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Vasileva ID, Samgina TY, Meng Z, Zubarev RA, Lebedev AT. EThcD Benefits for the Sequencing Inside Intramolecular Disulfide Cycles of Amphibian Intact Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1979-1988. [PMID: 37525119 DOI: 10.1021/jasms.3c00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Disulfide bonds formed by a pair of cysteine residues in the peptides' backbone represent a certain problem for their sequencing by means of mass spectrometry. As a rule, in proteomics, disulfide bonds should be cleaved before the analysis followed by some sort of chemical derivatization. That step is time-consuming and may lead to losses of minor peptides of the analyzed mixtures due to incomplete reaction, adsorption on the walls of the vials, etc. Certain problems in the de novo top-down sequencing of amphibian skin peptides are caused by the C-terminal disulfide loop, called the Rana box. Its reduction with or without subsequent derivatization was considered to be an unavoidable step before mass spectrometry. In the present study, EThcD demonstrated its efficiency in sequencing intact disulfide-containing peptides without any preliminary derivatization. Applied to the secretion of three frog species, EThcD provided the full sequence inside the intramolecular disulfide cycle for all S-S-containing peptides found in the samples, with the only exception being diarginine species. Proteolytic fragments, which are shorter than the original peptides, were helpful in some cases. HCD should be mentioned as a complementary tool to the EThcD tool, being useful as a confirmation method for some sequence details.
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Affiliation(s)
- Irina D Vasileva
- Lomonosov Moscow State University, Department of Organic Chemistry, 119991 Moscow, Russia
| | - Tatiana Yu Samgina
- Lomonosov Moscow State University, Department of Organic Chemistry, 119991 Moscow, Russia
| | - Zhaowei Meng
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Albert T Lebedev
- Lomonosov Moscow State University, Department of Organic Chemistry, 119991 Moscow, Russia
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2
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Quick MM, Crittenden CM, Rosenberg JA, Brodbelt JS. Characterization of Disulfide Linkages in Proteins by 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry. Anal Chem 2018; 90:8523-8530. [PMID: 29902373 PMCID: PMC6050148 DOI: 10.1021/acs.analchem.8b01556] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Deciphering disulfide bond patterns in proteins remains a significant challenge. In the present study, interlinked disulfide bonds connecting peptide chains are homolytically cleaved with 193 nm ultraviolet photodissociation (UVPD). Analysis of insulin showcased the ability of UVPD to cleave multiple disulfide bonds and provide sequence coverage of the peptide chains in the same MS/MS event. For proteins containing more complex disulfide bonding patterns, an approach combining partial reduction and alkylation mitigated disulfide scrambling and allowed assignment of the array of disulfide bonds. The 4 disulfide bonds of lysozyme and the 19 disulfide bonds of serotransferrin were characterized through LC/UVPD-MS analysis of nonreduced and partially reduced protein digests.
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3
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Ciccimaro E, Ranasinghe A, D’Arienzo C, Xu C, Onorato J, Drexler DM, Josephs JL, Poss M, Olah T. Strategy to Improve the Quantitative LC-MS Analysis of Molecular Ions Resistant to Gas-Phase Collision Induced Dissociation: Application to Disulfide-Rich Cyclic Peptides. Anal Chem 2014; 86:11523-7. [DOI: 10.1021/ac502678y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Eugene Ciccimaro
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Asoka Ranasinghe
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Celia D’Arienzo
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Carrie Xu
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Joelle Onorato
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | | | - Jonathan L. Josephs
- ThermoFisher Scientific, 355 River
Oaks Parkway, San Jose, California 95134, United States
| | - Michael Poss
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Timothy Olah
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
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4
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Qu J, Young R, Page BJ, Shen X, Tata N, Li J, Duan X, Fallavollita JA, Canty JM. Reproducible ion-current-based approach for 24-plex comparison of the tissue proteomes of hibernating versus normal myocardium in swine models. J Proteome Res 2014; 13:2571-84. [PMID: 24697261 PMCID: PMC4015685 DOI: 10.1021/pr5000472] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Hibernating
myocardium is an adaptive response to repetitive myocardial
ischemia that is clinically common, but the mechanism of adaptation
is poorly understood. Here we compared the proteomes of hibernating
versus normal myocardium in a porcine model with 24 biological replicates.
Using the ion-current-based proteomic strategy optimized in this study
to expand upon previous proteomic work, we identified differentially
expressed proteins in new molecular pathways of cardiovascular interest.
The methodological strategy includes efficient extraction with detergent
cocktail; precipitation/digestion procedure with high, quantitative
peptide recovery; reproducible nano-LC/MS analysis on a long, heated
column packed with small particles; and quantification based on ion-current
peak areas. Under the optimized conditions, high efficiency and reproducibility
were achieved for each step, which enabled a reliable comparison of
24 the myocardial samples. To achieve confident discovery of differentially
regulated proteins in hibernating myocardium, we used highly stringent
criteria to define “quantifiable proteins”. These included
the filtering criteria of low peptide FDR and S/N > 10 for peptide
ion currents, and each protein was quantified independently from ≥2
distinct peptides. For a broad methodological validation, the quantitative
results were compared with a parallel, well-validated 2D-DIGE analysis
of the same model. Excellent agreement between the two orthogonal
methods was observed (R = 0.74), and the ion-current-based
method quantified almost one order of magnitude more proteins. In
hibernating myocardium, 225 significantly altered proteins were discovered
with a low false-discovery rate (∼3%). These proteins are involved
in biological processes including metabolism, apoptosis, stress response,
contraction, cytoskeleton, transcription, and translation. This provides
compelling evidence that hibernating myocardium adapts to chronic
ischemia. The major metabolic mechanisms include a down-regulation
of mitochondrial respiration and an increase in glycolysis. Meanwhile,
cardioprotective and cytoskeletal proteins are increased, while cardiomyocyte
contractile proteins are reduced. These intrinsic adaptations to regional
ischemia maintain long-term cardiomyocyte viability at the expense
of contractile function.
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Affiliation(s)
- Jun Qu
- Department of Pharmaceutical Sciences, ‡Department of Biochemistry, §Department of Medicine, ∥Department of Physiology and Biophysics, ⊥The Center for Research in Cardiovascular Medicine, and #Center for Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo , Buffalo, New York 14214, United States
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5
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Samgina TY, Vorontsov EA, Gorshkov VA, Artemenko KA, Zubarev RA, Ytterberg JA, Lebedev AT. Collision-induced dissociation fragmentation inside disulfide C-terminal loops of natural non-tryptic peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1037-1044. [PMID: 23633018 DOI: 10.1007/s13361-013-0632-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/27/2013] [Accepted: 03/27/2013] [Indexed: 06/02/2023]
Abstract
Collision-induced dissociation (CID) spectra of long non-tryptic peptides are usually quite complicated and rather difficult to interpret. Disulfide bond formed by two cysteine residues at C-terminus of frog skin peptides precludes one to determine sequence inside the forming loop. Thereby, chemical modification of S-S bonds is often used in "bottom up" sequencing approach. However, low-energy CID spectra of natural non-tryptic peptides with C-terminal disulfide cycle demonstrate an unusual fragmentation route, which may be used to elucidate the "hidden" C-terminal sequence. Low charge state protonated molecules experience peptide bond cleavage at the N-terminus of C-terminal cysteine. The forming isomeric acyclic ions serve as precursors for a series of b-type ions revealing sequence inside former disulfide cycle. The reaction is preferable for peptides with basic lysine residues inside the cycle. It may also be activated by acidic protons of Asp and Glu residues neighboring the loop. The observed cleavages may be quite competitive, revealing the sequence inside disulfide cycle, although S-S bond rupture does not occur in this case.
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Affiliation(s)
- Tatiana Y Samgina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russian Federation
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6
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Jackson CA, Yadav N, Min S, Li J, Milliman EJ, Qu J, Chen YC, Yu MC. Proteomic analysis of interactors for yeast protein arginine methyltransferase Hmt1 reveals novel substrate and insights into additional biological roles. Proteomics 2013; 12:3304-14. [PMID: 22997150 DOI: 10.1002/pmic.201200132] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 09/06/2012] [Accepted: 09/10/2012] [Indexed: 01/07/2023]
Abstract
Protein arginine methylation is a PTM catalyzed by an evolutionarily conserved family of enzymes called protein arginine methyltransferases (PRMTs), with PRMT1 being the most conserved member of this enzyme family. This modification has emerged to be an important regulator of protein functions. To better understand the role of PRMTs in cellular pathways and functions, we have carried out a proteomic profiling experiment to comprehensively identify the physical interactors of Hmt1, the budding yeast homolog for human PRMT1. Using a dual-enzymatic digestion linear trap quadrupole/Orbitrap proteomic strategy, we identified a total of 108 proteins that specifically copurify with Hmt1 by tandem affinity purification. A reverse coimmunoprecipitation experiment was used to confirm Hmt1's physical association with Bre5, Mtr4, Snf2, Sum1, and Ssd1, five proteins that were identified as Hmt1-specific interactors in multiple biological replicates. To determine whether the identified Hmt1-interactors had the potential to act as an Hmt1 substrate, we used published bioinformatics algorithms that predict the presence and location of potential methylarginines for each identified interactor. One of the top hits from this analysis, Snf2, was experimentally confirmed as a robust substrate of Hmt1 in vitro. Overall, our data provide a feasible proteomic approach that aid in the better understanding of PRMT1's roles within a cell.
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Affiliation(s)
- Christopher A Jackson
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York 14260, USA
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7
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Echterbille J, Quinton L, Gilles N, De Pauw E. Ion Mobility Mass Spectrometry as a Potential Tool To Assign Disulfide Bonds Arrangements in Peptides with Multiple Disulfide Bridges. Anal Chem 2013; 85:4405-13. [DOI: 10.1021/ac303686w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Julien Echterbille
- Laboratory of Mass Spectrometry,
GIGA-R, Department of Chemistry, University of Liege, Liege, Belgium
| | - Loïc Quinton
- Laboratory of Mass Spectrometry,
GIGA-R, Department of Chemistry, University of Liege, Liege, Belgium
| | - Nicolas Gilles
- iBiTec-S,
SIMOPRO, Commissariat à l’Energie Atomique, Gif-sur-Yvette,
France
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry,
GIGA-R, Department of Chemistry, University of Liege, Liege, Belgium
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8
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Duan X, Dai L, Chen SC, Balthasar JP, Qu J. Nano-scale liquid chromatography/mass spectrometry and on-the-fly orthogonal array optimization for quantification of therapeutic monoclonal antibodies and the application in preclinical analysis. J Chromatogr A 2012; 1251:63-73. [PMID: 22770385 DOI: 10.1016/j.chroma.2012.06.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/28/2012] [Accepted: 06/01/2012] [Indexed: 01/29/2023]
Abstract
Therapeutic monoclonal antibodies (mAbs) constitute a group of highly effective agents for treating various refractory diseases. Nonetheless it is challenging to achieve selective and accurate quantification of mAb in pharmaceutical matrices, which is required by PK studies. Liquid chromatography/mass spectrometry under selected reaction monitoring mode (LC/SRM-MS) is emerging as an attractive alternative to immunoassays because of the high specificity and multiplexing capacity it provides, but may fall short in terms of sensitivity, reliability and quantitative accuracy. Moreover, the strategy for optimization of the MS conditions for many candidates of signature peptides (SP) and the selection of the optimal SP for quantification remains elusive. In this study, we employed a suite of technical advances to overcome these difficulties, which include: (i) a nano-LC/SRM-MS approach to achieve high analytical sensitivity, (ii) a high-resolution nano-LC/LTQ/Orbitrap for confident identification of candidate peptides, (iii) an on-the-fly orthogonal array optimization (OAO) method for the high-throughput, accurate and reproducible optimization for numerous candidate peptides in a single LC/MS run without using synthesized peptides, (iv) a comprehensive evaluation of stability of candidates in matrix using the optimized SRM parameters, (v) the use of two unique SP for quantification of one mAb to gauge possible degradation/modification in biological system and thus enhancing data reliability (e.g. rejection of data if the deviation between the two SP is greater than 25%) and (vi) the utilization of purified target protein as the calibrator to eliminate the risk of severe negative biases that could occur when a synthesized peptide is used as calibrator. To show a proof of concept, this strategy is applied in the quantification of cT84.66, a chimeric, anti-CEA antibody, in preclinical mouse models. A low detection limit of the mAb down to 3.2 ng/mL was achieved, which is substantially more sensitive than established immunoassay methods for anti-CEA antibodies. The quantitative method showed good linearity (within the range of 12.9 ng/mL to 32.3 μg/mL in plasma), accuracy and precision. Additionally, the ultra-low sample consumption (2 μL plasma per preparation) permits the acquisition of an entire set of time course data from the same mouse, which represents a prominent advantage for PK study using small-animal models. The developed method enabled an accurate PK investigation of cT84.66 in mice following intravenous and subcutaneous administrations at relatively low doses over an extended period of time. The strategy employed in this study can be easily adapted to the sensitive and accurate analysis of other mAb and therapeutic proteins.
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Affiliation(s)
- Xiaotao Duan
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Lipeng Dai
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260, USA; Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Shang-Chiung Chen
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Joseph P Balthasar
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Jun Qu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA.
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9
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Krishnatry AS, Kamei T, Wang H, Qu J, Fung HL. Identification of nitroglycerin-induced cysteine modifications of pro-matrix metalloproteinase-9. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:2291-2298. [PMID: 21766372 DOI: 10.1002/rcm.5118] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nitroglycerin (NTG), an important cardiovascular agent, has been shown recently to activate matrix metalloproteinase-9 (MMP-9) in biological systems, possibly leading to destabilization of atherosclerotic plaques. The chemical mechanism for this activation, particularly on the cysteine switch of the pro-form of MMP-9 (proMMP-9), has not been investigated and was examined here using nano-flow liquid chromatography coupled to mass spectrometry. In order to obtain high sequence coverage, two orthogonal enzymes (trypsin and GluC) were employed to digest the protein in parallel. Two complementary activation methods, collision-induced dissociation (CID) and electron-transfer dissociation (ETD), were employed for the identification of various modifications. A high-resolution Orbitrap analyzer was used to enable confident identification. Incubation of NTG with proMMP-9 resulted in the formation of an unstable thionitrate intermediate and oxidation of the cysteine switch to sulfinic and irreversible sulfonic acid derivatives. The unstable thionitrate modification was confirmed by both CID and ETD in the proteolytic peptides produced by both trypsin and GluC. Incubation of proMMP-9 with diethylenetriamine NONOate (a nitric oxide donor) led to sulfonic acid formation, but no observable sulfinic acid modification. Extensive tyrosine nitration by NTG was observed at Tyr-262, in close proximity to an oxidized Cys-256 of proMMP-9. The intramolecular interaction between these two residues toward NTG-induced oxidation was examined using a synthesized peptide representing the sequence in this domain, PWCSTTANYDTDDR, and the modification status was compared against an analog in which Cys was substituted by Ala. We observed a thionitrate product, extensive Cys oxidative modifications and enhanced tyrosine nitration with the Cys peptide but not with the Ala analog. Our results indicated that neighboring Cys and Tyr residues can facilitate each other's oxidation in the presence of NTG.
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Affiliation(s)
- Anu Shilpa Krishnatry
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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