1
|
Nakamura T, Hongo Y, Harada KI. Mobilize a Proton to Transform the Collision-Induced Dissociation Spectral Pattern of a Cyclic Peptide. Mass Spectrom (Tokyo) 2024; 13:A0144. [PMID: 38435076 PMCID: PMC10904930 DOI: 10.5702/massspectrometry.a0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024] Open
Abstract
The collision-induced dissociation (CID) behaviors of protonated molecules of anabaenopeptins, a group of cyanobacterial cyclic peptides, were investigated in detail using liquid chromatography-tandem mass spectrometry. Although anabaenopeptin A and B share a macrocyclic peptide structure, they give strikingly different fragmentation patterns; the former gives a variety of product ions including cleavages in the cyclic peptide structure, which is useful for structural analysis; whereas the latter gives far fewer product ions and no fragmentation in the cyclic moiety. Energy-resolved CID experiments clarified the mechanism behind the striking difference attributable to the difference in exocyclic amino acid residues, Tyr or Arg. The guanidino group in Arg-containing analogue, anabaenopeptin B, should be by far the most preferred protonation site; the proton would be sequestered at the guanidino group in the protonated molecule, with the lack of proton mobility prohibiting opening of the charge-directed fragmentation channels in the cyclic moiety. Enzymatic hydrolysis of the guanidino group to give citrullinated-anabaenopeptin B restored proton mobility. The fragmentation pattern of the citrullinated peptide became almost identical to that of anabaenopeptin A. The observed fragmentation behaviors of these cyclic peptides were consistent with those of linear peptides, which have been well understood based on the mobile proton model.
Collapse
Affiliation(s)
- Takemichi Nakamura
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science, 2–1 Hirosawa, Wako, Saitama 351–0198, Japan
| | - Yayoi Hongo
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science, 2–1 Hirosawa, Wako, Saitama 351–0198, Japan
| | - Ken-ichi Harada
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku, Nagoya 468–8503, Japan
| |
Collapse
|
2
|
Eggen MD, Merboth P, Neukirchner H, Glomb MA. Lipid Peroxidation Has Major Impact on Malondialdehyde-Derived but Only Minor Influence on Glyoxal and Methylglyoxal-Derived Protein Modifications in Carbohydrate-Rich Foods. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10271-10283. [PMID: 35968682 DOI: 10.1021/acs.jafc.2c04052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In the present work, the contribution of lipid peroxidation on modifications of lysine and arginine residues of proteins was investigated. Lipid peroxidation had a major impact on malondialdehyde-derived protein modifications; however, the influence on glyoxal and methylglyoxal-derived modifications in flat wafers was negligible. Therefore, vegetable oils (either linseed oil, sunflower oil, or coconut oil) were added to respective batters, and flat wafers were baked (150 °C, 3-10 min). Analysis of malondialdehyde indicated oxidation in linseed wafers, which was supported by the direct quantitation of three malondialdehyde protein adducts in the range of 0.09-23.5 mg/kg after enzymatic hydrolysis. In contrast, levels of free glyoxal and methylglyoxal were independent of the type of oil added, which was in line with the analysis of 13 advanced glycation end products. Comprehensive incubations of 40 mM N2-t-Boc-lysine (100 mM phosphate buffer, pH 7.4) with either 10% oil or an equimolar concentration of carbohydrates led to magnitudes higher (103-105) amounts of N6-carboxymethyl lysine, N6-glycolyl lysine, and N6-carboxyethyl lysine in the latter. Furthermore, malondialdehyde exceeded glyoxal and methylglyoxal in incubations of pure oils at 150 °C by factors of 30 and 100, respectively.
Collapse
Affiliation(s)
- Michael D Eggen
- Institute of Chemistry, Food Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle, Saale, Germany
| | - Paul Merboth
- Institute of Chemistry, Food Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle, Saale, Germany
| | - Helen Neukirchner
- Institute of Chemistry, Food Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle, Saale, Germany
| | - Marcus A Glomb
- Institute of Chemistry, Food Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle, Saale, Germany
| |
Collapse
|
3
|
Vandemoortele A, Babat P, Yakubu M, De Meulenaer B. Behavior of Malondialdehyde and Its Whey Protein Adducts during In Vitro Simulated Gastrointestinal Digestion. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11846-11854. [PMID: 32985186 DOI: 10.1021/acs.jafc.0c03947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The behavior of malondialdehyde and its whey protein adducts in aqueous buffer and fully hydrogenated coconut oil-in-water emulsions stabilized by Tween 20 or by whey protein was studied during in vitro gastrointestinal digestion. The malondialdehyde levels during in vitro digestion depended upon the kind of sample, the location of the whey protein, and the extent of adduct formation before digestion. During gastric digestion, degradation of acid-labile malondialdehyde-whey protein adducts as well as formation of new malondialdehyde adducts with hydrolyzed whey protein was suggested to occur, in addition to the earlier described equilibria with respect to the aldol self-condensation of malondialdehyde and its hydrolytic cleavage. After in vitro digestion, both malondialdehyde and its adducts were present in the digest with malondialdehyde recoveries varying between 55 and 86% depending upon the model system studied. To conclude, the reactivity of malondialdehyde toward (hydrolyzed) proteins does not stop at the point of ingestion.
Collapse
Affiliation(s)
- Angelique Vandemoortele
- NutriFOODchem Unit, Department of Food Technology, Safety and Health (Partner in Food2Know), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Pinar Babat
- NutriFOODchem Unit, Department of Food Technology, Safety and Health (Partner in Food2Know), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Mariam Yakubu
- NutriFOODchem Unit, Department of Food Technology, Safety and Health (Partner in Food2Know), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Bruno De Meulenaer
- NutriFOODchem Unit, Department of Food Technology, Safety and Health (Partner in Food2Know), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| |
Collapse
|
4
|
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
Collapse
Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
| |
Collapse
|
5
|
Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
|
6
|
Frost DC, Buchberger AR, Li L. Mass Defect-Based Dimethyl Pyrimidinyl Ornithine (DiPyrO) Tags for Multiplex Quantitative Proteomics. Anal Chem 2017; 89:10798-10805. [PMID: 28795795 PMCID: PMC7491675 DOI: 10.1021/acs.analchem.7b02098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have developed a novel amine-reactive mass defect-based chemical tag, dimethyl pyrimidinyl ornithine (DiPyrO), that is compact in size, is suitable for various biological samples, and enables highly multiplexed quantification of peptides at the MS1 level without increasing mass spectral complexity. The DiPyrO tag structure incorporates heavy isotopes in a variety of configurations to impart as much as 45.3 mDa or as little as 5.8 mDa per tag between labeled peptides. Notably, peptides containing lysine are labeled with two tags, doubling the imparted mass defect to up to 90.6 mDa for the duplex tags and effectively reducing the resolving power requirement compared to previously reported mass defect-based quantification approaches. This permits current and previous generation LTQ-Orbitrap platforms to perform confident quantitative analyses of two DiPyrO-labeled samples at 100K resolving power, whereas 3-plex and 6-plex quantifications are possible at 240K and 480K resolving powers, respectively. In this work, we discuss the design and synthesis of the DiPyrO tag, characterize its effect on labeled proteome analysis by nanoLC-MS2, and demonstrate proof-of-principle applications of the duplex and triplex tags for quantitative proteomics using high-resolution MS acquisition on the Orbitrap Elite and Orbitrap Fusion Lumos.
Collapse
Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Amanda R Buchberger
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
7
|
Nišavić M, Hozić A, Hameršak Z, Radić M, Butorac A, Duvnjak M, Cindrić M. High-Efficiency Microflow and Nanoflow Negative Electrospray Ionization of Peptides Induced by Gas-Phase Proton Transfer Reactions. Anal Chem 2017; 89:4847-4854. [DOI: 10.1021/acs.analchem.6b04466] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marija Nišavić
- Vinča
Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Amela Hozić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Zdenko Hameršak
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Martina Radić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Ana Butorac
- BIOCentre, Central
Lab Services, Zagreb, Croatia
| | - Marija Duvnjak
- Faculty
of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Mario Cindrić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| |
Collapse
|
8
|
Chaudhury S, Ghosh P, Parveen S, Dasgupta S. Glycation of human γB-crystallin: A biophysical investigation. Int J Biol Macromol 2017; 96:392-402. [DOI: 10.1016/j.ijbiomac.2016.12.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/28/2022]
|
9
|
Ning Z, Star AT, Mierzwa A, Lanouette S, Mayne J, Couture JF, Figeys D. A charge-suppressing strategy for probing protein methylation. Chem Commun (Camb) 2016; 52:5474-7. [PMID: 27021271 DOI: 10.1039/c6cc00814c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methylation of arginine and lysine (RK) residues play essential roles in epigenetics and the regulation of gene expression. However, research in this area is often hindered by the lack of effective tools for probing the protein methylation. Here, we present an antibody-free strategy to capture protein methylation on RK residues by using chemical reactions to eliminate the charges on un-modified RK residues and peptide N-termini. Peptides containing methylated RK residues remain positively charged and are then enriched by strong cation exchange chromatography, followed by high-resolution mass spectrometry identification.
Collapse
Affiliation(s)
- Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Alexandra Therese Star
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Anna Mierzwa
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Janice Mayne
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| |
Collapse
|
10
|
Kuyama H, Yoshizawa AC, Nakajima C, Hosako M, Tanaka K. Identification of human basic fetoprotein as glucose-6-phosphate isomerase by using N- and C-terminal sequence tags and terminal tag database. J Pharm Biomed Anal 2015; 112:116-25. [PMID: 25978494 DOI: 10.1016/j.jpba.2015.04.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
Abstract
Human basic fetoprotein (BFP), found in fetal serum and tissue extracts as well as in extracts of various cancer tissues, has long been known as a marker protein for cancers; however, the primary sequence has not yet been reported. This paper describes the identification of BFP using the N- and C-terminal amino acid sequence tags (Ac-AALTRDPQFQ and QQREARVQ, respectively) clarified by mass spectrometry-based methods, and a terminal tag database (ProteinCarta). In this study, BFP was identified as glucose-6-phosphate isomerase (G6PI_HUMAN).
Collapse
Affiliation(s)
- Hiroki Kuyama
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan.
| | - Akiyasu C Yoshizawa
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan.
| | - Chihiro Nakajima
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Mutsumi Hosako
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| |
Collapse
|
11
|
Fernandez A, Drozdzecki A, Hoogewijs K, Vassileva V, Madder A, Beeckman T, Hilson P. The GLV6/RGF8/CLEL2 peptide regulates early pericycle divisions during lateral root initiation. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5245-56. [PMID: 26163695 PMCID: PMC4526922 DOI: 10.1093/jxb/erv329] [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] [Indexed: 05/18/2023]
Abstract
Small peptides of the Arabidopsis GLV/RGF/CLEL family are involved in different developmental programmes, including meristem maintenance and gravitropic responses. In addition, our previous report suggested that they also participate in the formation of lateral roots. Specifically, GLV6 is transcribed during the first stages of primordium development and GLV6 overexpression results in a strong reduction of emerged lateral roots. To investigate the cause of this phenotype we analysed primordium development in gain-of-function (gof) mutants and found that GLV6 induces supernumerary pericycle divisions, hindering the formation of a dome-shaped primordium, a prerequisite for successful emergence. The GLV6 phenotype could be reproduced by ectopic expression of the gene only in xylem-pole pericycle cells. Furthermore, GLV6 seems to function at the very beginning of lateral root initiation because GLV6 excess-either gene overexpression or peptide treatment-disrupts the first asymmetric cell divisions required for proper primordium formation. Our results suggest that GLV6 acts during lateral root initiation controlling the patterning of the first pericycle divisions.
Collapse
Affiliation(s)
- Ana Fernandez
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Andrzej Drozdzecki
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Kurt Hoogewijs
- Department of Organic Chemistry, Ghent University, 9000 Ghent, Belgium
| | - Valya Vassileva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Annemieke Madder
- Department of Organic Chemistry, Ghent University, 9000 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium. INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France. AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| |
Collapse
|
12
|
Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 397] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
Collapse
Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
| | | |
Collapse
|
13
|
Autofluorescence of MDA-modified proteins as an in vitro and in vivo probe in oxidative stress analysis. Protein Cell 2015; 5:484-7. [PMID: 24691907 PMCID: PMC4026423 DOI: 10.1007/s13238-014-0052-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|
14
|
A sensitive quantification of the peptide apidaecin 1 isoforms in single bee tissues using a weak cation exchange pre-separation and nanocapillary liquid chromatography coupled with mass spectrometry. J Chromatogr A 2014; 1374:134-144. [DOI: 10.1016/j.chroma.2014.11.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 11/10/2014] [Accepted: 11/14/2014] [Indexed: 11/20/2022]
|
15
|
Yuan L, Mai A, Aubry AF, Arnold ME, Ji QC. Feasibility assessment of a novel selective peptide derivatization strategy for sensitivity enhancement for the liquid chromatography/tandem mass spectrometry bioanalysis of protein therapeutics in serum. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:705-712. [PMID: 24573801 DOI: 10.1002/rcm.6836] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/07/2014] [Accepted: 01/12/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Sensitivity is one major challenge limiting the application of liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods for bioanalysis of proteins. A novel selective peptide derivatization (SPD) strategy was proposed to improve assay sensitivity. The main concept of the SPD strategy is to selectively derivatize surrogate peptides of the target protein in the digests, while not derivatizing the abundant background peptides, thereby improving the separation of target peptides during sample extraction and chromatography, and increasing the sensitivity. Additional benefits may help improve sensitivity include (1) increased ionization efficiency; (2) improved fragmentation pattern; and (3) increased sample extraction recovery of target peptides. METHODS Feasibility assessment of the SPD strategy was conducted using BMS-986012, a monoclonal antibody, as the model protein, and with malondialdehyde (MDA) to selectively derivatize the arginine-containing surrogate peptide SLIY in tryptic-digested monkey serum samples. RESULTS The decreased polarity and basicity of the MDA-derivatized peptide SLIY (MDA-SLIY) helped improve its separation from the background peptides during solid-phase extraction (SPE) and chromatography. The recovery of MDA-SLIY was 36.1-44.2%, which was ~3-fold higher than the recovery of peptide SLIY (11.9-16.1%). There was no significant ion suppression for MDA-SLIY. Overall, SPD improved the sensitivity ~5-fold. SPD methodology was then successfully applied to the development of a sensitive LC/MS/MS assay for BMS-986012 in monkey serum. CONCLUSIONS This work demonstrates the feasibility of the SPD strategy for sensitivity enhancement. SPD can provide a simple, cost-efficient, and antibody-free sample preparation approach to improve sensitivity.
Collapse
Affiliation(s)
- Long Yuan
- Bioanalytical Sciences, Analytical & Bioanalytical Development, Bristol-Myers Squibb, Princeton, NJ, 08543, USA
| | | | | | | | | |
Collapse
|
16
|
Shuford CM, Muddiman DC. Capitalizing on the hydrophobic bias of electrospray ionization through chemical modification in mass spectrometry-based proteomics. Expert Rev Proteomics 2014; 8:317-23. [DOI: 10.1586/epr.11.24] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
17
|
Comparison of retention behavior of oligolysine and oligoarginine in ion-pairing chromatography using heptafluorobutyric acid. Anal Bioanal Chem 2013; 405:9739-46. [DOI: 10.1007/s00216-013-7397-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 09/21/2013] [Accepted: 09/23/2013] [Indexed: 12/01/2022]
|
18
|
Taniguchi K, Kuyama H, Kajihara S, Tanaka K. MALDI mass spectrometry-based sequence analysis of arginine-containing glycopeptides: improved fragmentation of glycan and peptide chains by modifying arginine residue. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:951-960. [PMID: 23893643 DOI: 10.1002/jms.3241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/20/2013] [Accepted: 05/27/2013] [Indexed: 06/02/2023]
Abstract
This paper describes an improved method for the sequence analysis of Arg-containing glycopeptide by MALDI mass spectrometry (MS). The method uses amino group derivatization (4-aza-6-(2,6-dimethyl-1-piperidinyl)-5-oxohexanoic acid N-succinimidyl ester) and removal (carboxypeptidase B) or modification (peptidylarginine deiminase 4) of the arginine residue of the peptide. The derivatization attaches a basic tertiary amine moiety onto the peptides, and the enzymatic treatment removes or modifies the arginine residue. Fragmentation of the resulting glycopeptide under low-energy collision-induced dissociation yielded a simplified ion series of both the glycan and the peptide that can facilitate their sequencing. The feasibility of the method was studied using α1 -acid glycoprotein-derived N-linked glycopeptides, and glycan and peptide in each glycopeptide were successfully sequenced by MALDI tandem MS (MS/MS).
Collapse
Affiliation(s)
- Kenichi Taniguchi
- Koichi Tanaka Laboratory of Advanced Science and Technology (KTLAST), Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto, 604-8511, Japan
| | | | | | | |
Collapse
|
19
|
Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FCS, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V. HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions. Anal Chem 2013; 85:3515-20. [PMID: 23448308 DOI: 10.1021/ac303239g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide sequence matching algorithms used for peptide identification by tandem mass spectrometry (MS/MS) enumerate theoretical peptides from the database, predict their fragment ions, and match them to the experimental MS/MS spectra. Here, we present an approach for scoring MS/MS identifications based on the high mass accuracy matching of precursor ions, the identification of a high intensity b1 fragment ion, and partial sequence tags from phenylthiocarbamoyl-derivatized peptides. This derivatization process boosts the b1 fragment ion signal, which turns it into a powerful feature for peptide identification. We demonstrate the effectiveness of our scoring system by implementing it on a computational tool called "HI-bone" and by identifying mass spectra of an Escherichia coli sample acquired on an Orbitrap Velos instrument using Higher-energy C-trap dissociation. Following this strategy, we identified 1614 peptide spectrum matches with a peptide false discovery rate (FDR) below 1%. These results were significantly higher than those from Mascot and SEQUEST using a similar FDR.
Collapse
Affiliation(s)
- Yasset Perez-Riverol
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Cubanacán, Playa, Ciudad de la Habana, Cuba
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Mehranpour A, Hashemnia S, Azamifar F. Synthesis of new malonaldehyde derivatives using 2-heteroaryl-substituted trimethinium salts. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2012.11.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
21
|
Arsene CG, Schulze D, Kratzsch J, Henrion A. High sensitivity mass spectrometric quantification of serum growth hormone by amphiphilic peptide conjugation. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1554-1560. [PMID: 23280743 DOI: 10.1002/jms.3094] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 08/15/2012] [Accepted: 08/16/2012] [Indexed: 06/01/2023]
Abstract
Amphiphilic peptide conjugation affords a significant increase in sensitivity with protein quantification by electrospray-ionization mass spectrometry. This has been demonstrated for human growth hormone (GH) in serum using N-(3-iodopropyl)-N,N,N-dimethyloctylammonium iodide as derivatizing reagent. The signal enhancement achieved is up to a factor of 5-6 and enables extension of the applicable concentration range down to the very low concentrations (≤ 1.0 µg/L) as encountered with clinical glucose suppression tests for patients with acromegaly. The method has been validated using a set of serum samples spiked with known amounts of recombinant 22 kDa GH in the range of 0.48 to 7.65 µg/L. The coefficient of variation (CV) calculated based on the deviation of results from the expected concentrations was 3.5%. The limit of detection (LoD) was determined as 0.1 µg/L and the limit of quantification (LoQ) as 0.4 µg/L. The potential of the method as a tool in clinical practice has been demonstrated with patient samples of about 1 µg/L.
Collapse
Affiliation(s)
- Cristian G Arsene
- Physikalisch-Technische Bundesanstalt, D-38116, Braunschweig, Germany.
| | | | | | | |
Collapse
|
22
|
QIAO XQ, Wang R, ZHANG LH, YANG GL, ZHANG YK. Recent Advancement of Chemical Derivatization and Its Applications to High Sensitive Analysis of Peptide in Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2012. [DOI: 10.1016/s1872-2040(11)60560-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
23
|
Recent Advancements in the LC- and GC-Based Analysis of Malondialdehyde (MDA): A Brief Overview. Chromatographia 2012; 75:433-440. [PMID: 22593603 PMCID: PMC3336054 DOI: 10.1007/s10337-012-2237-1] [Citation(s) in RCA: 296] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 03/23/2012] [Indexed: 11/05/2022]
Abstract
Malondialdehyde (MDA) is an end-product of lipid peroxidation and a side product of thromboxane A2 synthesis. Moreover, it is not only a frequently measured biomarker of oxidative stress, but its high reactivity and toxicity underline the fact that this molecule is more than “just” a biomarker. Additionally, MDA was proven to be a mutagenic substance. Having said this, it is evident that there is a major interest in the highly selective and sensitive analysis of this molecule in various matrices. In this review, we will provide a brief overview of the most recent developments and techniques for the liquid chromatography (LC) and gas chromatography (GC)-based analysis of MDA in different matrices. While the 2-thiobarbituric acid assay still is the most prominent methodology for determining MDA, several advanced techniques have evolved, including GC–MS(MS), LC–MS(MS) as well as several derivatization-based strategies.
Collapse
|
24
|
Miyashita M, Hanai Y, Awane H, Yoshikawa T, Miyagawa H. Improving peptide fragmentation by N-terminal derivatization with high proton affinity. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1130-1140. [PMID: 21488112 DOI: 10.1002/rcm.4962] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
An improved method of de novo peptide sequencing based on mass spectrometry using novel N-terminal derivatization reagents with high proton affinity has been developed. The introduction of a positively charged group into the N-terminal amino group of a peptide is known to enhance the relative intensity of b-ions in product ion spectra, allowing the easy interpretation of the spectra. However, the physicochemical properties of charge derivatization reagents required for efficient fragmentation remain unclear. In this study, we prepared several derivatization reagents with high proton affinity, which are thought to be appropriate for peptide fragmentation under low-energy collision-induced dissociation (CID) conditions, and examined their usefulness in de novo peptide sequencing. Comparison of the effects on fragmentation among three derivatization reagents having a guanidino or an amidino moiety, which differ in proton affinity, clearly indicated that there was an optimal proton affinity for efficient fragmentation of peptides. Among reagents tested in this study, derivatization with 4-amidinobenzoic acid brought about the most effective fragmentation. This derivatization approach will offer a novel de novo peptide sequencing method under low-energy CID conditions.
Collapse
Affiliation(s)
- Masahiro Miyashita
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan. ‐u.ac.jp
| | | | | | | | | |
Collapse
|
25
|
Kulevich SE, Frey BL, Kreitinger G, Smith LM. Alkylating tryptic peptides to enhance electrospray ionization mass spectrometry analysis. Anal Chem 2010; 82:10135-42. [PMID: 21114270 PMCID: PMC3075559 DOI: 10.1021/ac1019792] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A major limitation of mass spectrometry-based proteomics is inefficient and differential ionization during electrospray ionization (ESI). This leads to problems such as increased limits of detection and incomplete sequence coverage of proteins. Incomplete sequence coverage is especially problematic for analyses that require the detection and identification of specific peptides from a protein, such as the analysis of post-translational modifications. We describe here the development and use of aldehyde-based chemistry for the alkylation of peptide primary amines to increase peptide hydrophobicity, providing increased ionization efficiency and concomitant signal enhancement. When employed to modify the peptide products of protein tryptic digests, increased sequence coverage is obtained from combined modified and unmodified digests. To evaluate the utility of alkylation of peptides for selected reaction monitoring (SRM) assays, we alkylated a peptide from the protein Oct4, known to play a role in regulating stem cell differentiation. Increased chromatographic retention and ionization efficiency is observed for the alkylated Oct4 peptide compared to its unmodified form.
Collapse
Affiliation(s)
- Suzanne E. Kulevich
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Brian L. Frey
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Gloria Kreitinger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| |
Collapse
|
26
|
Shuford CM, Comins DL, Whitten JL, Burnett JC, Muddiman DC. Improving limits of detection for B-type natriuretic peptide using PC-IDMS: an application of the ALiPHAT strategy. Analyst 2010; 135:36-41. [PMID: 20024179 PMCID: PMC3129710 DOI: 10.1039/b919484c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Hydrophobic tagging of biomolecules has been reported by our group and others to increase their ionization efficiency during electrospray ionization and facilitate their detection by mass spectrometry. As such, hydrophobic tagging should provide a viable method for augmenting MS-based quantification of low abundance proteins by decreasing their detection limits. Herein we have evaluated two commercial alkylation reagents and several newly synthesized hydrophobic alkylation reagents for their utility in quantifying B-type Natriuretic Peptide, a low abundance cardiac biomarker, by protein cleavage isotope dilution mass spectrometry. For the cysteine containing tryptic peptide evaluated, a approximately 3.5-fold decrease in the detection limit was observed for the best performing hydrophobic reagent, 2-iodo-N-octylacetamide, relative to the commonly used alkylation reagent, iodoacetamide. Additionally, we have evaluated the use of nonpolar surface areas as a metric for assessing the effectiveness of the alkylation reagents in improving ESI response.
Collapse
Affiliation(s)
- Christopher M. Shuford
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - Daniel L. Comins
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - Jerry L. Whitten
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - John C. Burnett
- Division for Cardiovascular Disease, Mayo Clinic College of Medicine, Rochester, Minnesota 55905
| | - David C. Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
| |
Collapse
|
27
|
Williams DK, Comins DL, Whitten JL, Muddiman DC. Evaluation of the ALiPHAT method for PC-IDMS and correlation of limits-of-detection with nonpolar surface area. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:2006-12. [PMID: 19734056 PMCID: PMC2763965 DOI: 10.1016/j.jasms.2009.07.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/24/2009] [Accepted: 07/31/2009] [Indexed: 05/12/2023]
Abstract
PC-IDMS experiments for two peptides, laminin nonapeptide and the N-terminal tryptic peptide of prostate specific antigen, were performed utilizing a variety of alkylating reagents. These experiments were conducted to investigate how hydrophobicity influences the limits-of-detection (LOD) by altering their electrospray ionization response. Nonpolar surface areas were calculated for both peptides and all alkylating reagents to provide an estimate of the hydrophobicity of the differently alkylated peptides. Decreases in LOD by 2-fold were observed for both peptides between the best and worst performing combination of alkylating reagent. However, while an increase in hydrophobicity was found to aid in decreasing LOD to an extent, beyond a certain hydrophobicity, we observed a decrease.
Collapse
Affiliation(s)
| | | | | | - David C. Muddiman
- Author for Correspondence David C. Muddiman, Ph.D. W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, Phone: 919-513-0084, Fax: 919-513-7993,
| |
Collapse
|
28
|
Optimizing the performance of tin dioxide microspheres for phosphopeptide enrichment. Anal Chim Acta 2009; 638:51-7. [DOI: 10.1016/j.aca.2009.01.063] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 01/29/2009] [Accepted: 01/30/2009] [Indexed: 01/10/2023]
|
29
|
Kuyama H, Sonomura K, Shima K, Nishimura O, Tsunasawa S. An improved method for de novo sequencing of arginine-containing, Nalpha-tris(2,4,6-trimethoxyphenyl)phosphonium-acetylated peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:2063-2072. [PMID: 18521828 DOI: 10.1002/rcm.3587] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An improved method for de novo sequencing of arginine-containing peptides modified with succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-Ac-OSu) is reported. A tagging reagent, TMPP-Ac-OSu, was introduced to improve the sequence analysis of peptides owing to the simplified fragmentation pattern. However, peptides containing arginine residues did not fragment efficiently even after TMPP-Ac modification at their N-termini. This report describes how fragmentation efficiency of TMPP-Ac-modified arginine-containing peptides was significantly improved by modifying the guanidino group on the side chain of arginine with acetylacetone.
Collapse
Affiliation(s)
- Hiroki Kuyama
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan.
| | | | | | | | | |
Collapse
|
30
|
Onofrejova L, Leitner A, Lindner W. Malondialdehyde tagging improves the analysis of arginine oligomers and arginine-containing dendrimers by HPLC-MS. J Sep Sci 2008; 31:499-506. [PMID: 18210380 DOI: 10.1002/jssc.200700485] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The selective modification of arginine residues by malondialdehyde (MDA) was used to improve the mass spectrometric analysis of arginine oligomers (Arg(x), x = 4, 6, 7, 8, 9) and an arginine-containing dendrimeric peptide. MDA tagging significantly increased the hydrophobicity of the arginine side-chain and resulted in improved retention in RP HPLC of the oligoarginines using formic acid as mobile phase additive. This avoided the use of TFA to generate sufficient retention, as TFA was shown to lead to a dramatically reduced sensitivity (up to ten-fold for Arg(8) and Arg(9)) as a result of the strong signal suppression by ion pairing with multiple basic residues. MDA modification of Arg oligomers not only resulted in improved detection sensitivity for most of the peptides studied (e. g., more than six-fold for Arg(7)), but also greatly enhanced the quality of MS/MS spectra, in line with previous results for other peptides. Furthermore, MDA modification helped to identify major side products in a sample of a dendrimeric peptide, a class of peptides that is typically difficult to analyze by MS.
Collapse
Affiliation(s)
- Lucia Onofrejova
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Waehringer Strasse 38, Vienna, Austria
| | | | | |
Collapse
|
31
|
Foettinger A, Melmer M, Leitner A, Lindner W. Reaction of the Indole Group with Malondialdehyde: Application for the Derivatization of Tryptophan Residues in Peptides. Bioconjug Chem 2007; 18:1678-83. [PMID: 17705413 DOI: 10.1021/bc070001h] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method for the selective modification of tryptophan residues based on the reaction of malondialdehyde with the indole nitrogen of the tryptophan side chain at acidic conditions is presented. The condensation reaction is quantitative and leads to a substituted acrolein moiety with a remaining reactive aldehyde group. As is shown, this group can be further converted to a hydrazone using hydrazide compounds, but if hydrazine or phenylhydrazine are used, release of the free indole group is observed upon cleavage of the substitution. Alternatively, secondary amines such as pyrrolidine may also act as cleavage reagents. This general reaction scheme has been adapted and optimized for the derivatization of tryptophan-containing peptides and small N-heterocyclic compounds. It serves as the basis of a reversible tagging scheme for Trp-peptides or molecules of interest carrying indole structures as it allows the specific attachment and removal of a reactive group that may be used for a variety of purposes such as affinity tagging.
Collapse
Affiliation(s)
- Alexandra Foettinger
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
| | | | | | | |
Collapse
|
32
|
Foettinger A, Leitner A, Lindner W. Selective Enrichment of Tryptophan-Containing Peptides from Protein Digests Employing a Reversible Derivatization with Malondialdehyde and Solid-Phase Capture on Hydrazide Beads. J Proteome Res 2007; 6:3827-34. [PMID: 17655347 DOI: 10.1021/pr0702767] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method for the selective enrichment of tryptophan-containing peptides from complex peptide mixtures such as protein digests is presented. It is based on the reversible reaction of tryptophan with malondialdehyde and trapping of the derivatized Trp-peptides on hydrazide beads via the free aldehyde group of the modified peptides. The peptides are subsequently recovered in their native form by specific cleavage reactions for further (mass spectrometric) analysis. The method was optimized and evaluated using a tryptic digest of a mixture of 10 model proteins, demonstrating a significant reduction in sample complexity while still allowing the identification of all proteins. The applicability of the tryptophan-specific enrichment procedure to complex biological samples is demonstrated for a total yeast cell lysate. Analysis of the processed fraction by 1D-LC-MS/MS confirms the specificity of the enrichment procedure, as more than 85% of the peptides recovered from the enrichment step contained tryptophan. The reduction in sample complexity also resulted in the identification of additional proteins in comparison to the untreated lysate.
Collapse
Affiliation(s)
- Alexandra Foettinger
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria
| | | | | |
Collapse
|
33
|
Leitner A, Foettinger A, Lindner W. Improving fragmentation of poorly fragmenting peptides and phosphopeptides during collision-induced dissociation by malondialdehyde modification of arginine residues. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:950-9. [PMID: 17539043 DOI: 10.1002/jms.1233] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Despite significant technological and methodological advancements in peptide sequencing by mass spectrometry, analyzing peptides that exhibit only poor fragmentation upon collision-induced dissociation (CID) remains a challenge. A major cause for unfavorable fragmentation is insufficient proton 'mobility' due to charge localization at strongly basic sites, in particular, the guanidine group of arginine. We have recently demonstrated that the conversion of the guanidine group of the arginine side chain by malondialdehyde (MDA) is a convenient tool to reduce the basicity of arginine residues and can have beneficial effects for peptide fragmentation. In the present work, we have focused on peptides that typically yield incomplete sequence information in CID-MS/MS experiments. Energy-resolved tandem MS experiments were carried out on angiotensins and arginine-containing phosphopeptides to study in detail the influence of the modification step on the fragmentation process. MDA modification dramatically improved the fragmentation behavior of peptides that exhibited only one or two dominant cleavages in their unmodified form. Neutral loss of phosphoric acid from phosphopeptides carrying phosphoserine and threonine residues was significantly reduced in favor of a higher abundance of fragment ions. Complementary experiments were carried out on three different instrumental platforms (triple-quadrupole, 3D ion trap, quadrupole-linear ion trap hybrid) to ascertain that the observation is a general effect.
Collapse
Affiliation(s)
- Alexander Leitner
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria.
| | | | | |
Collapse
|
34
|
Frahm JL, Bori ID, Comins DL, Hawkridge AM, Muddimana DC. Achieving Augmented Limits of Detection for Peptides with Hydrophobic Alkyl Tags. Anal Chem 2007; 79:3989-95. [PMID: 17477508 DOI: 10.1021/ac070558q] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The wide range of protein concentrations found in biological matrixes presents a formidable analytical challenge in proteomics experiments. It is predicted that low-abundance proteins are the likely clinically relevant targets in disease-based proteomics analyses. To effectively analyze low-abundance proteins by electrospray ionization mass spectrometry, limits of detection must be improved upon. Previous studies have demonstrated hydrophobicity is a main determinant of the electrospray ionization response. One would expect to improve the electrospray ionization response of a hydrophilic peptide by making it more hydrophobic, thus increasing the molecule's affinity for the surface of the electrospray droplet, thereby allowing the molecule to more effectively compete for charge. In this report, we demonstrate a strategy to increase the electrospray ionization response of cysteine-containing peptides with the addition of an octylcarboxyamidomethyl modification via alkylation chemistry, which we name the ALiPHAT strategy (augmented limits of detection for peptides with hydrophobic alkyl tags). We demonstrate the relative increase in electrospray ionization response of peptides with an octylcarboxyamidomethyl modification compared to carboxyamidomethyl-modified peptides upon LC-MS analysis. Furthermore, we show the octylcarboxyamidomethyl group does not fragment or undergo neutral loss during collision-induced dissociation. Collectively, our results demonstrate the feasibility of the octylcarboxyamidomethyl modification to improve limits of detection for cysteine-containing peptides.
Collapse
Affiliation(s)
- Jennifer L Frahm
- Department of Chemistry and W.M. Keck FT-ICR Mass Spectrometry Laboratory, North Carolina State University, Dabney Hall, Raleigh, North Carolina 27695-8204, USA
| | | | | | | | | |
Collapse
|
35
|
Leitner A, Lindner W. Chemistry meets proteomics: the use of chemical tagging reactions for MS-based proteomics. Proteomics 2007; 6:5418-34. [PMID: 16972287 DOI: 10.1002/pmic.200600255] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As proteomics matures from a purely descriptive to a function-oriented discipline of the life sciences, there is strong demand for novel methodologies that increase the depth of information that can be obtained from proteomic studies. MS has long played a central role for protein identification and characterization, often in combination with dedicated chemical modification reactions. Today, chemistry is helping to advance the field of proteomics in numerous ways. In this review, we focus on those methodologies that have a significant impact for the large-scale study of proteins and peptides. This includes approaches that allow the introduction of affinity tags for the enrichment of subclasses of peptides or proteins and strategies for in vitro stable isotope labeling for quantification purposes, among others. Particular attention is given to the study of PTMs where recent advancements have been promising, but many interesting targets are not yet being addressed.
Collapse
Affiliation(s)
- Alexander Leitner
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Vienna, Austria.
| | | |
Collapse
|