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Samgina TY, Mazur DM, Lebedev AT. Assessing the Efficacy of Protease Inactivation for the Preservation of Bioactive Amphibian Skin Peptides. Int J Mol Sci 2024; 25:8759. [PMID: 39201446 PMCID: PMC11354720 DOI: 10.3390/ijms25168759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/03/2024] [Accepted: 08/08/2024] [Indexed: 09/02/2024] Open
Abstract
The skin of amphibians is a rich source of peptides with a wide range of biological activities. They are stored in secretory granules in an inactive form. Upon stimulation, they are secreted together with proteases into the skin. Once activated, they rapidly exert their biological effects, including fighting microorganisms and predators, while their excess is immediately destroyed by the released proteases. To keep bioactive peptides in their initial form, it is necessary to inhibit these enzymes. Several inhibitors for this purpose have previously been mentioned; however, there has not been any reliable comparison of their efficiency so far. Here, we studied the efficiency of methanol and hydrochloric and formic acids, as well as phenylmethylsulfonyl fluoride, in the inhibition of nine frog peptides with the known sequence, belonging to five families in the secretion of Pelophylax esculentus. The results demonstrated that methanol had the highest inhibitory efficiency, while phenylmethylsulfonyl fluoride was the least efficient, probably due to its instability in aqueous media. Possible cleavages between certain amino acid residues in the sequence were established for each of the inhibitors. These results may be helpful for future studies on the nature of proteases and on prediction of the possible cleavage sites in novel peptides.
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Affiliation(s)
- Tatiana Yu. Samgina
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China; (T.Y.S.); (D.M.M.)
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitrii M. Mazur
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China; (T.Y.S.); (D.M.M.)
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Albert T. Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China; (T.Y.S.); (D.M.M.)
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
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Samgina TY, Vasileva ID, Trebše P, Torkar G, Surin AK, Meng Z, Zubarev RA, Lebedev AT. Tandem Mass Spectrometry de novo Sequencing of the Skin Defense Peptides of the Central Slovenian Agile Frog Rana dalmatina. Molecules 2023; 28:7118. [PMID: 37894596 PMCID: PMC10608968 DOI: 10.3390/molecules28207118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Peptides released on frogs' skin in a stress situation represent their only weapon against micro-organisms and predators. Every species and even population of frog possesses its own peptidome being appropriate for their habitat. Skin peptides are considered potential pharmaceuticals, while the whole peptidome may be treated as a taxonomic characteristic of each particular population. Continuing the studies on frog peptides, here we report the peptidome composition of the Central Slovenian agile frog Rana dalmatina population. The detection and top-down de novo sequencing of the corresponding peptides was conducted exclusively by tandem mass spectrometry without using any chemical derivatization procedures. Collision-induced dissociation (CID), higher energy collision-induced dissociation (HCD), electron transfer dissociation (ETD) and combined MS3 method EThcD with stepwise increase of HCD energy were used for that purpose. MS/MS revealed the whole sequence of the detected peptides including differentiation between isomeric Leu/Ile, and the sequence portion hidden in the disulfide cycle. The array of the discovered peptide families (brevinins 1 and 2, melittin-related peptides (MRPs), temporins and bradykinin-related peptides (BRPs)) is quite similar to that of R. temporaria. Since the genome of this frog remains unknown, the obtained results were compared with the recently published transcriptome of R. dalmatina.
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Affiliation(s)
- Tatiana Yu. Samgina
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Irina D. Vasileva
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Polonca Trebše
- Faculty of Health Sciences, University of Ljubljana Zdravstvena Pot 5, 1000 Ljubljana, Slovenia;
| | - Gregor Torkar
- Department for Biology, Chemistry and Home Economics, University of Ljubljana Faculty of Education, Kardeljeva Ploščad 16, 1000 Ljubljana, Slovenia;
| | - Alexey K. Surin
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, 142290 Moscow, Russia;
| | - Zhaowei Meng
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (Z.M.); (R.A.Z.)
| | - Roman A. Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (Z.M.); (R.A.Z.)
- The National Medical Research Center for Endocrinology, 115478 Moscow, Russia
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Albert T. Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
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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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Tolpina MD, Vasileva ID, Samgina TY. Modern Approaches in de novo Sequencing of Nontryptic Peptides of Ranid and Hylid Frogs by Means of Mass Spectrometry: A Review. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822130081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Samgina TY, Vasileva ID, Trebse P, Torkar G, Surin AK, Meng Z, Zubarev RA, Lebedev AT. Mass Spectrometry Differentiation between Rana arvalis Populations Based on Their Skin Peptidome Composition. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1480-1491. [PMID: 35820801 DOI: 10.1021/jasms.2c00084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Skin secretion of amphibians often represents the only weapon of these species against pathogens and predators. Peptides constitute the major portion of active molecules of that weapon and may be treated as potential pharmaceuticals for future generations. The first step of their efficient use involves establishing of their primary structure, i.e., sequencing. De novo sequencing by means of mass spectrometry was applied to Rana arvalis species, collected in the spring 2021 in Central Slovenia (vicinity of Ljubljana). HPLC-ESI-HRMS/MS with Orbitrap instruments was used to establish the skin peptidome of these species and compare it with the earlier identified skin peptidome of the Moscow population of Rana arvalis. Application of CID, HCD, ETD, and EThcD enabled detecting and sequencing 18 peptides; five of them were novel and may be treated as possible biomarkers of the Ljubljana population of Rana arvalis. Interestingly, representatives of two peptide families (temporins and brevinins 2) were not found in the Moscow population. MS3 modes, first of all EThcD, demonstrated their great potential in the de novo sequencing, including extraction of the sequence information from the intact peptides with disulfide cycle (rana box) in their structure and differentiation of isomeric Leu/Ile residues. Thus, all six isomeric residues were reliably distinguished in the novel melittin-related peptide AK-23-1. In addition, another post-translational modification dealing with carbonylation of the N-terminal Gly of novel temporin AVa was established using the MS3 mode. The obtained results demonstrate the efficiency of the use of MS3 tools in proteomics/peptidomics.
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Affiliation(s)
- Tatiana Yu Samgina
- Lomonosov Moscow State University, Department of Organic Chemistry, Moscow 119991 Russia
| | - Irina D Vasileva
- Lomonosov Moscow State University, Department of Organic Chemistry, Moscow 119991 Russia
| | - Polonca Trebse
- University of Ljubljana Faculty of Health Sciences, Zdravstvena pot 5, Ljubljana 1000 Slovenia
- MASSECO d.o.o. Erazmova 20, Postojna 6230, Slovenia
| | - Gregor Torkar
- University of Ljubljana Faculty of Education, Department for Biology, Chemistry and Home Economics, Kardeljeva ploščad 16, Ljubljana 1000 Slovenia
| | - Alexey K Surin
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow 142290, Russia
| | - Zhaowei Meng
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177 Sweden
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177 Sweden
| | - Albert T Lebedev
- Lomonosov Moscow State University, Department of Organic Chemistry, Moscow 119991 Russia
- MASSECO d.o.o. Erazmova 20, Postojna 6230, Slovenia
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Lebedev AT, Vasileva ID, Samgina TY. FT-MS in the de novo top-down sequencing of natural nontryptic peptides. MASS SPECTROMETRY REVIEWS 2022; 41:284-313. [PMID: 33347655 DOI: 10.1002/mas.21678] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
The present review covers available results on the application of FT-MS for the de novo sequencing of natural peptides of various animals: cones, bees, snakes, amphibians, scorpions, and so forth. As these peptides are usually bioactive, the animals efficiently use them as a weapon against microorganisms or higher animals including predators. These peptides represent definite interest as drugs of future generations since the mechanism of their activity is completely different in comparison with that of the modern antibiotics. Utilization of those peptides as antibiotics can eliminate the problem of the bacterial resistance development. Sequence elucidation of these bioactive peptides becomes even more challenging when the species genome is not available and little is known about the protein origin and other properties of those peptides in the study. De novo sequencing may be the only option to obtain sequence information. The benefits of FT-MS for the top-down peptide sequencing, the general approaches of the de novxxo sequencing, the difficult cases involving sequence coverage, isobaric and isomeric amino acids, cyclization of short peptides, the presence of posttranslational modifications will be discussed in the review.
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Affiliation(s)
- Albert T Lebedev
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Irina D Vasileva
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Y Samgina
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
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Samgina TY, Vasileva ID, Kovalev SV, Trebse P, Torkar G, Surin AK, Zubarev RA, Lebedev AT. Differentiation of Central Slovenian and Moscow populations of Rana temporaria frogs using peptide biomarkers of temporins family. Anal Bioanal Chem 2021; 413:5333-5347. [PMID: 34235566 DOI: 10.1007/s00216-021-03506-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022]
Abstract
Skin secretion represents the only means of defense for the majority of frog species. That phenomenon is based on the fact that the main components of the secretion are peptides demonstrating greatly varying types of bioactivity. They fulfill regulatory functions, fight microorganisms and may be even helpful against predators. These peptides are considered to be rather promising pharmaceuticals of future generation as according to the present knowledge microorganisms are unlikely to develop resistance to them. Mass spectrometry sequencing of these peptides is the most efficient first step of their study providing reliably their primary structures, i.e., amino acids sequence and S-S bond motif. Besides discovering new bioactive peptides, mass spectrometry appears to be an efficient tool of taxonomy studies, allowing for distinguishing not only between closely related species, but also between populations of the same species. Application of several tandem mass spectrometry tools (CID, HCD, ETD, EThcD) available with Orbitrap mass analyzer allowed us to obtain full sequence of about 60 peptides in the secretion of Slovenian population of brown ranid frog Rana temporaria. The problem of sequence inside C-terminal cycle formed by two Cys and differentiation of isomeric Leu and Ile residues was done in top-down mode without any derivatization steps. Besides general biomarkers of Rana temporaria species, Central Slovenian population of Rana temporaria demonstrates six novel temporins and one brevinin 1, which may be treated as biomarkers of that population.
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Affiliation(s)
- T Yu Samgina
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia.
| | - I D Vasileva
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - S V Kovalev
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - P Trebse
- University of Ljubljana Faculty of Health Sciences, Zdravstvena pot 5, 1000, Ljubljana, Slovenia
| | - G Torkar
- Department for Biology, Chemistry and Home Economics, University of Ljubljana Faculty of Education, Kardeljeva ploščad 16, 1000, Ljubljana, Slovenia
| | - A K Surin
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow, 142290, Russia
| | - R A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, 17177, Stockholm, Sweden.,Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
| | - A T Lebedev
- Department of Organic Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia.
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Samgina TY, Tolpina MD, Surin AK, Kovalev SV, Bosch RA, Alonso IP, Garcia FA, Gonzalez Lopez LJ, Lebedev AT. Manual mass spectrometry de novo sequencing of the anionic host defense peptides of the Cuban Treefrog Osteopilus septentrionalis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9061. [PMID: 33527491 DOI: 10.1002/rcm.9061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE Host defense peptides accumulated in the skin glands of the animals constitute the basis of the adaptive and immune system of amphibians. The peptidome of the Cuban frog Osteopilus septentrionalis was established using tandem mass spectrometry as the best analytical tool to elucidate the sequence of these peptides. METHODS Manual interpretation of complementary collision-induced dissociation (CID), higher energy collision-induced dissociation (HCD), and electron transfer dissociation (ETD) tandem mass spectra recorded with an Orbitrap Elite mass spectrometer in liquid chromatography/mass spectrometry (LC/MS) mode was used to sequence the peptide components of the frog skin secretion, obtained by mild electrostimulation. RESULTS Although the vast majority of amphibian peptides discovered so far are cationic, surprisingly only anionic peptides were identified in the skin secretion of the Cuban frog Osteopilus septentrionalis. Mass spectrometry allowed the sequences to be established of 16 representatives of new peptide families: septenins 1 and septenins 2. The highest sequence coverage when dealing with these anionic peptides was obtained with CID normalized collision energy 35 and HCD normalized collision energy 28. CONCLUSIONS Mirror-symmetrical peptides are sequenced using N-terminal acetylation. Acetylated Ser is reliably distinguished from isomeric Glu by the loss of ketene from b-ions containing the corresponding residue. Calculations of the physicochemical and structural properties of the discovered anionic septenins 1 and 2 allowed the mechanism of their interaction with microbe cells to be postulated.
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Affiliation(s)
- Tatiana Y Samgina
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Maria D Tolpina
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Alexey K Surin
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow, 142290, Russia
| | - Sergey V Kovalev
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Roberto Alonso Bosch
- Museum of Natural History "Felipe Poey", Faculty of Biology, University of Havana, Havana, Cuba
| | - Isel Pascual Alonso
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | | | - Luis Javier Gonzalez Lopez
- Mass Spectrometry Laboratory, Department of Proteomics, Center for Genetic Engineering and Biotechnology, PO Box 6162, Havana, Cuba
| | - Albert T Lebedev
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
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Konovalov AI, Antipin IS, Burilov VA, Madzhidov TI, Kurbangalieva AR, Nemtarev AV, Solovieva SE, Stoikov II, Mamedov VA, Zakharova LY, Gavrilova EL, Sinyashin OG, Balova IA, Vasilyev AV, Zenkevich IG, Krasavin MY, Kuznetsov MA, Molchanov AP, Novikov MS, Nikolaev VA, Rodina LL, Khlebnikov AF, Beletskaya IP, Vatsadze SZ, Gromov SP, Zyk NV, Lebedev AT, Lemenovskii DA, Petrosyan VS, Nenaidenko VG, Negrebetskii VV, Baukov YI, Shmigol’ TA, Korlyukov AA, Tikhomirov AS, Shchekotikhin AE, Traven’ VF, Voskresenskii LG, Zubkov FI, Golubchikov OA, Semeikin AS, Berezin DB, Stuzhin PA, Filimonov VD, Krasnokutskaya EA, Fedorov AY, Nyuchev AV, Orlov VY, Begunov RS, Rusakov AI, Kolobov AV, Kofanov ER, Fedotova OV, Egorova AY, Charushin VN, Chupakhin ON, Klimochkin YN, Osyanin VA, Reznikov AN, Fisyuk AS, Sagitullina GP, Aksenov AV, Aksenov NA, Grachev MK, Maslennikova VI, Koroteev MP, Brel’ AK, Lisina SV, Medvedeva SM, Shikhaliev KS, Suboch GA, Tovbis MS, Mironovich LM, Ivanov SM, Kurbatov SV, Kletskii ME, Burov ON, Kobrakov KI, Kuznetsov DN. Modern Trends of Organic Chemistry in Russian Universities. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2018. [DOI: 10.1134/s107042801802001x] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Samgina TY, Kovalev SV, Tolpina MD, Trebse P, Torkar G, Lebedev AT. EThcD Discrimination of Isomeric Leucine/Isoleucine Residues in Sequencing of the Intact Skin Frog Peptides with Intramolecular Disulfide Bond. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:842-852. [PMID: 29299834 DOI: 10.1007/s13361-017-1857-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/19/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Our scientific interests involve de novo sequencing of non-tryptic natural amphibian skin peptides including those with intramolecular S-S bond by means of exclusively mass spectrometry. Reliable discrimination of the isomeric leucine/isoleucine residues during peptide sequencing by means of mass spectrometry represents a bottleneck in the workflow for complete automation of the primary structure elucidation of these compounds. MS3 is capable of solving the problem. Earlier we demonstrated the advanced efficiency of ETD-HCD method to discriminate Leu/Ile in individual peptides by consecutive application of ETD to the polyprotonated peptides followed by HCD applied to the manually selected primary z-ions with the targeted isomeric residues at their N-termini and registration of the characteristic w-ions. Later this approach was extended to deal with several (4-7) broad band mass ranges, without special isolation of the primary z-ions. The present paper demonstrates an advanced version of this method when EThcD is applied in the whole mass range to a complex mixture of natural non-tryptic peptides without their separation and intermediate isolation of the targeted z-ions. The proposed EThcD method showed over 81% efficiency for the large natural peptides with intact disulfide ring, while the interfering process of radical site migration is suppressed. Due to higher speed and sensitivity, the proposed EThcD approach facilitates the analytical procedure and allows for the automation of the entire experiment and data processing. Moreover, in some cases it gives a chance to establish the nature of the residues in the intact intramolecular disulfide loops. Graphical Abstract ᅟ.
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Affiliation(s)
- Tatiana Yu Samgina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Sergey V Kovalev
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Miriam D Tolpina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Polonca Trebse
- Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Torkar
- Faculty of Education, University of Ljubljana, Ljubljana, Slovenia
| | - Albert T Lebedev
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia.
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Kovalyov SV, Zhokhov SS, Onoprienko LV, Vaskovsky BV, Lebedev AT. Exploration of doubtful cases of leucine and isoleucine discrimination in mass spectrometric peptide sequencing by electron-transfer and higher-energy collision dissociation-based method. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:376-384. [PMID: 29183199 DOI: 10.1177/1469066717730705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Electron-transfer dissociation (ETD) and electron-transfer and higher-energy collision dissociation (EThcD) spectra of short tryptic peptides with leucine/isoleucine residues in neighboring positions demonstrate intensive w-ions. On the contrary, u-ions possess very low intensities (if present at all). Therefore radical site migration is negligible in the applied conditions while ETD (EThcD) spectra allow for the reliable discrimination of the isomeric residues in the sequencing process. The presence of a fragment ion 43.055 mass units lower than z2-ion of peptides with IK sequence at their C-termini was shown to be a result of alternative fragmentation starting from the loss of propylammonium ion from the doubly protonated peptide molecule and formation of an oxazole fragment ion.
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Affiliation(s)
- Sergey V Kovalyov
- 1 Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Sergey S Zhokhov
- 1 Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Ludmila V Onoprienko
- 2 Shemyakin-Ovchinnikov Insitiute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Boris V Vaskovsky
- 2 Shemyakin-Ovchinnikov Insitiute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Albert T Lebedev
- 1 Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
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Zhokhov SS, Kovalyov SV, Samgina TY, Lebedev AT. An EThcD-Based Method for Discrimination of Leucine and Isoleucine Residues in Tryptic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1600-1611. [PMID: 28447219 DOI: 10.1007/s13361-017-1674-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/18/2017] [Accepted: 03/20/2017] [Indexed: 06/07/2023]
Abstract
An EThcD-based approach for the reliable discrimination of isomeric leucine and isoleucine residues in peptide de novo sequencing procedure has been proposed. A multistage fragmentation of peptide ions was performed with Orbitrap Elite mass spectrometer in electrospray ionization mode. At the first stage, z-ions were produced by ETD or ETcaD fragmentation of doubly or triply charged peptide precursor ions. These primary ions were further fragmented by HCD with broad-band ion isolation, and the resulting w-ions showed different mass for leucine and isoleucine residues. The procedure did not require manual isolation of specific z-ions prior to HCD stage. Forty-three tryptic peptides (3 to 27 residues) obtained by trypsinolysis of human serum albumin (HSA) and gp188 protein were analyzed. To demonstrate a proper solution for radical site migration problem, three non-tryptic peptides were also analyzed. A total of 93 leucine and isoleucine residues were considered and 83 of them were correctly identified. The developed approach can be a reasonable substitution for additional Edman degradation procedure, which is still used in peptide sequencing for leucine and isoleucine discrimination. Graphical Abstract ᅟ.
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Affiliation(s)
- Sergey S Zhokhov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1 Bld. 3, 119991, Moscow, Russia
| | - Sergey V Kovalyov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1 Bld. 3, 119991, Moscow, Russia
| | - Tatiana Yu Samgina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1 Bld. 3, 119991, Moscow, Russia
| | - Albert T Lebedev
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1 Bld. 3, 119991, Moscow, Russia.
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Samgina TY, Artemenko KA, Bergquist J, Trebse P, Torkar G, Tolpina MD, Lebedev AT. Differentiation of frogs from two populations belonging to the Pelophylax esculentus complex by LC-MS/MS comparison of their skin peptidomes. Anal Bioanal Chem 2016; 409:1951-1961. [PMID: 28012108 DOI: 10.1007/s00216-016-0143-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/22/2016] [Accepted: 12/09/2016] [Indexed: 12/27/2022]
Abstract
LC-MS/MS was applied to establish the composition of the skin peptidome of a Slovenian green frog belonging to the Pelophylax esculentus complex. As this was similar to the peptidome of the Moscow population of Pelophylax ridibundus, it allowed us to identify the Slovenian frog from the Pelophylax esculentus complex as Pelophylax ridibundus. The sequences of six new peptides from the brevinin 2 family are reported for the first time on the basis of manual interpretation of their tandem mass spectra. The structural similarity of the brevinin 2 peptides from the Moscow and Slovenian populations of Pelophylax ridibundus enables peptides from this family to be utilized as biomarkers for Pelophylax ridibundus inter- and intraspecies differentiation, and the proposed approach can be used as an analytical tool for differentiating the corresponding species and populations. The potential biological activities of the novel peptides were estimated by 2D mass mapping. The results allowed us to classify all of the available peptides belonging to the brevinin 2 family. Graphical Abstract Intraspecies identification within the green frog complex.
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Affiliation(s)
- Tatiana Yu Samgina
- Department of Chemistry, Moscow State University, Leninskie Gori 1/3, 119991, Moscow, Russian Federation
| | - Konstantin A Artemenko
- Department of Chemistry-Biomedical Center, Analytical Chemistry, Uppsala University, Uppsala, 75124, Sweden
| | - Jonas Bergquist
- Department of Chemistry-Biomedical Center, Analytical Chemistry, Uppsala University, Uppsala, 75124, Sweden
| | - Polonca Trebse
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, 1000, Ljubljana, Slovenia
| | - Gregor Torkar
- Faculty of Education, University of Ljubljana, Kardeljeva ploščad 16, 1000, Ljubljana, Slovenia
| | - Miriam D Tolpina
- Department of Chemistry, Moscow State University, Leninskie Gori 1/3, 119991, Moscow, Russian Federation
| | - Albert T Lebedev
- Department of Chemistry, Moscow State University, Leninskie Gori 1/3, 119991, Moscow, Russian Federation.
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Samgina TY, Tolpina MD, Trebse P, Torkar G, Artemenko KA, Bergquist J, Lebedev AT. LTQ Orbitrap Velos in routine de novo sequencing of non-tryptic skin peptides from the frog Rana latastei with traditional and reliable manual spectra interpretation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:265-276. [PMID: 27071218 DOI: 10.1002/rcm.7436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RATIONALE Mass spectrometry has shown itself to be the most efficient tool for the sequencing of peptides. However, de novo sequencing of novel natural peptides is significantly more challenging in comparison with the same procedure applied for the tryptic peptides. To reach the goal in this case it is essential to select the most efficient methods of triggering fragmentation and combine all the possible complementary techniques. METHODS Collision-induced dissociation (CID), high-energy collision dissociation (HCD), and electron-transfer dissociation (ETD) tandem mass spectra recorded with a LTQ Orbitrap Velos instrument were used for the elucidation of the sequence of the natural non-tryptic peptides from the skin secretion of Rana latastei. Manual interpretation of the spectra was applied. RESULTS The combined approach using CID, HCD, and ETD tandem mass spectra of the multiprotonated peptides in various charge states, as well as of their proteolytic fragments, allowed the sequences of seven novel peptides from the skin secretion of Rana latastei to be established. CONCLUSIONS Manual mass spectrometry sequencing of natural non-tryptic peptides from the skin secretion of Rana latastei provided the opportunity to work successfully with these species and demonstrated once again its advantage over automatic approaches.
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Samgina TY, Vorontsov EA, Gorshkov VA, Artemenko KA, Zubarev RA, Lebedev AT. Mass spectrometric de novo sequencing of natural non-tryptic peptides: comparing peculiarities of collision-induced dissociation (CID) and high energy collision dissociation (HCD). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2595-2604. [PMID: 25366406 DOI: 10.1002/rcm.7049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE Mass spectrometry has shown itself as the most efficient tool for the sequencing of peptides. However, de novo sequencing of novel natural peptides is significantly more challenging in comparison with the same procedure applied for the tryptic peptides. To reach the goal in this case it is essential to select the most useful methods of triggering fragmentation and combine complementary techniques. METHODS Comparison of low-energy collision-induced dissociation (CID) and higher energy collision-induced dissociation (HCD) modes for sequencing of the natural non-tryptic peptides with disulfide bonds and/or several proline residues in the backbone was achieved using an LTQ FT Ultra Fourier transform ion cyclotron resonance (FTICR) mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) equipped with a 7 T magnet and an LTQ Orbitrap Velos ETD (Thermo Fisher Scientific, Bremen, Germany) instrument. Peptide fractions were obtained by high-performance liquid chromatography (HPLC) separation of frog skin secretion samples from ten species of Rana temporaria, caught in the Kolomna district of Moscow region (Russia). RESULTS HCD makes the b/y series longer and more pronounced, thus increasing sequence coverage. Fragment ions due to cleavages at the C-termini of proline residues make the sequencing more reliable and may be used to detect missed cleavages in the case of tryptic peptides. Another HCD peculiarity involves formation of pronounced inner fragment ions (secondary y(n)b(m) ion series formed from the abundant primary y-ions). Differences in de novo sequencing of natural non-tryptic peptides with CID and HCD, involving thorough manual expert interpretation of spectra and two automatic sequencing algorithms, are discussed. CONCLUSIONS Although HCD provides better results, a combination of CID and HCD data may notably increase reliability of de novo sequencing. Several pairs of b2 /a2 -ions may be formed in HCD, complicating the spectra. Automatic de novo sequencing with the available programs remains less efficient than the manual one, independently of the collision energy.
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Affiliation(s)
- Tatyana Yu Samgina
- Department of Chemistry, Moscow State University, Russian Federation, 119991, Leninskie Gory 1/3, Moscow, Russia
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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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Zaikin VG, Sysoev AA. Review: mass spectrometry in Russia. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2013; 19:399-452. [PMID: 24378462 DOI: 10.1255/ejms.1248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The present review covers the main research in the area of mass spectrometry from the 1990s which was about the same time as the Russian Federation emerged from the collapse of the Soviet Union (USSR). It consists of two main parts-application of mass spectrometry to chemistry and related fields and creation and development of mass spectrometric technique. Both traditional and comparatively new mass spectrometric methods were used to solve various problems in organic chemistry (reactivity of gas-phase ions, structure elucidation and problems of identification, quantitative and trace analysis, differentiation of stereoisomers, derivatization approaches etc.), biochemistry (proteomics and peptidomics, lipidomics), medical chemistry (mainly the search of biomarkers, pharmacology, doping control), environmental, petrochemistry, polymer chemistry, inorganic and physical chemistry, determination of natural isotope ratio etc. Although a lot of talented mass spectrometrists left Russia and moved abroad after the collapse of the Soviet Union, the vitality of the mass spectral community proved to be rather high, which allowed the continuation of new developments in the field of mass spectrometric instrumentation. They are devoted to improvements in traditional magnetic sector mass spectrometers and the development of new ion source types, to analysis and modification of quadrupole, time-of-flight (ToF) and ion cyclotron resonance (ICR) analyzers. The most important achievements are due to the creation of multi-reflecting ToF mass analyzers. Special attention was paid to the construction of compact mass spectrometers, particularly for space exploration, of combined instruments, such as ion mobility spectrometer/mass spectrometer and accelerating mass spectrometers. The comparatively young Russian Mass Spectrometry Society is working hard to consolidate the mass spectrometrists from Russia and foreign countries, to train young professionals on new appliances and regularly holds conferences on mass spectrometry. For ten years, a special journal Mass-spektrometria has published papers on all disciplines of mass spectrometry.
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Affiliation(s)
- Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky prospect 29, 119991 Moscow, Russian Federation.
| | - Alexander A Sysoev
- National Research Nuclear University MEPhI, Kashirskoe Shosse 31, 115409 Moscow, Russian Federation
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Samgina TY, Vorontsov EA, Gorshkov VA, Artemenko KA, Nifant'ev IE, Kanawati B, Schmitt-Kopplin P, Zubarev RA, Lebedev AT. Novel cysteine tags for the sequencing of non-tryptic disulfide peptides of anurans: ESI-MS study of fragmentation efficiency. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2246-2255. [PMID: 21979873 DOI: 10.1007/s13361-011-0247-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 05/31/2023]
Abstract
Mass spectrometry faces considerable difficulties in de novo sequencing of long non-tryptic peptides with S-S bonds. Long disulfide-containing peptides brevinins 1E and 2Ec from frog Rana ridibunda were reduced and alkylated with nine novel and three known derivatizing agents. Eight of the novel reagents are maleimide derivatives. Modified samples were subjected to MS/MS studies on FT-ICR and Orbitrap mass spectrometers using CAD/HCD or ECD/ETD techniques. Procedures, fragmentation patterns, and sequence coverage for two peptides modified with 12 tags are described. ECD/ETD and CAD fragmentation revealed complementary sequence information. Higher-energy collisionally activated dissociation (HCD) sufficiently enhanced y-ions formation for brevinin 1E, but not for brevinin 2Ec. Some novel tags [N-benzylmaleimide, N-(2,6-dimethylphenyl)maleimide] along with known N-phenylmaleimide and iodoacetic acid showed high total sequence coverage taking into account combined ETD and HCD fragmentation. Moreover, modification of long (34 residues) brevinin 2Ec with N-benzylmaleimide or N-(2,6-dimethylphenyl)maleimide yielded high sequence coverage and full C-terminal sequence determination with ECD alone.
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Affiliation(s)
- Tatyana Y Samgina
- Department of Chemistry, Moscow State University, Russian Federation, 119991 Leninskie Gory 1/3, Moscow, Russia
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Samgina TY, Gorshkov VA, Vorontsov YA, Artemenko KA, Ogourtsov SV, Zubarev RA, Lebedev AT. Investigation of skin secretory peptidome of Rana lessonae frog by mass spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1134/s1061934811130120] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Vorontsov EA, Samgina TY, Gorshkov VA, Poljakov NB, Nifant'ev IE, Lebedev AT. Matrix-assisted laser desorption/ionization-post source decay fragmentation of cystine- containing amphibian peptides with novel cysteine tags. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2011; 17:73-83. [PMID: 21625031 DOI: 10.1255/ejms.1110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Long disulphide-containing peptides brevinins 1E and 2Ec from the skin secretion of the frog Rana ridibunda were reduced and alkylated with ten novel and three known derivatizing agents. Nine of novel reagents are maleimide derivatives. The peptides were also reduced with DTT directly onto the MALDI target without alkylation. Modified samples were subjected to MALDI-PSD study. Procedures, fragmentation patterns, fragment ion signal abundances and sequence coverage for two peptides modified with thirteen tags (or on-plate reduced) are described. The fast on-plate procedure for reduction/alkylation was applied to Rana ridibunda crude secretion, providing intensive signals of derivatized peptides. The corresponding ions may be used for the MS/MS sequencing procedure.
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Samgina TY, Gorshkov VA, Vorontsov EA, Bagrov VV, Nifant’ev IE, Lebedev AT. New cysteine-modifying reagents: Efficiency of derivatization and influence on the signals of the protonated molecules of disulfide-containing peptides in matrix-assisted laser desorption/ionization mass spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1134/s1061934810130034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Analysis of intact proteins by tandem mass spectrometry has mostly been confined to high-end mass spectrometry platforms. This protocol describes the application of routine HPLC to separate proteins, MALDI-ToF mass spectrometry to interrogate intact protein species and electron transfer dissociation/proton transfer reaction within a quadrupole ion trap to perform tandem mass spectrometry.
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Affiliation(s)
- Sarah R Hart
- Michael Barber Centre for Mass Spectrometry, University of Manchester, Manchester, UK
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Voinov VG, Beckman JS, Deinzer ML, Barofsky DF. Electron-capture dissociation (ECD), collision-induced dissociation (CID) and ECD/CID in a linear radio-frequency-free magnetic cell. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3028-30. [PMID: 19685479 PMCID: PMC3057201 DOI: 10.1002/rcm.4209] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- Valery G. Voinov
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
- Pacific Institute of Bioorganic Chemistry, Vladivostok 690022, Russia
- Correspondence to: V. G. Voinov, Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA.
| | - Joseph S. Beckman
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | - Max L. Deinzer
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
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Artemenko KA, Zubarev AR, Samgina TY, Lebedev AT, Savitski MM, Zubarev RA. Two Dimensional Mass Mapping as a General Method of Data Representation in Comprehensive Analysis of Complex Molecular Mixtures. Anal Chem 2009; 81:3738-45. [DOI: 10.1021/ac802532j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Konstantin A. Artemenko
- Division of Molecular Biometry, Institute for Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, Department of Organic Chemistry, Moscow State University, Moscow, Russia, and Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Alexander R. Zubarev
- Division of Molecular Biometry, Institute for Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, Department of Organic Chemistry, Moscow State University, Moscow, Russia, and Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Tatiana Yu Samgina
- Division of Molecular Biometry, Institute for Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, Department of Organic Chemistry, Moscow State University, Moscow, Russia, and Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Albert T. Lebedev
- Division of Molecular Biometry, Institute for Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, Department of Organic Chemistry, Moscow State University, Moscow, Russia, and Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Mikhail M. Savitski
- Division of Molecular Biometry, Institute for Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, Department of Organic Chemistry, Moscow State University, Moscow, Russia, and Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Roman A. Zubarev
- Division of Molecular Biometry, Institute for Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, Department of Organic Chemistry, Moscow State University, Moscow, Russia, and Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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Samgina TY, Artemenko KA, Gorshkov VA, Ogourtsov SV, Zubarev RA, Lebedev AT. De novo sequencing of peptides secreted by the skin glands of the Caucasian Green Frog Rana ridibunda. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:3517-3525. [PMID: 18855342 DOI: 10.1002/rcm.3759] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Amphibian skin glands are known to secrete various types of bioactive peptides. The array of these peptides is specific for every frog species. The present research deals with the identification of peptides isolated from the skin secretion of the Marsh frog R. ridibunda inhabiting the Kolkhida Canyon of the Caucasian region. The research is based on comprehensive high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) analysis of intact and chemically modified peptides. In particular, an oxidation procedure was applied directly to the crude skin secretion to open S--S loops whereas N-terminal acetylation was additionally carried out for one individual peptide. Sequences were determined by manual interpretation of electron capture dissociation (ECD) and collisionally induced dissociation (CID) tandem mass spectra. A total of 29 peptides were identified in the skin secretion of the Caucasian Marsh frog. The peptide profile is represented with disulfide-containing peptides belonging to the brevinin, esculentin and ranatuerin families, neuropeptides of the bradykinin and bombesin families. Two identified peptides belonging to the ranatuerins are the first peptides of this family discovered in the skin secretions of European frogs. Ten of the identified peptides coincide with those reported earlier for the European Edible frog. Another ten are identical to those found in R. ridubunda from the Moscow region. This fact verifies the described method as being an efficient analytical tool to compare intra- and interspecific variabilities.
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Creese AJ, Cooper HJ. The effect of phosphorylation on the electron capture dissociation of peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1263-74. [PMID: 18585055 PMCID: PMC2570175 DOI: 10.1016/j.jasms.2008.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 05/15/2008] [Accepted: 05/16/2008] [Indexed: 05/13/2023]
Abstract
The effect of site and frequency of phosphorylation on the electron capture dissociation of peptide ions has been investigated. The ECD of a suite of synthetic peptides (APLSFRGSLPKSYVK; one unmodified, three singly-phosphorylated, three-doubly phosphorylated, and one triply-phosphorylated); two tryptic phosphopeptides (YKVPQLEIVPN(p)SAEER, alpha-casein and FQ(p)SEEQQQTEDELQDK, beta-casein) and their unmodified counterparts, were determined over a range of ECD cathode potentials. The results show that, for doubly-charged precursor ions, the presence of phosphorylation has a deleterious effect on ECD sequence coverage. The fragmentation patterns observed suggest that for peptides with multiple basic residues, the phospho-groups exist in their deprotonated form and form salt-bridges with protonated amino acid side chains. The fragmentation observed for the acidic tryptic peptides suggested the presence of noncovalent interactions, which were perturbed on phosphorylation. Increasing the ECD electron energy significantly improves sequence coverage. Alternatively, improved sequence coverage can be achieved by performing ECD on triply-charged precursor ions. The findings are important for the understanding of gas-phase fragmentation of phosphopeptides.
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Affiliation(s)
| | - Helen J. Cooper
- Address reprint requests to Dr. H. J. Cooper, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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Quan Z, Zhou M, Chen W, Chen T, Walker B, Shaw C. Novel brevinins from Chinese piebald odorous frog (Huia schmackeri) skin deduced from cloned biosynthetic precursors. Peptides 2008; 29:1456-60. [PMID: 18423796 DOI: 10.1016/j.peptides.2008.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/07/2008] [Accepted: 03/10/2008] [Indexed: 11/23/2022]
Abstract
Antimicrobial peptides represent the most characterized and diverse class of peptides within the defensive skin secretions of anuran amphibians. With an ever expanding database of primary structures, the current accepted rules for nomenclature have become increasingly difficult to apply to peptides whose primary structural attributes are either unique or that fall between those that define existing groups. An additional factor that adds to the confusion is the regular re-classification or revision of existing taxa. In the present study, we have identified five new antimicrobial peptide homologs in the defensive skin secretion of the Chinese piebald odorous frog, Huia schmackeri (formerly Rana (Odorrana) schmackeri), by cloning of their respective biosynthetic precursors. As these peptides are obvious homologs of the brevinin-1 and brevinin-2 families we have named these in accordance: (1) brevinin-1HS1, (2) brevinin-2HS1, (3) brevinin-2HS2, (4) brevinin-2HS3 and (5) brevinin-1HS2. The reasons for adopting these names are discussed. It is clear that with an ever-increasing number of amphibian skin antimicrobial peptides appearing in the literature that a consistent nomenclature scheme needs to be established.
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Affiliation(s)
- Zhenzhen Quan
- Molecular Therapeutics Research, School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK
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Samgina TY, Artemenko KA, Gorshkov VA, Poljakov NB, Lebedev AT. Oxidation versus carboxamidomethylation of S-S bond in ranid frog peptides: pro and contra for de novo MALDI-MS sequencing. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:479-487. [PMID: 18280749 DOI: 10.1016/j.jasms.2007.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 12/20/2007] [Accepted: 12/20/2007] [Indexed: 05/25/2023]
Abstract
Five natural peptides isolated from ranid skin secretions of European frog species of Rana ridibunda and Rana arvalis (molecular masses 3516, 2674, 2636, 1874, and 1810 Da) were studied by MALDI-TOF/TOF to compare two procedures of disulfide bond cleavage: (1) performic oxidation and (2) reduction/carboxamidomethylation. The processes are relevant for the elucidation of the amino acid sequence inside the seven-member cystine ring at the C-terminus. The results clearly demonstrated that oxidation of the disulfide bond led to notably higher abundances of b- and y-ions, corresponding to the C-terminal peptide bonds, than reduction/carboxamidomethylation. This conclusion is true for all five peptides studied. Besides that, the oxidation procedure is simpler than carboxamidomethylation, as it is a one-step process with no purification required. The oxidation is more reproducible. The results were similar each time the peptide was subjected to the process. It was successfully applied to all five peptides while reduction/carboxamidomethylation failed in the case of brevinin-1Ra, despite all variations of reaction conditions.
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