 DOI: 10.1021/ac403579s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The ability to acquire highly accurate quantitative data is an increasingly important part of any proteomics experiment, whether shotgun or top-down approaches are used. We recently developed a quantitation strategy for peptides based on neutron encoding, or NeuCode SILAC, which uses closely spaced heavy isotope-labeled amino acids and high-resolution mass spectrometry to provide quantitative data. We reasoned that the strategy would also be applicable to intact proteins and could enable robust, multiplexed quantitation for top-down experiments. We used yeast lysate labeled with either (13)C6(15)N2-lysine or (2)H8-lysine, isotopologues of lysine that are spaced 36 mDa apart. Proteins having such close spacing cannot be distinguished during a medium resolution scan, but upon acquiring a high-resolution scan, the two forms of the protein with each amino acid are resolved and the quantitative information revealed. An additional benefit NeuCode SILAC provides for top down is that the spacing of the isotope peaks indicates the number of lysines present in the protein, information that aids in identification. We used NeuCode SILAC to quantify several hundred isotope distributions, manually identify and quantify proteins from 1:1, 3:1, and 5:1 mixed ratios, and demonstrate MS(2)-based quantitation using ETD.
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Affiliation(s)
- Timothy W Rhoads
- Department of Chemistry, ‡Department of Biomolecular Chemistry, §Genome Center, and ∇Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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