1
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Joyce AW, Searle BC. Computational approaches to identify sites of phosphorylation. Proteomics 2024; 24:e2300088. [PMID: 37897210 DOI: 10.1002/pmic.202300088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Due to their oftentimes ambiguous nature, phosphopeptide positional isomers can present challenges in bottom-up mass spectrometry-based workflows as search engine scores alone are often not enough to confidently distinguish them. Additional scoring algorithms can remedy this by providing confidence metrics in addition to these search results, reducing ambiguity. Here we describe challenges to interpreting phosphoproteomics data and review several different approaches to determine sites of phosphorylation for both data-dependent and data-independent acquisition-based workflows. Finally, we discuss open questions regarding neutral losses, gas-phase rearrangement, and false localization rate estimation experienced by both types of acquisition workflows and best practices for managing ambiguity in phosphosite determination.
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Affiliation(s)
- Alex W Joyce
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Brian C Searle
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
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2
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Lau JKC, Hopkinson AC, Siu KWM. Phosphate Migration versus the Loss of Phosphoric Acid in Protonated Phosphopeptides: A Computational Study. J Phys Chem B 2024; 128:504-514. [PMID: 38190618 DOI: 10.1021/acs.jpcb.3c06767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Residue-specific phosphorylation is a protein post-translational modification that regulates cellular functions. Experimental determination of the exact sites of protein phosphorylation provides an understanding of the signaling and processes at work for a given cellular state. Any experimental artifact that involves migration of the phosphate group during measurement is a concern, as the outcome can lead to erroneous conclusions that may confound studies on cellular signal transduction. Herein, we examine computationally the mechanism by which a phosphate group migrates from one serine residue to another serine in monoprotonated pentapeptides [BA-pSer-Gly-Ser-BB + H]+ → [BA-Ser-Gly-pSer-BB + H]+ (where BA and BB are different combinations of the three basic amino acids, histidine, lysine, and arginine). In addition to moving the phosphate group, the overall mechanism involves transferring a proton from the N-terminal amino acid, BA, to the C-terminal amino acid, BB. This is not a synchronous process, and there is a key high-energy intermediate, structure C, that is zwitterionic with both the basic amino acids protonated and the phosphate group attached to both serine residues and carrying a negative charge. The barriers to moving the phosphate group are calculated to be in the range of 219-274 kJ mol-1 at the B3LYP/6-31G(d) level. These barriers are systematically slightly lower and in good agreement with single-point energy calculations at both M06-2X/6-311++G(d,p) and MP2/6-31++G(d,p) levels. The competitive reaction, loss of phosphoric acid from the protonated pentapeptides, has a barrier in the range of 176-202 kJ mol-1 at the B3LYP/6-31G(d) level. Extension of the theory to M06-2X/6-311++G(d,p)//B3LYP/6-31G(d) and MP2/6-31++G(d,p)// B3LYP/6-31G(d) gives higher values for the loss of phosphoric acid, falling in the range of 196-226 kJ mol-1; these are comparable to the barriers against phosphate migration at the same levels of theory. For larger peptides His-pSer-(Gly)n-Ser-His, where n has values from 2 to 5, the barriers against the loss of phosphoric acid are higher than those against the phosphate group migration. This difference is most pronounced and significant when n = 4 and 5 (the differences are approximately 80 kJ mol-1 under the single-point energy calculations at the M06-2X and MP2 levels). Energy differences using two more recent functionals, M08-HX and MN15, on His-pSer-(Gly)n-Ser-His, where n = 1 and 5, are in good agreement with the M06-2X and MP2 calculations. These results provide the mechanistic rationale for phosphate migration versus other competing reactions in the gas phase under tandem mass spectrometry conditions.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
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3
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Searle BC, Chien A, Koller A, Hawke D, Herren AW, Kim Kim J, Lee KA, Leib RD, Nelson AJ, Patel P, Ren JM, Stemmer PM, Zhu Y, Neely BA, Patel B. A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development. Mol Cell Proteomics 2023; 22:100639. [PMID: 37657519 PMCID: PMC10561125 DOI: 10.1016/j.mcpro.2023.100639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Recent advances in methodology have made phosphopeptide analysis a tractable problem for many proteomics researchers. There are now a wide variety of robust and accessible enrichment strategies to generate phosphoproteomes while free or inexpensive software tools for quantitation and site localization have simplified phosphoproteome analysis workflow tremendously. As a research group under the Association for Biomolecular Resource Facilities umbrella, the Proteomics Standards Research Group has worked to develop a multipathway phosphopeptide standard based on a mixture of heavy-labeled phosphopeptides designed to enable researchers to rapidly develop assays. This mixture contains 131 mass spectrometry vetted phosphopeptides specifically chosen to cover as many known biologically interesting phosphosites as possible from seven different signaling networks: AMPK signaling, death and apoptosis signaling, ErbB signaling, insulin/insulin-like growth factor-1 signaling, mTOR signaling, PI3K/AKT signaling, and stress (p38/SAPK/JNK) signaling. Here, we describe a characterization of this mixture spiked into a HeLa tryptic digest stimulated with both epidermal growth factor and insulin-like growth factor-1 to activate the MAPK and PI3K/AKT/mTOR pathways. We further demonstrate a comparison of phosphoproteomic profiling of HeLa performed independently in five labs using this phosphopeptide mixture with data-independent acquisition. Despite different experimental and instrumentation processes, we found that labs could produce reproducible, harmonized datasets by reporting measurements as ratios to the standard, while intensity measurements showed lower consistency between labs even after normalization. Our results suggest that widely available, biologically relevant phosphopeptide standards can act as a quantitative "yardstick" across laboratories and sample preparations enabling experimental designs larger than a single laboratory can perform. Raw data files are publicly available in the MassIVE dataset MSV000090564.
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Affiliation(s)
- Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.
| | - Allis Chien
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | | | - Anthony W Herren
- UC Davis Genome Center, Proteomics Core, University of California Davis, Davis California, USA
| | - Jenny Kim Kim
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Kimberly A Lee
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Ryan D Leib
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | - Purvi Patel
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Jian Min Ren
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Paul M Stemmer
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Yiying Zhu
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Bhavin Patel
- Thermo Fisher Scientific, Rockford, Illinois, USA
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4
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Daly LA, Clarke CJ, Po A, Oswald SO, Eyers CE. Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond. Chem Commun (Camb) 2023; 59:11484-11499. [PMID: 37681662 PMCID: PMC10521633 DOI: 10.1039/d3cc02909c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
Post-translational modifications (PTMs) are ubiquitous and key to regulating protein function. Understanding the dynamics of individual PTMs and their biological roles requires robust characterisation. Mass spectrometry (MS) is the method of choice for the identification and quantification of protein modifications. This article focusses on the MS-based analysis of those covalent modifications that induce a mass shift of +80 Da, notably phosphorylation and sulfation, given the challenges associated with their discrimination and pinpointing the sites of modification on a polypeptide chain. Phosphorylation in particular is highly abundant, dynamic and can occur on numerous residues to invoke specific functions, hence robust characterisation is crucial to understanding biological relevance. Showcasing our work in the context of other developments in the field, we highlight approaches for enrichment and site localisation of phosphorylated (canonical and non-canonical) and sulfated peptides, as well as modification analysis in the context of intact proteins (top down proteomics) to explore combinatorial roles. Finally, we discuss the application of native ion-mobility MS to explore the effect of these PTMs on protein structure and ligand binding.
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Affiliation(s)
- Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Christopher J Clarke
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Allen Po
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Sally O Oswald
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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5
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Borotto NB, Richards TK. Rapid Online Oxidation of Proteins and Peptides via Electrospray-Accelerated Ozonation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2078-2086. [PMID: 36194498 DOI: 10.1021/jasms.2c00182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mass spectrometry-based analyses of protein conformation continue to grow in utilization due their speed, low sample requirements, and applicability to most protein systems. These techniques typically rely on chemical derivatization of proteins and as with all label-based analyses must ensure the integrity of the protein conformation throughout the duration of the labeling reaction. Hydroxyl radical footprinting of proteins and the recently developed fast fluoroalkylation of proteins attempt to bypass this consideration via rapid reactions that occur on time scales faster than protein folding, but they often require microfluidic setups or electromagnetic radiation sources. In this work, we demonstrate that ozonation of proteins and peptides, which normally occurs in the second to minute time scales, can be accelerated to the submillisecond to millisecond time scale with an electrospray ionization source. This rapid ozonation results in selective labeling of tryptophan and methionine residues. When applied to cytochrome C and carbonic anhydrase, this labeling technique is sensitive to solution conditions and correlates with solution-phase analyses of conformation. While significant work is still needed to characterize this fast chemical labeling strategy, it requires no complicated sample handling, electromagnetic radiation sources, or microfluidic systems outside of the electrospray source and may represent a facile alternative to other rapid labeling technologies that are utilized today.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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6
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Zhang Y, Dreyer B, Govorukhina N, Heberle AM, Končarević S, Krisp C, Opitz CA, Pfänder P, Bischoff R, Schlüter H, Kwiatkowski M, Thedieck K, Horvatovich PL. Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics. Anal Chem 2022; 94:10893-10906. [PMID: 35880733 PMCID: PMC9366746 DOI: 10.1021/acs.analchem.2c01036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
With increasing sensitivity and accuracy in mass spectrometry,
the tumor phosphoproteome is getting into reach. However, the selection
of quantitation techniques best-suited to the biomedical question
and diagnostic requirements remains a trial and error decision as
no study has directly compared their performance for tumor tissue
phosphoproteomics. We compared label-free quantification (LFQ), spike-in-SILAC
(stable isotope labeling by amino acids in cell culture), and tandem
mass tag (TMT) isobaric tandem mass tags technology for quantitative
phosphosite profiling in tumor tissue. Compared to the classic SILAC
method, spike-in-SILAC is not limited to cell culture analysis, making
it suitable for quantitative analysis of tumor tissue samples. TMT
offered the lowest accuracy and the highest precision and robustness
toward different phosphosite abundances and matrices. Spike-in-SILAC
offered the best compromise between these features but suffered from
a low phosphosite coverage. LFQ offered the lowest precision but the
highest number of identifications. Both spike-in-SILAC and LFQ presented
susceptibility to matrix effects. Match between run (MBR)-based analysis
enhanced the phosphosite coverage across technical replicates in LFQ
and spike-in-SILAC but further reduced the precision and robustness
of quantification. The choice of quantitative methodology is critical
for both study design such as sample size in sample groups and quantified
phosphosites and comparison of published cancer phosphoproteomes.
Using ovarian cancer tissue as an example, our study builds a resource
for the design and analysis of quantitative phosphoproteomic studies
in cancer research and diagnostics.
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Affiliation(s)
- Yang Zhang
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands.,Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Benjamin Dreyer
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Alexander M Heberle
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Saša Končarević
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt/Main, Germany
| | - Christoph Krisp
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christiane A Opitz
- Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Department of Neurology, National Center for Tumor Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Pauline Pfänder
- Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Bioscience, Heidelberg University, 69117 Heidelberg, Germany
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Groningen 9700 AD, The Netherlands.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen 9700 AD, The Netherlands
| | - Kathrin Thedieck
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands.,Department of Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26129 Oldenburg, Germany
| | - Peter L Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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7
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Ramasamy P, Vandermarliere E, Vranken WF, Martens L. Panoramic Perspective on Human Phosphosites. J Proteome Res 2022; 21:1894-1915. [PMID: 35793420 DOI: 10.1021/acs.jproteome.2c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation is the most common reversible post-translational modification of proteins and is key in the regulation of many cellular processes. Due to this importance, phosphorylation is extensively studied, resulting in the availability of a large amount of mass spectrometry-based phospho-proteomics data. Here, we leverage the information in these large-scale phospho-proteomics data sets, as contained in Scop3P, to analyze and characterize proteome-wide protein phosphorylation sites (P-sites). First, we set out to differentiate correctly observed P-sites from false-positive sites using five complementary site properties. We then describe the context of these P-sites in terms of the protein structure, solvent accessibility, structural transitions and disorder, and biophysical properties. We also investigate the relative prevalence of disease-linked mutations on and around P-sites. Moreover, we assess the structural dynamics of P-sites in their phosphorylated and unphosphorylated states. As a result, we show how large-scale reprocessing of available proteomics experiments can enable a more reliable view on proteome-wide P-sites. Furthermore, adding the structural context of proteins around P-sites helps uncover possible conformational switches upon phosphorylation. Moreover, by placing sites in different biophysical contexts, we show the differential preference in protein dynamics at phosphorylated sites when compared to the nonphosphorylated counterparts.
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Affiliation(s)
- Pathmanaban Ramasamy
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Centre for Structural Biology, VIB, 1050 Brussels, Belgium
| | | | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Centre for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
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8
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Paris J, Theisen A, Marzullo BP, Haris A, Morgan TE, Barrow MP, O’Hara J, O’Connor PB. Multimodal Tandem Mass Spectrometry Techniques for the Analysis of Phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1126-1133. [PMID: 35604791 PMCID: PMC9264387 DOI: 10.1021/jasms.1c00353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Collisionally activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), ultraviolet photodissociation (UVPD), electron capture dissociation and electron detachment dissociation (EDD) experiments were conducted on a set of phosphopeptides, in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation patterns were compared and varied according to the fragmentation mechanisms and the composition of the peptides. CAD and IRMPD produced similar fragmentation profiles of the phosphopeptides, while UVPD produced a large number of complementary fragments. Electron-based dissociation techniques displayed lower fragmentation efficiencies, despite retaining the labile phosphate group, and drastically different fragmentation profiles. EDD produced complex spectra whose interpretation proved challenging.
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Affiliation(s)
- Johanna Paris
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alina Theisen
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Bryan P. Marzullo
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Anisha Haris
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tomos E. Morgan
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark P. Barrow
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - John O’Hara
- UCB, 216 Bath Road, Slough SL1 3WE, United
Kingdom
| | - Peter B. O’Connor
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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9
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Sun L, Mo A, Lu P. Proteomic-, Phosphoproteomic-, and Acetylomic-Based Mass Spectrometry to Identify Tissue-Specific Protein Complexes and Phosphorylation in Plant Gametogenesis. Methods Mol Biol 2022; 2484:13-22. [PMID: 35461441 DOI: 10.1007/978-1-0716-2253-7_2] [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] [Indexed: 06/14/2023]
Abstract
Using proteomics to analyze phosphorylation, acetylation, and other posttranslational modifications has been a very important method in biological research. Here we take the rice meiotic anther as an example to introduce the experimentally verified proteomic analysis methods of plant tissue-specific phosphorylation and acetylation, including total protein extraction, trypsin digestion, phosphopeptide enrichment by TiO2 microcolumn, affinity enrichment of lysine-acetylated peptides, desalting, Nano UHPLC-MS/MS analysis, database search and data analysis, and bioinformatic analysis.
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Affiliation(s)
- Lu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Aowei Mo
- School of Life Sciences, Fudan University, Shanghai, China
| | - Pingli Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China.
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10
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Liu X, Fields R, Schweppe DK, Paulo JA. Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. Expert Rev Proteomics 2021; 18:795-807. [PMID: 34652972 DOI: 10.1080/14789450.2021.1994390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Protein phosphorylation is a primary mechanism of signal transduction in cellular systems. Isobaric tagging can be used to investigate alterations in phosphorylation events in sample multiplexing experiments where quantification extends across all conditions. As such, innovations in tandem mass tag methods can facilitate the expansion of the depth and breadth of phosphoproteomic analyses. AREAS COVERED This review discusses the current state of tandem mass tag-centric phosphoproteomics and highlights advances in reagent chemistry, instrumentation, data acquisition, and data analysis. We stress that approaches for phosphoproteomic investigations require high-specificity enrichment, sensitive detection, and accurate phosphorylation site localization. EXPERT OPINION Tandem mass tag-centric phosphoproteomics will continue to be an important conduit for our understanding of signal transduction in living organisms. We anticipate that progress in phosphopeptide enrichment methodologies, enhancements in instrumentation and data acquisition technologies, and further refinements in analytical strategies will be key to the discovery of biologically relevant findings from phosphoproteomics studies.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, USA
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11
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Fang Z, Chowdhury SM. Dual-Stage Neutral Loss Tandem Mass Spectrometric Strategy for Confident Identification of Protein Prenylation. Anal Chem 2021; 93:13169-13176. [PMID: 34558911 DOI: 10.1021/acs.analchem.1c01617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein prenylation is an important post-translational modification that regulates protein interactions, localizations, and signaling pathways in normal functioning of eukaryotic cells. It is also a critical step in the oncogenic developments of various cancers. Direct identification of native protein prenylation by mass spectrometry (MS) has been challenging due to high hydrophobicity and the lack of an efficient enrichment technique. Prior MS studies of prenylation revealed that prenyl peptides readily generate high-intensity fragments after neutral loss of the prenyl group (R group), and more recent investigation of oxidized prenyl peptides discovered more consistent neutral loss of the oxidized prenyl group (RSOH group). Here, a dual-stage neutral loss MS3 (DS-NLMS3)-based strategy is therefore developed by combining both gas-phase cleavable properties of the prenyl thioether bond and mono-oxidized thioether to improve the large-scale identification of prenylation. Both neutral losses can individually and distinctively confirm the prenylation type in MS2 and the sequence of the prenyl peptide upon targeted MS3 fragmentation. This dual-faceted NLMS3 strategy significantly improves the confidence in the identification of protein prenylation from large-scale samples, which enables the unambiguous identification of prenylated sites of the spiked low-abundance farnesyl peptide and native prenyl proteins from mouse macrophage cells, even without prior enrichment during sample preparation. The ease of incorporating this strategy into the prenylation study workflow and minimum disruption to the biological lipidome are advantageous for unraveling unknown native protein prenylation and further developments in profiling and quantifying prenylome.
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Affiliation(s)
- Zixiang Fang
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
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12
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Paulo JA, Schweppe DK. Advances in quantitative high-throughput phosphoproteomics with sample multiplexing. Proteomics 2021; 21:e2000140. [PMID: 33455035 DOI: 10.1002/pmic.202000140] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
Eukaryotic protein phosphorylation modulates nearly every major biological process. Phosphorylation regulates protein activity, mediates cellular signal transduction, and manipulates cellular structure. Consequently, the dysregulation of kinase and phosphatase pathways has been linked to a multitude of diseases. Mass spectrometry-based proteomic techniques are increasingly used for the global interrogation of perturbations in phosphorylation-based cellular signaling. Strategies for studying phosphoproteomes require high-specificity enrichment, sensitive detection, and accurate localization of phosphorylation sites with advanced LC-MS/MS techniques and downstream informatics. Sample multiplexing with isobaric tags has also been integral to recent advancements in throughput and sensitivity for phosphoproteomic studies. Each of these facets of phosphoproteomics analysis present distinct challenges and thus opportunities for improvement and innovation. Here, we review current methodologies, explore persistent challenges, and discuss the outlook for isobaric tag-based quantitative phosphoproteomic analysis.
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Affiliation(s)
- Joao A Paulo
- Harvard Medical School, Boston, Massachusetts, USA
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13
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Conti BJ, Leicht AS, Kirchdoerfer RN, Sussman MR. Mass spectrometric based detection of protein nucleotidylation in the RNA polymerase of SARS-CoV-2. Commun Chem 2021; 4:41. [PMID: 34189273 PMCID: PMC8238455 DOI: 10.1038/s42004-021-00476-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 02/22/2021] [Indexed: 02/08/2023] Open
Abstract
Coronaviruses, like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), encode a nucleotidyl transferase in the N-terminal (NiRAN) domain of the nonstructural protein (nsp) 12 protein within the RNA dependent RNA polymerase. Here we show the detection of guanosine monophosphate (GMP) and uridine monophosphate-modified amino acids in nidovirus proteins using heavy isotope-assisted mass spectrometry (MS) and MS/MS peptide sequencing. We identified lysine-143 in the equine arteritis virus (EAV) protein, nsp7, as a primary site of in vitro GMP attachment via a phosphoramide bond. In SARS-CoV-2 replicase proteins, we demonstrate nsp12-mediated nucleotidylation of nsp7 lysine-2. Our results demonstrate new strategies for detecting GMP-peptide linkages that can be adapted for higher throughput screening using mass spectrometric technologies. These data are expected to be important for a rapid and timely characterization of a new enzymatic activity in SARS-CoV-2 that may be an attractive drug target aimed at limiting viral replication in infected patients.
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Affiliation(s)
- Brian J. Conti
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI USA
| | - Andrew S. Leicht
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI USA
| | - Robert N. Kirchdoerfer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI USA
| | - Michael R. Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI USA
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14
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The challenge of detecting modifications on proteins. Essays Biochem 2020; 64:135-153. [PMID: 31957791 DOI: 10.1042/ebc20190055] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.
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15
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Steckel A, Uray K, Kalló G, Csosz É, Schlosser G. Investigation of Neutral Losses and the Citrulline Effect for Modified H4 N-Terminal Pentapeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:565-573. [PMID: 31967473 PMCID: PMC7309534 DOI: 10.1021/jasms.9b00036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 05/15/2023]
Abstract
Tandem mass spectrometry is an indispensable tool in proteomics used for protein sequencing and quantitation. On the basis of the sequential fragments usually generated from peptide ions via collision-induced dissociation, electron-transfer dissociation, or a combination of the two, probabilistic database search engines could be used for the identification of the peptides. The correct localization of posttranslational modifications (PTMs) poses a more challenging problem than the general identification of proteins. Histones are involved in the regulation of DNA transcription via the wealth of PTMs on their N-terminal tail. In this study, we analyzed the histone H4 peptide SGRGK incorporating four different posttranslational modifications: citrullination, acetylation, phosphorylation, and arginine methylation at various positions. The pentapeptides model the enzymatic cleavage of the N-terminal tail of human histone H4 protein by LysC protease. Fragmentation of the peptides was investigated using higher-energy collisional dissociation (HCD), electron-transfer dissociation (ETD), and electron-transfer higher-energy collisional dissociation (EThcD) on an ultrahigh resolution and mass accuracy instrument. We found that while all three techniques have their unique characteristics, advantages, and pitfalls, EThcD generated the most fragment ion-rich spectra. Despite potential ambiguities regarding exact fragment identities, full sequence coverage and PTM mapping may also be achievable. We also found novel neutral losses from the charge-reduced precursors characteristic to citrullination in ETD and EThcD which may be used in proteomic applications. N-Terminal acetylation and arginine methylation could also be confirmed by their characteristic neutral losses from the charge-reduced precursors.
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Affiliation(s)
- Arnold Steckel
- Hevesy György PhD School of Chemistry,
ELTE Eötvös Loránd University, Budapest,
Pázmány Péter sétány 1/A, 1117,
Hungary
- MTA-ELTE Research Group of Peptide Chemistry,
ELTE Eötvös Loránd University, Budapest,
Pázmány Péter sétány 1/A, 1117,
Hungary
| | - Katalin Uray
- MTA-ELTE Research Group of Peptide Chemistry,
ELTE Eötvös Loránd University, Budapest,
Pázmány Péter sétány 1/A, 1117,
Hungary
| | - Gergo Kalló
- Proteomics Core Facility, Department of Biochemistry and
Molecular Biology, Faculty of Medicine, University of Debrecen,
Debrecen, Nagyerdei krt. 98, 4032, Hungary
| | - Éva Csosz
- Proteomics Core Facility, Department of Biochemistry and
Molecular Biology, Faculty of Medicine, University of Debrecen,
Debrecen, Nagyerdei krt. 98, 4032, Hungary
| | - Gitta Schlosser
- MTA-ELTE Research Group of Peptide Chemistry,
ELTE Eötvös Loránd University, Budapest,
Pázmány Péter sétány 1/A, 1117,
Hungary
- Department of Analytical Chemistry, ELTE
Eötvös Loránd University, Budapest,
Pázmány Péter sétány 1/A, 1117,
Hungary
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16
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Shih M, McLuckey SA. Ion/ion Charge Inversion/Attachment in Conjunction with Dipolar DC Collisional Activation as a Selective Screen for Sulfo- and Phosphopeptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 444:116181. [PMID: 37064606 PMCID: PMC10104595 DOI: 10.1016/j.ijms.2019.116181] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We describe a gas-phase approach for the rapid screening of polypeptide anions for phosphorylation or sulfonation based on binding strengths to guanidinium-containing reagent ions. The approach relies on the generation of a complex via reaction of mixtures of deprotonated polypeptide anions with dicationic guanidinium-containing reagent ions and subsequent dipolar DC collisional activation of the complexes. The relative strengths of the electrostatic interactions of guanidinium with deprotonated acidic sites follows the order carboxylate<phosph(on)ate<sulf(on)ate. The differences between the binding strengths at these sites allows for the use of an appropriately selected dipolar DC amplitude to lead to significantly different dissociation rates for complexes derived from unmodified peptides versus phosphorylated and sulfated peptides. The difference in binding strengths between guanidinium and phosph(on)ate versus guanidinium and sulf(on)ate is sufficiently great to allow for the dissociation of a large fraction of phosphopeptide complexes with the dissociation of a much smaller fraction of sulfopeptide complexes. DFT calculations and experimental data with model peptides and with a mixture of tryptic peptides spiked with phosphopeptides are presented to illustrate and support this approach. Dissociation rate data are presented that demonstrate the differences in binding strengths for different anion charge-bearing sites and that reveal the DDC conditions most likely to provide the greatest discrimination between unmodified peptides, phosphopeptides, and sulfopeptides.
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Affiliation(s)
- Mack Shih
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Address reprint requests to: Dr. Scott A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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17
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Bailey LS, Alves M, Galy N, Patrick AL, Polfer NC. Mechanistic insights into intramolecular phosphate group transfer during collision induced dissociation of phosphopeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:449-458. [PMID: 30860300 DOI: 10.1002/jms.4351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/22/2019] [Accepted: 03/04/2019] [Indexed: 05/28/2023]
Abstract
We report on the rearrangement chemistry of model phosphorylated peptides during collision-induced dissociation (CID), where intramolecular phosphate group transfers are observed from donor to acceptor residues. Such "scrambling" could result in inaccurate modification localization, potentially leading to misidentifications. Systematic studies presented herein provide mechanistic insights for the unusually high phosphate group rearrangements presented some time ago by Reid and coworkers (Proteomics 2013, 13 [6], 964-973). It is postulated here that a basic residue like histidine can play a key role in mediating the phosphate group transfer by deprotonating the serine acceptor site. The proposed mechanism is consistent with the observation that fast collisional activation by collision-cell CID and higher-energy collisional dissociation (HCD) can shut down rearrangement chemistry. Additionally, the rearrangement chemistry is highly dependent on the charge state of the peptide, mirroring previous studies that less rearrangement is observed under mobile proton conditions.
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Affiliation(s)
- Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Mélanie Alves
- Département de chimie, UFR 926, Sorbonne Université, Paris, France
| | - Nicolas Galy
- Département de chimie, Université Paul Sabatier, Toulouse, France
| | - Amanda L Patrick
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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18
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Affiliation(s)
- Clement
M. Potel
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
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19
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Fredenhagen A, Kühnöl J, Kittelmann M, Oberer L. Gas-Phase Rearrangement of the O-Glucuronide of Vildagliptin Forms Product-Ion Fragments Suggesting Wrongly an N-Glucuronide. Drug Metab Dispos 2018; 47:189-193. [PMID: 30567879 DOI: 10.1124/dmd.118.085597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/17/2018] [Indexed: 11/22/2022] Open
Abstract
The O-glucuronide of vildagliptin, a dipeptidyl peptidase 4 inhibitor, is a major metabolite in monkeys and a minor metabolite in humans, rats, and dogs. Its product ion spectrum shows fragments that can be explained only by an N-glucuronide. Biotransformation using rat liver yielded milligram amounts of the O-glucuronide, and its structure was assigned unambiguously by nuclear magnetic resonance. The tandem mass spectra (MS/MS) of this compound was investigated in detail using MSn and accurate mass spectrometers and was identical to the animal metabolite. Thus, the MS/MS fragments suggesting an N-glucuronide had to be formed by gas-phase rearrangement. This gas-phase rearrangement can be observed on quadrupole time-of-flight and ion-trap mass instruments. The literature on gas-phase rearrangements is reviewed.
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Affiliation(s)
- Andreas Fredenhagen
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Basel, Switzerland
| | - Jürgen Kühnöl
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Basel, Switzerland
| | - Matthias Kittelmann
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Basel, Switzerland
| | - Lukas Oberer
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Basel, Switzerland
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20
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Commodore JJ, Cassady CJ. Electron transfer dissociation mass spectrometry of acidic phosphorylated peptides cationized with trivalent praseodymium. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:1178-1188. [PMID: 30221809 PMCID: PMC6291000 DOI: 10.1002/jms.4291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 06/08/2023]
Abstract
The lanthanide ion praseodymium, Pr(III), was employed to study metallated ion formation and electron transfer dissociation (ETD) of 27 biological and model highly acidic phosphopeptides. All phosphopeptides investigated form metallated ions by electrospray ionization (ESI) that can be studied by ETD to yield abundant sequence information. The ions formed are [M + Pr - H]2+ , [M + Pr]3+ , and [M + Pr + H]4+ . All biological phosphopeptides with a chain length of seven or more residues generate [M + Pr]3+ . For biological phosphopeptides, [M + Pr]3+ undergoes more backbone cleavage by ETD than [M + Pr - H]2+ and, in some cases, full sequence coverage occurs. Acidic model phosphorylated hexa-peptides and octa-peptides, composed of alanine residues and one phosphorylated residue, form exclusively [M + Pr - H]2+ by ESI. Limited sequence information is obtained by ETD of [M + Pr - H]2+ with only metallated product ions being generated. For two biological phosphopeptides, [M + Pr + H]4+ is observed and may be due to the presence of at least one residue with a highly basic side chain that facilitates the addition of an extra proton. For the model phosphopeptides, more sequence coverage occurs when the phosphorylated residue is in the middle of the sequence than at either the N- or C-terminus. ETD of the metallated precursor ions formed by ESI generates exclusively metallated and nonmetallated c- and z-ions for the biological phosphopeptides, while metallated c-ions, z-ions, and a few y-ions form for the model phosphopeptides. Most of the product ions contain the phosphorylated residue indicating that the metal ion binds predominantly at the deprotonated phosphate group. The results of this study indicate that ETD is a promising tool for sequencing highly acidic phosphorylated peptides by metal adduction with Pr (III) and, by extension, all nonradioactive lanthanide metal ions.
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Affiliation(s)
| | - Carolyn J Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama, USA
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21
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Chouinard CD, Nagy G, Webb IK, Shi T, Baker ES, Prost SA, Liu T, Ibrahim YM, Smith RD. Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry. Anal Chem 2018; 90:10889-10896. [PMID: 30118596 PMCID: PMC6211290 DOI: 10.1021/acs.analchem.8b02397] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphoproteomics greatly augments proteomics and holds tremendous potential for insights into the modulation of biological systems for various disease states. However, numerous challenges hinder conventional methods in terms of measurement sensitivity, throughput, quantification, and capabilities for confident phosphopeptide and phosphosite identification. In this work, we report the first example of integrating structures for lossless ion manipulations ion mobility-mass spectrometry (SLIM IM-MS) with online reversed-phase liquid chromatography (LC) to evaluate its potential for addressing the aforementioned challenges. A mixture of 51 heavy-labeled phosphopeptides was analyzed with a SLIM IM module having integrated ion accumulation and long-path separation regions. The SLIM IM-MS provided limits of detection as low as 50-100 pM (50-100 amol/μL) for several phosphopeptides, with the potential for significant further improvements. In addition, conventionally problematic phosphopeptide isomers could be resolved following an 18 m SLIM IM separation. The 2-D LC-IM peak capacity was estimated as ∼9000 for a 90 min LC separation coupled to an 18 m SLIM IM separation, considerably higher than LC alone and providing a basis for both improved identification and quantification, with additional gains projected with the future use of longer path SLIM IM separations. Thus, LC-SLIM IM-MS offers great potential for improving the sensitivity, separation, and throughput of phosphoproteomics analyses.
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Affiliation(s)
- Christopher D. Chouinard
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ian K. Webb
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erin S. Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Spencer A. Prost
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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22
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DeGraan-Weber N, Zhao B, Reilly JP. Unusual fragmentation of derivatized cysteine-containing peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1491-1496. [PMID: 29874404 PMCID: PMC6430700 DOI: 10.1002/rcm.8196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Modification of cysteines by aminoethylation results in side chains similar to those of lysine. Trypsin cleaves at this modified residue and this labeling method can facilitate the analysis of proteins, specifically antibodies. In this work, the ability to identify peptides containing aminoethylated cysteines is investigated through digestion, covalent labeling, and low-energy ion fragmentation. METHODS A prototype antibody was reduced, aminoethylated, and digested with either Lys-N or Glu-C. The resulting peptides were amidinated with SMTA and analyzed by PSD in a MALDI-TOF/TOF mass spectrometer or by CID in an ESI ion trap/orbitrap mass spectrometer. RESULTS PSD and CID fragmentation of peptides with an amidinated aminoethylated cysteine can produce an intense characteristic loss from this modified residue. A neutral loss of 118 Da or charged loss of 119 Da is observed when peptides have low charges. This fragment can form when the cysteine is located in any position in the peptide. The rationalization for this ion is that the amidino group can be initially neutral or protonated and initiates fragmentation. CONCLUSIONS The combination of a dual-labeling technique and low-energy fragmentation produces an abundant diagnostic ion for the analysis of cysteine-containing peptides. These 118 and 119 Da losses are observed when protons are sequestered.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405
| | - Bingqing Zhao
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405
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23
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A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis. Proteomes 2017; 5:proteomes5020011. [PMID: 28387712 PMCID: PMC5489772 DOI: 10.3390/proteomes5020011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022] Open
Abstract
Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.
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24
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Penkert M, Yates LM, Schümann M, Perlman D, Fiedler D, Krause E. Unambiguous Identification of Serine and Threonine Pyrophosphorylation Using Neutral-Loss-Triggered Electron-Transfer/Higher-Energy Collision Dissociation. Anal Chem 2017; 89:3672-3680. [DOI: 10.1021/acs.analchem.6b05095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Martin Penkert
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Department
of Chemistry, Brook-Taylor-Straße
2, 12489 Berlin, Germany
| | - Lisa M. Yates
- Princeton University, Department of Chemistry, Frick Chemistry Building, Washington
Road, Princeton, New Jersey 08544, United States
| | - Michael Schümann
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
| | - David Perlman
- Princeton University, Department of Molecular Biology, 119 Lewis Thomas Laboratory, Washington
Road, Princeton, New Jersey 08544, United States
| | - Dorothea Fiedler
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Department
of Chemistry, Brook-Taylor-Straße
2, 12489 Berlin, Germany
| | - Eberhard Krause
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
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25
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Everley RA, Huttlin EL, Erickson AR, Beausoleil SA, Gygi SP. Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags. J Proteome Res 2016; 16:1069-1076. [PMID: 27978624 DOI: 10.1021/acs.jproteome.6b00487] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While developing a multiplexed phosphotyrosine peptide quantification assay, an unexpected observation was made: significant neutral loss from phosphotyrosine (pY) containing peptides. Using a 2000-member peptide library, we sought to systematically investigate this observation by comparing unlabeled peptides with the two highest-plex isobaric tags (iTRAQ8 and TMT10) across CID, HCD, and ETD fragmentation using high resolution high mass accuracy Orbitrap instrumentation. We found pY peptide neutral loss behavior was consistent with reduced proton mobility, and does not occur during ETD. The site of protonation at the peptide N-terminus changes from a primary to a tertiary amine as a result of TMT labeling which would increase the gas phase basicity and reduce proton mobility at this site. This change in fragmentation behavior has implications during instrument method development and interpretation of MS/MS spectra, and therefore ensuing follow-up studies. We show how sites not localized to tyrosine by search and site localization algorithms can be confidently reassigned to tyrosine using neutral loss and phosphotyrosine immonium ions. We believe these findings will be of general interest to those studying pY signal transduction using isobaric tags.
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Affiliation(s)
- Robert A Everley
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States.,Laboratory of Systems Pharmacology, Harvard Medical School , Boston, Massachusetts 02115 United States
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Alison R Erickson
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Sean A Beausoleil
- Cell Signaling Technology, Inc. , Danvers, Massachusetts 01923, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
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26
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Baird MA, Shvartsburg AA. Localization of Post-Translational Modifications in Peptide Mixtures via High-Resolution Differential Ion Mobility Separations Followed by Electron Transfer Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2064-2070. [PMID: 27644938 PMCID: PMC7063994 DOI: 10.1007/s13361-016-1498-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/28/2016] [Accepted: 08/31/2016] [Indexed: 05/02/2023]
Abstract
Precise localization of post-translational modifications (PTMs) on proteins and peptides is an outstanding challenge in proteomics. While electron transfer dissociation (ETD) has dramatically advanced PTM analyses, mixtures of localization variants that commonly coexist in cells often require prior separation. Although differential or field asymmetric waveform ion mobility spectrometry (FAIMS) achieves broad variant resolution, the need for standards to identify the features has limited the utility of approach. Here we demonstrate full a priori characterization of variant mixtures by high-resolution FAIMS coupled to ETD and the procedures to systematically extract the FAIMS spectra for all variants from such data. Graphical Abstract ᅟ.
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Affiliation(s)
- Matthew A Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS, 67260-0051, USA
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS, 67260-0051, USA.
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27
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Vandermarliere E, Stes E, Gevaert K, Martens L. Resolution of protein structure by mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:653-665. [PMID: 25536908 DOI: 10.1002/mas.21450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Typically, mass spectrometry is used to identify the peptides present in a complex peptide mixture and subsequently the precursor proteins. As such, mass spectrometry focuses mainly on the primary structure, the (modified) amino acid sequence of peptides and proteins. In contrast, the three-dimensional structure of a protein is typically determined with protein X-ray crystallography or NMR. Despite the close relationship between these two aspects of protein studies (sequence and structure), mass spectrometry and structure determination are not frequently combined. Nevertheless, this combination of approaches, dubbed conformational proteomics, can offer insight into the function, working mechanism, and conformational status of a protein. In this review, we will discuss the developments at the intersection of mass spectrometry-based proteomics and protein structure determination and start from a brief overview of the classic approaches to identify protein structure along with their advantages and disadvantages. We will subsequently discuss the ability of mass spectrometry to overcome some of the hurdles of these classic methods. Finally, we will provide an outlook on the interplay of mass spectrometry and protein structure determination, and highlight several recent experiments in which mass spectrometry was successfully used to either aid or complement structure elucidation. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:653-665, 2016.
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Affiliation(s)
- Elien Vandermarliere
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium
| | - Elisabeth Stes
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium
| | - Lennart Martens
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium.
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium.
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Solari FA, Dell'Aica M, Sickmann A, Zahedi RP. Why phosphoproteomics is still a challenge. MOLECULAR BIOSYSTEMS 2016; 11:1487-93. [PMID: 25800119 DOI: 10.1039/c5mb00024f] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite continuous improvements phosphoproteomics still faces challenges that are often neglected, e.g. partially poor recovery of phosphopeptide enrichment, assessment of phosphorylation stoichiometry, label-free quantification, poor behavior during chromatography, and general limitations of peptide-centric proteomics. Here we critically discuss current limitations that need consideration in both qualitative and quantitative studies.
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Affiliation(s)
- Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
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29
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Identification, Quantification, and Site Localization of Protein Posttranslational Modifications via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:345-382. [PMID: 27975226 DOI: 10.1007/978-3-319-41448-5_17] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Posttranslational modifications (PTMs) are important biochemical processes for regulating various signaling pathways and determining specific cell fate. Mass spectrometry (MS)-based proteomics has been developed extensively in the past decade and is becoming the standard approach for systematic characterization of different PTMs on a global scale. In this chapter, we will explain the biological importance of various PTMs, summarize key innovations in PTMs enrichment strategies, high-performance liquid chromatography (HPLC)-based fractionation approaches, mass spectrometry detection methods, and lastly bioinformatic tools for PTMs related data analysis. With great effort in recent years by the proteomics community, highly efficient enriching methods and comprehensive resources have been developed. This chapter will specifically focus on five major types of PTMs; phosphorylation, glycosylation, ubiquitination/sumosylation, acetylation, and methylation.
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30
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Chai Y, Xiong X, Yue L, Jiang Y, Pan Y, Fang X. Intramolecular Halogen Transfer via Halonium Ion Intermediates in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:161-167. [PMID: 26383734 DOI: 10.1007/s13361-015-1261-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
The fragmentation of halogen-substituted protonated amines and quaternary ammonium ions (R(1)R(2)R(3)N(+)CH2(CH2)nX, where X = F, Cl, Br, I, n = 1, 2, 3, 4) was studied by electrospray ionization tandem mass spectrometry. A characteristic fragment ion (R(1)R(2)R(3)N(+)X) resulting from halogen transfer was observed in collision-induced dissociation. A new mechanism for the intramolecular halogen transfer was proposed that involves a reactive intermediate, [amine/halonium ion]. A potential energy surface scan using DFT calculation for CH2-N bond cleavage process of protonated 2-bromo-N,N-dimethylethanamine supports the formation of this intermediate. The bromonium ion intermediate-involved halogen transfer mechanism is supported by an examination of the ion/molecule reaction between isolated ethylenebromonium ion and triethylamine, which generates the N-bromo-N,N,N-triethylammonium cation. For other halogens, Cl and I also can be involved in similar intramolecular halogen transfer, but F cannot be involved. With the elongation of the carbon chain between the halogen (bromine as a representative example) and amine, the migration ability of halogen decreases. When the carbon chain contains two or three CH2 units (n = 1, 2), formal bromine cation transfer can take place, and the transfer is easier when n = 1. When the carbon chain contains four or five CH2 units (n = 3, 4), formal bromine cation transfer does not occur, probably because the five- and six-membered cyclic bromonium ions are very stable and do not donate the bromine to the amine.
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Affiliation(s)
- Yunfeng Chai
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | | | - Lei Yue
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - You Jiang
- National Institute of Metrology, Beijing, 100013, China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China.
| | - Xiang Fang
- National Institute of Metrology, Beijing, 100013, China.
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31
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Stover ML, Plummer CE, Miller SR, Cassady CJ, Dixon DA. Gas-Phase Acidities of Phosphorylated Amino Acids. J Phys Chem B 2015; 119:14604-21. [DOI: 10.1021/acs.jpcb.5b08616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele L. Stover
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Chelsea E. Plummer
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Sean R. Miller
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Carolyn J. Cassady
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - David A. Dixon
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
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Ye J, Zhang Z, Long H, Zhang Z, Hong Y, Zhang X, You C, Liang W, Ma H, Lu P. Proteomic and phosphoproteomic analyses reveal extensive phosphorylation of regulatory proteins in developing rice anthers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:527-44. [PMID: 26360816 DOI: 10.1111/tpj.13019] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 05/18/2023]
Abstract
Anther development, particularly around the time of meiosis, is extremely crucial for plant sexual reproduction. Meanwhile, cell-to-cell communication between somatic (especial tapetum) cells and meiocytes are important for both somatic anther development and meiosis. To investigate possible molecular mechanisms modulating protein activities during anther development, we applied high-resolution mass spectrometry-based proteomic and phosphoproteomic analyses for developing rice (Oryza sativa) anthers around the time of meiosis (RAM). In total, we identified 4984 proteins and 3203 phosphoproteins with 8973 unique phosphorylation sites (p-sites). Among those detected here, 1544 phosphoproteins are currently absent in the Plant Protein Phosphorylation DataBase (P3 DB), substantially enriching plant phosphorylation information. Mapman enrichment analysis showed that 'DNA repair','transcription regulation' and 'signaling' related proteins were overrepresented in the phosphorylated proteins. Ten genetically identified rice meiotic proteins were detected to be phosphorylated at a total of 25 p-sites; moreover more than 400 meiotically expressed proteins were revealed to be phosphorylated and their phosphorylation sites were precisely assigned. 163 putative secretory proteins, possibly functioning in cell-to-cell communication, are also phosphorylated. Furthermore, we showed that DNA synthesis, RNA splicing and RNA-directed DNA methylation pathways are extensively affected by phosphorylation. In addition, our data support 46 kinase-substrate pairs predicted by the rice Kinase-Protein Interaction Map, with SnRK1 substrates highly enriched. Taken together, our data revealed extensive protein phosphorylation during anther development, suggesting an important post-translational modification affecting protein activity.
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Affiliation(s)
- Juanying Ye
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Zaibao Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Haifei Long
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Zhimin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yue Hong
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Chenjiang You
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Wanqi Liang
- State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Pingli Lu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
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Patrick AL, Polfer NC. H2SO4 and SO3 transfer reactions in a sulfopeptide-basic peptide complex. Anal Chem 2015; 87:9551-4. [PMID: 26335182 DOI: 10.1021/acs.analchem.5b02479] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report on the intermolecular transfer of sulfuric acid (H2SO4) and sulfur trioxide (SO3) from an acidic sulfopeptide (sSE) to a basic peptide (R3); this is achieved by subjecting a noncovalent complex of sSE + R3 to collisional activation in a quadrupole ion trap. The product ions resulting from the sulfo-group transfers were characterized by MS(3) experiments. Peak assignments were additionally supported by isotope-labeling and energy-resolved collision induced dissiciation (CID) experiments. The observed reactions and their potential implications for proteomics and post-translational modification discovery experiments are discussed.
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Affiliation(s)
- Amanda L Patrick
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
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Brown R, Stuart SA, Houel S, Ahn NG, Old WM. Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1128-42. [PMID: 25851653 PMCID: PMC4509682 DOI: 10.1007/s13361-015-1109-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 05/14/2023]
Abstract
Collision-induced dissociation (CID) remains the predominant mass spectrometry-based method for identifying phosphorylation sites in complex mixtures. Unfortunately, the gas-phase reactivity of phosphoester bonds results in MS/MS spectra dominated by phosphoric acid (H3PO4) neutral loss events, suppressing informative peptide backbone cleavages. To understand the major drivers of H3PO4 neutral loss, we performed robust nonparametric statistical analysis of local and distal sequence effects on the magnitude and variability of neutral loss, using a collection of over 35,000 unique phosphopeptide MS/MS spectra. In contrast to peptide amide dissociation pathways, which are strongly influenced by adjacent amino acid side chains, we find that neutral loss of H3PO4 is affected by both proximal and distal sites, most notably basic residues and the peptide N-terminal primary amine. Previous studies have suggested that protonated basic residues catalyze neutral loss through direct interactions with the phosphate. In contrast, we find that nearby basic groups decrease neutral loss regardless of mobility class, an effect only seen by stratifying spectra by charge-mobility. The most inhibitory bases are those immediately N-terminal to the phosphate, presumably because of steric hindrances in catalyzing neutral loss. Further evidence of steric effects is shown by the presence of proline, which can dramatically reduce the presence of neutral loss when between the phosphate and a possible charge donor. In mobile proton spectra, the N-terminus is the strongest predictor of high neutral loss, with proximity to the N-terminus essential for peptides to exhibit the highest levels of neutral loss.
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Affiliation(s)
- Robert Brown
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Scott A. Stuart
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | | | - Natalie G. Ahn
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309
| | - William M. Old
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
- Corresponding author: William M. Old, Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, Phone: 303-492-5519, Fax: 303-492-2439,
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Bertran-Vicente J, Schümann M, Hackenberger CPR, Krause E. Gas-Phase Rearrangement in Lysine Phosphorylated Peptides During Electron-Transfer Dissociation Tandem Mass Spectrometry. Anal Chem 2015; 87:6990-4. [PMID: 26110354 DOI: 10.1021/acs.analchem.5b01389] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tandem mass spectrometry (MS/MS) strategies coupled with collision-induced dissociation (CID) or radical-driven fragmentation techniques such as electron-capture dissociation (ECD) or electron-transfer dissociation (ETD) have been successfully used for comprehensive phosphoproteome analysis. However, the unambiguous characterization of the phosphorylation site remains a significant challenge due to phosphate-related neutral losses and gas-phase rearrangements, which have been observed during CID. In particular, for the analysis of labile N-phosphorylated peptides, ECD and ETD are emerging as a complementary method. In contrast to CID, the phosphorylation site of histidine, arginine, and lysine phosphorylated peptides can be characterized by ETD. Here, we present a study on the application of ETD for analysis of phospholysine (pLys) peptides. We show that, depending on the charge state of the precursor ion as well as the presence of basic amino acid side chains, phosphate transfer reactions during the ETD process can be observed leading to ambiguous fragment ion spectra. Basically, pLys is stable under ETD conditions allowing an unambiguous assignment of the site of phosphorylation, but some factors/parameters have to be considered to avoid gas-phase rearrangement which would lead to false positive results in phosphoproteomic studies.
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Affiliation(s)
- Jordi Bertran-Vicente
- †Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany.,§Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Michael Schümann
- †Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
| | - Christian P R Hackenberger
- †Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany.,‡Department Chemie, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Eberhard Krause
- †Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
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36
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Linke D, Koudelka T, Becker A, Tholey A. Identification and relative quantification of phosphopeptides by a combination of multi-protease digestion and isobaric labeling. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:919-926. [PMID: 26407306 DOI: 10.1002/rcm.7185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/18/2015] [Accepted: 02/25/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The identification and the determination of the extent of protein phosphorylation are major prerequisites for the comparative analysis of this important posttranslational modification of proteins in different biological situations. High sequence coverages and the availability of straightforward quantification methods are necessary to achieve these goals. METHODS Phosphoproteins and non-phosphorylated analogues separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were digested using four different proteases (trypsin, chymotrypsin, elastase and GluC) and the digests were isobarically labeled using eight-plex iTRAQ. The combined labeled digests were subsequently enriched using titanium dioxide and both the phosphorylated and non-phosphorylated fractions were analyzed by liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS). The influence of different data analysis algorithms (Percolator or False Discovery Rate) on the outcome of analysis was investigated. RESULTS Almost complete sequence coverage could be achieved upon application of a multi-protease approach. The formation of peptides of different lengths and physicochemical properties allowed the identification and the mapping of all phosphorylation sites in the investigated model proteins. The introduction of isobaric labels allowed quantification of different peptides of the same phosphorylation site with more than one peptide, leading to significantly improved statistical confidence. CONCLUSIONS A workflow for the straightforward comparative analysis of protein phosphorylation in samples of low complexity, e.g. isolated proteins, was developed. The workflow is transferable to other posttranslational modifications.
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Affiliation(s)
- Dennis Linke
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung und Bioanalytik, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Tomas Koudelka
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung und Bioanalytik, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Alexander Becker
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung und Bioanalytik, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Andreas Tholey
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung und Bioanalytik, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
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37
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Wright MJ, Thomas RL, Stanford PE, Horvath AR. Multiple Reaction Monitoring with Multistage Fragmentation (MRM3) Detection Enhances Selectivity for LC-MS/MS Analysis of Plasma Free Metanephrines. Clin Chem 2015; 61:505-13. [DOI: 10.1373/clinchem.2014.233551] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Abstract
BACKGROUND
LC-MS/MS with multiple reaction monitoring (MRM) is a powerful tool for quantifying target analytes in complex matrices. However, the technique lacks selectivity when plasma free metanephrines are measured. We propose the use of multistage fragmentation (MRM3) to improve the analytical selectivity of plasma free metanephrine measurement.
METHODS
Metanephrines were extracted from plasma with weak cation exchange solid-phase extraction before separation by hydrophilic interaction liquid chromatography. We quantified normetanephrine and metanephrine by either MRM or MRM3 transitions m/z 166→134→79 and m/z 180→149→121, respectively.
RESULTS
Over a 6-month period, approximately 1% (n = 21) of patient samples showed uncharacterized coeluting substances that interfered with the routine assay, resulting in an inability to report results. Quantification with MRM3 removed these interferences and enabled measurement of the target compounds. For patient samples unaffected by interferences, Deming regression analysis demonstrated a correlation between MRM3 and MRM methods of y = 1.00x − 0.00 nmol/L for normetanephrine and y = 0.99x + 0.03 nmol/L for metanephrine. Between the MRM3 method and the median of all LC-MS/MS laboratories enrolled in a quality assurance program, the correlations were y = 0.97x + 0.03 nmol/L for normetanephrine and y = 1.03x − 0.04 nmol/L for metanephrine. Imprecision for the MRM3 method was 6.2%–7.0% for normetanephrine and 6.1%–9.9% for metanephrine (n = 10). The lower limits of quantification for the MRM3 method were 0.20 nmol/L for normetanephrine and 0.16 nmol/L for metanephrine.
CONCLUSIONS
The use of MRM3 technology improves the analytical selectivity of plasma free metanephrine quantification by LC-MS/MS while demonstrating sufficient analytical sensitivity and imprecision.
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Affiliation(s)
- Michael J Wright
- Department of Clinical Chemistry and Endocrinology, South Eastern Area Laboratory Services (SEALS), Prince of Wales Hospitals, Sydney, Australia
| | - Rebecca L Thomas
- Department of Clinical Chemistry and Endocrinology, South Eastern Area Laboratory Services (SEALS), Prince of Wales Hospitals, Sydney, Australia
| | - Phoebe E Stanford
- Department of Clinical Chemistry and Endocrinology, South Eastern Area Laboratory Services (SEALS), Prince of Wales Hospitals, Sydney, Australia
| | - Andrea R Horvath
- Department of Clinical Chemistry and Endocrinology, South Eastern Area Laboratory Services (SEALS), Prince of Wales Hospitals, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
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Lee DCH, Jones AR, Hubbard SJ. Computational phosphoproteomics: from identification to localization. Proteomics 2015; 15:950-63. [PMID: 25475148 PMCID: PMC4384807 DOI: 10.1002/pmic.201400372] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/31/2014] [Accepted: 11/26/2014] [Indexed: 01/08/2023]
Abstract
Analysis of the phosphoproteome by MS has become a key technology for the characterization of dynamic regulatory processes in the cell, since kinase and phosphatase action underlie many major biological functions. However, the addition of a phosphate group to a suitable side chain often confounds informatic analysis by generating product ion spectra that are more difficult to interpret (and consequently identify) relative to unmodified peptides. Collectively, these challenges have motivated bioinformaticians to create novel software tools and pipelines to assist in the identification of phosphopeptides in proteomic mixtures, and help pinpoint or "localize" the most likely site of modification in cases where there is ambiguity. Here we review the challenges to be met and the informatics solutions available to address them for phosphoproteomic analysis, as well as highlighting the difficulties associated with using them and the implications for data standards.
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Affiliation(s)
- Dave C H Lee
- Faculty of Life Sciences, University of ManchesterManchester, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
| | - Simon J Hubbard
- Faculty of Life Sciences, University of ManchesterManchester, UK
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Maccarrone G, Filiou MD. Protein profiling and phosphoprotein analysis by isoelectric focusing. Methods Mol Biol 2015; 1295:293-303. [PMID: 25820730 DOI: 10.1007/978-1-4939-2550-6_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein profiling enables the qualitative characterization of a proteome of interest. Phosphorylation is a post-translational modification with regulatory functions in a plethora of cell processes. We present an experimental workflow for simultaneous analysis of the proteome and phosphoproteome with no additional enrichment for phosphoproteins/phosphopeptides. Our approach is based on isoelectric focusing (IEF) which allows the separation of peptide mixtures on an immobilized pH gradient (IPG) according to their isoelectric point. Due to the negative charge of the phosphogroup, most of the phosphopeptides migrate toward acidic pH values. Peptides and phosphopeptides are then identified by mass spectrometry (MS) and phosphopeptide spectra are manually checked for the assignment of phosphorylation sites. Here, we apply this methodology to investigate synaptosome extracts from whole mouse brain. IEF-based peptide separation is an efficient method for peptide and phosphopeptide identification.
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Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L. The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry. Proteomics 2014; 15:554-66. [PMID: 25367160 DOI: 10.1002/pmic.201400132] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/22/2014] [Accepted: 10/28/2014] [Indexed: 01/06/2023]
Abstract
Human embryonic stem cells (hESCs) have received considerable attention due to their therapeutic potential and usefulness in understanding early development and cell fate commitment. In order to appreciate the unique properties of these pluripotent, self-renewing cells, we have performed an in-depth multidimensional fractionation followed by LC-MS/MS analysis of the hESCs harvested from defined media to elucidate expressed, phosphorylated, O-linked β-N-acetylglucosamine (O-GlcNAc) modified, and secreted proteins. From the triplicate analysis, we were able to assign more than 3000 proteins with less than 1% false-discovery rate. This analysis also allowed us to identify nearly 500 phosphorylation sites and 68 sites of O-GlcNAc modification with the same high confidence. Investigation of the phosphorylation sites allowed us to deduce the set of kinases that are likely active in these cells. We also identified more than 100 secreted proteins of hESCs that likely play a role in extracellular matrix formation and remodeling, as well as autocrine signaling for self-renewal and maintenance of the undifferentiated state. Finally, by performing in-depth analysis in triplicate, spectral counts were obtained for these proteins and posttranslationally modified peptides, which will allow us to perform relative quantitative analysis between these cells and any derived cell type in the future.
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Affiliation(s)
- Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
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Hoffmann WD, Jackson GP. Charge transfer dissociation (CTD) mass spectrometry of peptide cations using kiloelectronvolt helium cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1939-43. [PMID: 25231159 DOI: 10.1007/s13361-014-0989-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/23/2014] [Accepted: 07/27/2014] [Indexed: 05/04/2023]
Abstract
A kiloelectronvolt beam of helium ions is used to ionize and fragment precursor peptide ions starting in the 1+ charge state. The electron affinity of helium cations (24.6 eV) exceeds the ionization potential of protonated peptides and can therefore be used to abstract an electron from--or charge exchange with--the isolated precursor ions. Kiloelectronvolt energies are used, (1) to overcome the Coulombic repulsion barrier between the cationic reactants, (2) to overcome ion-defocussing effects in the ion trap, and (3) to provide additional activation energy. Charge transfer dissociation (CTD) of the [M+H](+) precursor of Substance P gives product ions such as [M+H](2+•) and a dominant series of a ions in both the 1+ and 2+ charge states. These observations, along with the less-abundant a + 1 ions, are consistent with ultraviolet photodissociation (UVPD) results of others and indicate that C-C(α) cleavages are possible through charge exchange with helium ions. Although the efficiencies and timescale of CTD are not yet suitable for on-line chromatography, this new approach to ion activation provides an additional potential tool for the interrogation of gas phase ions.
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Affiliation(s)
- William D Hoffmann
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506, USA
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42
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Borotto NB, Degraan-Weber N, Zhou Y, Vachet RW. Label scrambling during CID of covalently labeled peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1739-46. [PMID: 25056863 PMCID: PMC4163129 DOI: 10.1007/s13361-014-0962-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/26/2014] [Accepted: 07/01/2014] [Indexed: 05/14/2023]
Abstract
Covalent labeling along with mass spectrometry is finding more use as a means of studying the higher order structure of proteins and protein complexes. Diethylpyrocarbonate (DEPC) is an increasingly used reagent for these labeling experiments because it is capable of modifying multiple residues at the same time. Pinpointing DEPC-labeled sites on proteins is typically needed to obtain more resolved structural information, and tandem mass spectrometry after protein proteolysis is often used for this purpose. In this work, we demonstrate that in certain instances, scrambling of the DEPC label from one residue to another can occur during collision-induced dissociation (CID) of labeled peptide ions, resulting in ambiguity in label site identity. From a preliminary study of over 30 labeled peptides, we find that scrambling occurs in about 25% of the peptides and most commonly occurs when histidine residues are labeled. Moreover, this scrambling appears to occur more readily under non-mobile proton conditions, meaning that low charge-state peptide ions are more prone to this reaction. For all peptides, we find that scrambling does not occur during electron transfer dissociation, which suggests that this dissociation technique is a safe alternative to CID for correct label site identification.
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Affiliation(s)
| | | | | | - Richard W. Vachet
- Corresponding author; address reprint requests to: Richard Vachet, Department of Chemistry, Life Sciences Laboratory, 240 Thatcher Way, University of Massachusetts, Amherst, MA 01003,
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43
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Popov IA, Indeikina MI, Pekov SI, Starodubtseva NL, Kononikhin AS, Nikolaeva MI, Kukaev EN, Kostyukevich YI, Kozin SA, Makarov AA, Nikolaev EN. Estimation of phosphorylation level of amyloid-beta isolated from human blood plasma: Ultrahigh-resolution mass spectrometry. Mol Biol 2014. [DOI: 10.1134/s0026893314040098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Gonzalez-Sanchez MB, Lanucara F, Hardman GE, Eyers CE. Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2014; 367:28-34. [PMID: 25844054 PMCID: PMC4375673 DOI: 10.1016/j.ijms.2014.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/14/2014] [Accepted: 04/22/2014] [Indexed: 05/26/2023]
Abstract
The hydrogen bonds and electrostatic interactions that form between the protonated side chain of a basic residue and the negatively charged phosphate of a phosphopeptide can play crucial roles in governing their dissociation pathways under low-energy collision-induced dissociation (CID). Understanding how phosphoramidate (i.e. phosphohistidine, phospholysine and phosphoarginine), rather than phosphomonoester-containing peptides behave during CID is paramount in investigation of these problematic species by tandem mass spectrometry. To this end, a synthetic peptide containing either phosphohistidine (pHis) or phospholysine (pLys) was analyzed by ESI-MS using a Paul-type ion trap (AmaZon, Bruker) and by traveling wave ion mobility-mass spectrometry (Synapt G2-Si, Waters). Analysis of the products of low-energy CID demonstrated formation of a doubly 'phosphorylated' product ion arising from intermolecular gas-phase phosphate transfer within a phosphopeptide dimer. The results are explained by the formation of a homodimeric phosphohistidine (pHis) peptide non-covalent complex (NCX), likely stabilized by the electrostatic interaction between the pHis phosphate group and the protonated C-terminal lysine residue of the peptide. To the best of our knowledge this is the first report of intermolecular gas-phase phosphate transfer from one phosphopeptide to another, leading to a doubly phosphorylated peptide product ion.
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Affiliation(s)
- Maria-Belen Gonzalez-Sanchez
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Francesco Lanucara
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Gemma E. Hardman
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Claire E. Eyers
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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45
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Recent developments and applications of electron transfer dissociation mass spectrometry in proteomics. Amino Acids 2014; 46:1625-34. [PMID: 24687149 DOI: 10.1007/s00726-014-1726-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 03/07/2014] [Indexed: 12/30/2022]
Abstract
Electron transfer dissociation (ETD) has been developed recently as an efficient ion fragmentation technique in mass spectrometry (MS), being presently considered a step forward in proteomics with real perspectives for improvement, upgrade and application. Available also on affordable ion trap mass spectrometers, ETD induces specific N-Cα bond cleavages of the peptide backbone with the preservation of the post-translational modifications and generation of product ions that are diagnostic for the modification site(s). In addition, in the last few years ETD contributed significantly to the development of top-down approaches which enable tandem MS of intact protein ions. The present review, covering the last 5 years highlights concisely the major achievements and the current applications of ETD fragmentation technique in proteomics. An ample part of the review is dedicated to ETD contribution in the elucidation of the most common posttranslational modifications, such as phosphorylation and glycosylation. Further, a brief section is devoted to top-down by ETD method applied to intact proteins. As the last few years have witnessed a major expansion of the microfluidics systems, a few considerations on ETD in combination with chip-based nanoelectrospray (nanoESI) as a platform for high throughput top-down proteomics are also presented.
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46
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Lanucara F, Chiavarino B, Scuderi D, Maitre P, Fornarini S, Crestoni ME. Kinetic control in the CID-induced elimination of H3PO4 from phosphorylated serine probed using IRMPD spectroscopy. Chem Commun (Camb) 2014; 50:3845-8. [PMID: 24589658 DOI: 10.1039/c4cc00877d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy was used to assay the structural features of the fragment ions resulting from the elimination of H3PO4 in the Collision-Induced Dissociation (CID) of protonated serine. The results are interpreted with the aid of density functional theory calculations. Experiment and theory point to an aziridine-ring structure, implying participation of the vicinal amino group in the formation of this species. This finding constitutes a benchmark for investigating the same process in the CID of phosphorylated peptides.
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Affiliation(s)
- Francesco Lanucara
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, M17DN Manchester, UK.
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47
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Lanucara F, Chi Hoo Lee D, Eyers CE. Unblocking the sink: improved CID-based analysis of phosphorylated peptides by enzymatic removal of the basic C-terminal residue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:214-225. [PMID: 24297471 PMCID: PMC3899453 DOI: 10.1007/s13361-013-0770-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 06/02/2023]
Abstract
A one-step enzymatic reaction for improving the collision-induced dissociation (CID)-based tandem mass spectrometry (MS/MS) analysis of phosphorylated peptides in an ion trap is presented. Carboxypeptidase-B (CBP-B) was used to selectively remove C-terminal arginine or lysine residues from phosphorylated tryptic/Lys-C peptides prior to their MS/MS analysis by CID with a Paul-type ion trap. Removal of this basic C-terminal residue served to limit the extent of gas-phase neutral loss of phosphoric acid (H3PO4), favoring the formation of diagnostic b and y ions as determined by an increase in both the number and relative intensities of the sequence-specific product ions. Such differential fragmentation is particularly valuable when the H3PO4 elimination is so predominant that localizing the phosphorylation site on the peptide sequence is hindered. Improvement in the quality of tandem mass spectral data generated by CID upon CBP-B treatment resulted in greater confidence both in assignment of the phosphopeptide primary sequence and for pinpointing the site of phosphorylation. Higher Mascot ion scores were also generated, combined with lower expectation values and higher delta scores for improved confidence in site assignment; Ascore values also improved. These results are rationalized in accordance with the accepted mechanisms for the elimination of H3PO4 upon low energy CID and insights into the factors dictating the observed dissociation pathways are presented. We anticipate this approach will be of utility in the MS analysis of phosphorylated peptides, especially when alternative electron-driven fragmentation techniques are not available.
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Affiliation(s)
- Francesco Lanucara
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Dave Chi Hoo Lee
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN UK
| | - Claire E. Eyers
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
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48
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Cui L, Yapici I, Borhan B, Reid GE. Quantification of competing H3PO4 versus HPO3 + H2O neutral losses from regioselective 18O-labeled phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:141-148. [PMID: 24249041 DOI: 10.1007/s13361-013-0744-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/26/2013] [Accepted: 08/28/2013] [Indexed: 06/02/2023]
Abstract
Abundant neutral losses of 98 Da are often observed upon ion trap CID-MS/MS of protonated phosphopeptide ions. Two competing fragmentation pathways are involved in this process, namely, the direct loss of H3PO4 from the phosphorylated residue and the combined losses of HPO3 and H2O from the phosphorylation site and from an additional site within the peptide, respectively. These competing pathways produce product ions with different structures but the same m/z values, potentially limiting the utility of CID-MS(3) for phosphorylation site localization. To quantify the relative contributions of these pathways and to determine the conditions under which each pathway predominates, we have examined the ion trap CID-MS/MS fragmentation of a series of regioselective (18)O-phosphate ester labeled phosphopeptides prepared using novel solution-phase amino acid synthesis and solid-phase peptide synthesis methodologies. By comparing the intensity of the -100 Da (-H3PO3 (18)O) versus -98 Da (-[HPO3 + H2O]) neutral loss product ions formed upon MS/MS, quantification of the two pathways was achieved. Factors that affect the extent of formation of the competing neutral losses were investigated, with the combined loss pathway predominantly occurring under conditions of limited proton mobility, and with increased combined losses observed for phosphothreonine compared with phosphoserine-containing peptides. The combined loss pathway was found to be less dominant under ion activation conditions associated with HCD-MS/MS. Finally, the contribution of carboxylic acid functional groups and backbone amide bonds to the water loss in the combined loss fragmentation pathway was determined via methyl esterification and by examination of a phosphopeptide lacking side-chain hydroxyl groups.
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Affiliation(s)
- Li Cui
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
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49
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Zhang XN, Mo C, Garrett WM, Cooper B. Phosphothreonine 218 is required for the function of SR45.1 in regulating flower petal development in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2014; 9:e29134. [PMID: 25763493 PMCID: PMC4203572 DOI: 10.4161/psb.29134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 05/19/2023]
Abstract
RNA splicing is crucial to the production of mature mRNAs (mRNA). In Arabidopsis thaliana, the protein Arginine/Serine-rich 45 (SR45) acts as an RNA splicing activator and initiates the spliceosome assembly. SR45 is alternatively spliced into 2 isoforms. Isoform 1 (SR45.1) plays an important role in the flower petal development whereas isoform 2 (SR45.2) is important for root growth. In this study, we used immunoprecipitation to isolate an SR45.1-GFP fusion protein from transgenic plants complementing a null mutant, sr45-1. Mass spectrometry suggested a single phosphorylation event in a peptide from the alternatively spliced region unique to SR45.1. Substituting alanine for threonine 218, a candidate site for phosphorylation, did not complement the sr45-1 mutant with narrow flower petals whereas substituting aspartic acid or glutamic acid for threonine 218 did complement the sr45-1 mutant. Mass spectrometry also revealed that other proteins involved in the spliceosome co-precipitated with SR45.1, and RT-qPCR revealed that phosphorylation of threonine 218 promotes the function of SR45.1 in promoting the constitutive splicing of SR30 mRNA. This is the first demonstration of a specific phosphorylation site that differentially regulates the function of a plant splicing activator in physiologically and morphologically distinct plant tissues.
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Affiliation(s)
- Xiao-Ning Zhang
- Department of Biology; Saint Bonaventure University; Saint Bonaventure, NY USA
- Correspondence to: Xiao-Ning Zhang,
| | - Cecilia Mo
- Department of Biology; Saint Bonaventure University; Saint Bonaventure, NY USA
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory; USDA-ARS; Beltsville, MD USA
| | - Bret Cooper
- Soybean Genomics and Improvement Laboratory; USDA-ARS; Beltsville, MD USA
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50
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Smith SA, Kalcic CL, Cui L, Reid GE. Femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) of deprotonated phosphopeptide anions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2807-2817. [PMID: 24214867 DOI: 10.1002/rcm.6750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Radical-directed dissociation techniques provide structural information which is complementary to that from conventional collision-induced dissociation (CID). The analysis of phosphopeptide anions is warranted due to their relatively acidic character. As femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) is uniquely initiated by field ionization, an investigation is warranted to determine whether fsLID may provide novel analytical utility for phosphopeptide anions. METHODS Twenty-three synthetic deprotonated phosphopeptide anions were introduced into a three-dimensional quadrupole ion trap mass spectrometer via electrospray ionization. The ion trap was interfaced with a near-IR (802 nm) ultrashort-pulsed (35 fs FWHM) ultrahigh-powered (peak power ~10(14) W/cm(2)) laser system. Performance comparisons are made with other techniques applied to phosphopeptide anion analysis, including CID, electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), activated electron photodetachment dissociation (activated-EPD), and ultraviolet photodissociation (UVPD). RESULTS FsLID-MS/MS of multiply deprotonated phosphopeptide anions provides sequence information via phosphorylation-intact a/x ions in addition to other sequence ions, satellite ions, and side-chain losses. Novel fragmentation processes include selective c-ion formation N-terminal to Ser/Thr and a phosphorylation-specific correlation between xn -98 ion abundances and phosphorylation at the n(th) residue. Sequencing-quality data required about 30 s of signal averaging. fsLID-MS/MS of singly deprotonated phosphopeptides did not yield product anions with stable trajectories, despite significant depletion of the precursor. CONCLUSIONS Multiply deprotonated phosphopeptide anions were sequenced via negative-mode fsLID-MS/MS, with phosphosite localization facilitated by a/x ion series in addition to diagnostic x(n)-98 ions. fsLID-MS/MS is qualitatively competitive with other techniques. Further efficiency enhancements (e.g., implementation on a linear trap or/and higher pulse frequencies) may permit sequence analyses on chromatographic timescales.
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Affiliation(s)
- Scott A Smith
- RTSF Mass Spectrometry & Metabolomics Core, Michigan State University, East Lansing, MI, 48824, USA
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