1
|
Samgina TY, Vasileva ID, Zubarev RA, Lebedev AT. EThcD as a Unique Tool for the Top-Down De Novo Sequencing of Intact Natural Ranid Amphibian Peptides. Anal Chem 2024; 96:12057-12064. [PMID: 38979842 DOI: 10.1021/acs.analchem.4c02109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
De novo sequencing of any novel peptide/protein is a difficult task. Full sequence coverage, isomeric amino acid residues, inter- and intramolecular S-S bonds, and numerous other post-translational modifications make the investigators employ various chemical modifications, providing a variety of specific fragmentation MSn patterns. The chemical processes are time-consuming, and their yields never reach 100%, while the subsequent purification often leads to the loss of minor components of the initial peptide mixture. Here, we present the advantages of the EThcD method that enables establishing the full sequence of natural intact peptides of ranid frogs in de novo top-down mode without any chemical modifications. The method provides complete sequence coverage, including the cyclic disulfide section, and reliable identification of isomeric leucine/isoleucine residues. The proposed approach demonstrated its efficiency in the analysis of peptidomes of ranid frogs from several populations of Rana arvalis, Rana temporaria, and Pelophylax esculentus complexes.
Collapse
Affiliation(s)
- Tatiana Yu Samgina
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Irina D Vasileva
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177, Sweden
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russia
| | - Albert T Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| |
Collapse
|
2
|
Sedláčková S, Hubálek M, Vrkoslav V, Blechová M, Kozlík P, Cvačka J. Positive Effect of Acetylation on Proteomic Analysis Based on Liquid Chromatography with Atmospheric Pressure Chemical Ionization and Photoionization Mass Spectrometry. Molecules 2023; 28:molecules28093711. [PMID: 37175121 PMCID: PMC10180487 DOI: 10.3390/molecules28093711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
A typical bottom-up proteomic workflow comprises sample digestion with trypsin, separation of the hydrolysate using reversed-phase HPLC, and detection of peptides via electrospray ionization (ESI) tandem mass spectrometry. Despite the advantages and wide usage of protein identification and quantification, the procedure has limitations. Some domains or parts of the proteins may remain inadequately described due to inefficient detection of certain peptides. This study presents an alternative approach based on sample acetylation and mass spectrometry with atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI). These ionizations allowed for improved detection of acetylated peptides obtained via chymotrypsin or glutamyl peptidase I (Glu-C) digestion. APCI and APPI spectra of acetylated peptides often provided sequence information already at the full scan level, while fragmentation spectra of protonated molecules and sodium adducts were easy to interpret. As demonstrated for bovine serum albumin, acetylation improved proteomic analysis. Compared to ESI, gas-phase ionizations APCI and APPI made it possible to detect more peptides and provide better sequence coverages in most cases. Importantly, APCI and APPI detected many peptides which passed unnoticed in the ESI source. Therefore, analytical methods based on chymotrypsin or Glu-C digestion, acetylation, and APPI or APCI provide data complementary to classical bottom-up proteomics.
Collapse
Affiliation(s)
- Simona Sedláčková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12800 Prague, Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
| | - Vladimír Vrkoslav
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
| | - Miroslava Blechová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
| | - Petr Kozlík
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12800 Prague, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12800 Prague, Czech Republic
| |
Collapse
|
3
|
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]
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
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: 4] [Impact Index Per Article: 1.3] [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.
Collapse
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
| |
Collapse
|
8
|
Zaikin VG, Borisov RS. Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry. Crit Rev Anal Chem 2021; 52:1287-1342. [PMID: 33557614 DOI: 10.1080/10408347.2021.1873100] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.
Collapse
Affiliation(s)
- Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| |
Collapse
|
9
|
Discussion of the protein characterization techniques used in the identification of membrane protein targets corresponding to tumor cell aptamers. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.11.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
10
|
Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
Collapse
Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
11
|
Popławska M, Błażewicz A. Identification of a novel growth hormone releasing peptide (a glycine analogue of GHRP-2) in a seized injection vial. Drug Test Anal 2018; 11:162-167. [DOI: 10.1002/dta.2467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 07/02/2018] [Accepted: 07/09/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Magdalena Popławska
- Counterfeit Medicinal Products and Designer Drugs Department; National Medicines Institute; Warsaw Poland
| | - Agata Błażewicz
- Counterfeit Medicinal Products and Designer Drugs Department; National Medicines Institute; Warsaw Poland
| |
Collapse
|
12
|
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]
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Kuchibhotla B, Kola SR, Medicherla JV, Cherukuvada SV, Dhople VM, Nalam MR. Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1216-1226. [PMID: 28349438 DOI: 10.1007/s13361-017-1606-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/30/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Bhanuramanand Kuchibhotla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Sankara Rao Kola
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Jagannadham V Medicherla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Swamy V Cherukuvada
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Vishnu M Dhople
- Department of Functional Genomics, University Medicine Greifswald, Interface Institute Genetics & Functional Genomics, D-17475, Greifswald, Germany
| | - Madhusudhana Rao Nalam
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India.
| |
Collapse
|
16
|
Saha B, Bhattacharya SG. Charting novel allergens from date palm pollen (Phoenix sylvestris) using homology driven proteomics. J Proteomics 2017; 165:1-10. [PMID: 28535932 DOI: 10.1016/j.jprot.2017.05.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/05/2017] [Accepted: 05/17/2017] [Indexed: 11/19/2022]
Abstract
Pollen grains from Phoenix sylvestris (date palm), a commonly cultivated tree in India has been found to cause severe allergic diseases in an increasing percentage of hypersensitive individuals. To unearth its allergenic components, pollen protein were profiled by two-dimensional gel electrophoresis followed by immunoblotting with date palm pollen sensitive patient sera. Allergens were identified by MALDI-TOF/TOF employing a layered proteomic approach combining conventional database dependent search and manual de novo sequencing followed by homology-based search as Phoenix sylvestris is unsequenced. Derivatization of tryptic peptides by acetylation has been demonstrated to differentiate the 'b' from the 'y' ions facilitating efficient de novo sequencing. Ten allergenic proteins were identified, out of which six showed homology with known allergens while others were reported for the first time. Amongst these, isoflavone reductase, beta-conglycinin, S-adenosyl methionine synthase, 1, 4 glucan synthase and beta-galactosidase were commonly reported as allergens from coconut pollen and presumably responsible for cross-reactivity. One of the allergens had IgE binding epitope recognized by its glycan moiety. The allergenic potency of date palm pollen has been demonstrated using in vitro tests. The identified allergens can be used to develop vaccines for immunotherapy against date palm pollen allergy. THE SIGNIFICANCE OF THE STUDY Identification of allergenic proteins from sources harboring them is essential in developing therapeutic interventions. This is the first comprehensive study on the identification of allergens from Phoenix sylvestris (date palm) pollen, one of the major aeroallergens in India using a proteomic approach. Proteomic methods are being increasingly used to identify allergens. However, since many of these proteins arise from species which are un-sequenced, it becomes difficult to interpret those using conventional proteomics. Date palm being an unsequenced species, the IgE-reactive proteins have been identified using a stratified proteomic workflow incorporating manual de novo sequencing and homology-based proteomics. This study also gives an insight into the presence of glycan nature of the IgE binding epitopes. Five proteins have been found to be common with coconut pollen allergens and presumably responsible for cross-reactivity. These can be used in diagnostics to differentiate patient cohorts allergic to both coconut and date palm pollen from true date palm pollen allergic subjects. This would also determine better specific immunotherapy regimes between the two cohorts. The allergens identified herein have potential towards vaccine development in date palm pollen allergy as well as in enriching the existing catalogue of allergenic proteins.
Collapse
Affiliation(s)
- Bodhisattwa Saha
- Division of Plant Biology, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Swati Gupta Bhattacharya
- Division of Plant Biology, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India.
| |
Collapse
|
17
|
Milyushkin AL, Laktyushina AA, Buryak AK. Identification of peptides with protected functional groups by chromatography, mass spectrometry, and molecular statistics. Russ Chem Bull 2017. [DOI: 10.1007/s11172-017-1699-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
Sayegh RSR, Batista IDFC, de Melo RL, Riske KA, Daffre S, Montich G, da Silva Junior PI. Longipin: An Amyloid Antimicrobial Peptide from the Harvestman Acutisoma longipes (Arachnida: Opiliones) with Preferential Affinity for Anionic Vesicles. PLoS One 2016; 11:e0167953. [PMID: 27997568 PMCID: PMC5172563 DOI: 10.1371/journal.pone.0167953] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 11/22/2016] [Indexed: 12/24/2022] Open
Abstract
In contrast to vertebrate immune systems, invertebrates lack an adaptive response and rely solely on innate immunity in which antimicrobial peptides (AMPs) play an essential role. Most of them are membrane active molecules that are typically unstructured in solution and adopt secondary/tertiary structures upon binding to phospholipid bilayers. This work presents the first characterization of a constitutive AMP from the hemolymph of an Opiliones order animal: the harvestman Acutisoma longipes. This peptide was named longipin. It presents 18 aminoacid residues (SGYLPGKEYVYKYKGKVF) and a positive net charge at neutral pH. No similarity with other AMPs was observed. However, high sequence similarity with heme-lipoproteins from ticks suggested that longipin might be a protein fragment. The synthetic peptide showed enhanced antifungal activity against Candida guilliermondii and C. tropicalis yeasts (MIC: 3.8–7.5 μM) and did not interfered with VERO cells line viability at all concentrations tested (200–0.1 μM). This selectivity against microbial cells is related to the highest affinity of longipin for anionic charged vesicles (POPG:POPC) compared to zwitterionic ones (POPC), once microbial plasma membrane are generally more negatively charged compared to mammalian cells membrane. Dye leakage from carboxyfluorescein-loaded POPG:POPC vesicles suggested that longipin is a membrane active antimicrobial peptide and FT-IR spectroscopy showed that the peptide chain is mainly unstructured in solution or in the presence of POPC vesicles. However, upon binding to POPG:POPC vesicles, the FT-IR spectrum showed bands related to β-sheet and amyloid-like fibril conformations in agreement with thioflavin-T binding assays, indicating that longipin is an amyloid antimicrobial peptide.
Collapse
Affiliation(s)
- Raphael Santa Rosa Sayegh
- Programa Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- * E-mail: (RSSS); (PISJ)
| | - Isabel de Fátima Correia Batista
- Unidade de Sequenciamento de Proteínas e Peptídeos, Instituto Butantan, São Paulo, Brazil
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, Brazil
| | - Robson Lopes de Melo
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
| | - Karin A. Riske
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sirlei Daffre
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Guillermo Montich
- Centro de Investigaciones en Quimica Biológica de Córdoba (CIQUIBIC, UNC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pedro Ismael da Silva Junior
- Programa Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- * E-mail: (RSSS); (PISJ)
| |
Collapse
|
20
|
Proteolytic degradation and deactivation of amphibian skin peptides obtained by electrical stimulation of their dorsal glands. Anal Bioanal Chem 2016; 408:3761-8. [PMID: 26975184 DOI: 10.1007/s00216-016-9462-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/24/2016] [Accepted: 03/01/2016] [Indexed: 10/22/2022]
Abstract
Amphibians are among the oldest creatures on our planet. Their only defensive weapon efficient against microorganisms and predators involves their skin secretion. The wide range of biological activities of the peptides in the skin secretion of amphibians makes these compounds rather interesting for generation of prospective pharmaceuticals. The first step in studying these molecules requires their structures to be established. Mass spectrometry is the most powerful tool for this purpose. The sampling and sample preparation stages preceding mass spectrometry experiments appear to be rather crucial. The results obtained here demonstrate that these preparation procedures might lead to partial or complete loss of the bioactive peptides in the secretion. Five minutes in water was enough to completely destroy all of the bioactive peptides in the skin secretion of the marsh frog (Rana ridibunda); even immediate addition of methanol to the water solution of the peptides did not prevent partial destruction. Concerted effort should be directed towards development of the most efficient procedure to keep the secreted peptides intact. Graphical Abstract ᅟ.
Collapse
|
21
|
Plaviak A, Osburn S, Patterson K, van Stipdonk MJ. Even-electron [M-H](+) ions generated by loss of AgH from argentinated peptides with N-terminal imine groups. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:69-80. [PMID: 26661972 DOI: 10.1002/rcm.7415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/24/2015] [Accepted: 10/04/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Experiments were performed to probe the creation of apparent even-electron, [M-H](+) ions by CID of Ag-cationized peptides with N-terminal imine groups (Schiff bases). METHODS Imine-modified peptides were prepared using condensation reactions with aldehydes. Ag(+) -cationized precursors were generated by electrospray ionization (ESI). Tandem mass spectrometry (MS(n) ) and collision-induced dissociation (CID) were performed using a linear ion trap mass spectrometer. RESULTS Loss of AgH from peptide [M + Ag](+) ions, at the MS/MS stage, creates closed-shell [M-H](+) ions from imine-modified peptides. Isotope labeling unambiguously identifies the imine C-H group as the source of H eliminated in AgH. Subsequent CID of the [M-H](+) ions generated sequence ions that are analogous to those produced from [M + H](+) ions of the imine-modified peptides. CONCLUSIONS Experiments show (a) formation of novel even-electron peptide cations by CID and (b) the extent to which sequence ions (conventional b, a and y ions) are generated from peptides with fixed charge site and thus lacking a conventional mobile proton.
Collapse
Affiliation(s)
- Alexandra Plaviak
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| | - Sandra Osburn
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| | - Khiry Patterson
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| | - Michael J van Stipdonk
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| |
Collapse
|
22
|
Lebedev AT, Damoc E, Makarov AA, Samgina TY. Discrimination of Leucine and Isoleucine in Peptides Sequencing with Orbitrap Fusion Mass Spectrometer. Anal Chem 2014; 86:7017-22. [DOI: 10.1021/ac501200h] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Albert T. Lebedev
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow, 119991, Russia
| | - Eugen Damoc
- ThermoFisher Scientific (Bremen) GmbH, Hanna-Kunath Strasse 11, 28199, Bremen, Germany
| | - Alexander A. Makarov
- ThermoFisher Scientific (Bremen) GmbH, Hanna-Kunath Strasse 11, 28199, Bremen, Germany
| | - Tatiana Yu. Samgina
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow, 119991, Russia
| |
Collapse
|
23
|
The fate of b-ions in the two worlds of collision-induced dissociation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2843-8. [DOI: 10.1016/j.bbapap.2013.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/14/2013] [Accepted: 08/16/2013] [Indexed: 11/21/2022]
|
24
|
Robotham SA, Kluwe C, Cannon JR, Ellington A, Brodbelt JS. De novo sequencing of peptides using selective 351 nm ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:9832-8. [PMID: 24050806 DOI: 10.1021/ac402309h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although in silico database search methods remain more popular for shotgun proteomics methods, de novo sequencing offers the ability to identify peptides derived from proteins lacking sequenced genomes and ones with subtle splice variants or truncations. Ultraviolet photodissociation (UVPD) of peptides derivatized by selective attachment of a chromophore at the N-terminus generates a characteristic series of y ions. The UVPD spectra of the chromophore-labeled peptides are simplified and thus amenable to de novo sequencing. This method resulted in an observed sequence coverage of 79% for cytochrome C (eight peptides), 47% for β-lactoglobulin (five peptides), 25% for carbonic anhydrase (six peptides), and 51% for bovine serum albumin (33 peptides). This strategy also allowed differentiation of proteins with high sequence homology as evidenced by de novo sequencing of two variants of green fluorescent protein.
Collapse
Affiliation(s)
- Scott A Robotham
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | | | | | | | | |
Collapse
|
25
|
Horvatić A, Dodig I, Vuletić T, Pavoković D, Hameršak Z, Butorac A, Cindrić M. Comparison between Enhanced MALDI In-source Decay by Ammonium Persulfate and N- or C-Terminal Derivatization Methods for Detailed Peptide Structure Determination. Anal Chem 2013; 85:3940-7. [DOI: 10.1021/ac303436n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anita Horvatić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Ivana Dodig
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | | | | | - Zdenko Hameršak
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | | | - Mario Cindrić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Bąchor R, Cydzik M, Rudowska M, Kluczyk A, Stefanowicz P, Szewczuk Z. Sensitive electrospray mass spectrometry analysis of one-bead-one-compound peptide libraries labeled by quaternary ammonium salts. Mol Divers 2012; 16:613-8. [PMID: 22740104 DOI: 10.1007/s11030-012-9377-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 05/28/2012] [Indexed: 11/26/2022]
Abstract
A rapid and straightforward method for high-throughput analysis of single resin beads from one-bead-one-compound combinatorial libraries with high resolution electrospray ionization tandem mass spectrometry (HR ESI-MS/MS) is presented. The application of an efficient method of peptide derivatization by quaternary ammonium salts (QAS) formation increases ionization efficiency and reduces the detection limit, allowing analysis of trace amounts of compounds by ESI-MS. Peptides, synthesized on solid support, contain a new cleavable linker composed of a Peg spacer (9-aza-3,6,12,15-tetraoxa-10-on-heptadecanoic acid), lysine with ɛ-amino group marked by the N,N,N-triethylglycine salt, and methionine, which makes possible the selective cleavage by cyanogen bromide. Even a small portion of peptides derivatized by QAS cleaved from a single resin bead is sufficient for sequencing by HR ESI-MS/MS experiments. The developed strategy was applied to a small training library of α chymotrypsin substrates. The obtained results confirm the applicability of the proposed method in combinatorial chemistry.
Collapse
Affiliation(s)
- Remigiusz Bąchor
- University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | | | | | | | | | | |
Collapse
|
28
|
Song J, Kim HJ. Matrix-assisted laser desorption/ionization mass spectrometry peptide sequencing utilizing selective N-terminal bromoacetylation. Anal Biochem 2011; 423:269-76. [PMID: 22178914 DOI: 10.1016/j.ab.2011.11.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/21/2011] [Accepted: 11/21/2011] [Indexed: 10/14/2022]
Abstract
In tandem mass spectrometric peptide sequencing, simplifying the mass spectrum is often desirable. The b-series ions were distinguished from the y-series ions in the MALDI TOF-TOF spectra by incorporating a bromine-tag to the N-terminal amino group through rapid and selective acetylation using bromoacetic anhydride without blocking the lysine and tyrosine residues. The 51:49 ratio of Br-79 and Br-81 isotopes facilitated identification of ions carrying the tag. With the Br-tag in the b-series ions, N-terminal sequencing of tryptic peptides from hemoglobin as well as model peptides was straightforward. When the b-ions were low in intensity, ions without the Br-tag were identified as y-ions and used for sequencing.
Collapse
Affiliation(s)
- Jinsu Song
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | | |
Collapse
|
29
|
Zhang D, Liu H, Zhang S, Chen X, Li S, Zhang C, Hu X, Bi K, Chen X, Jiang Y. An effective method for de novo peptide sequencing based on phosphorylation strategy and mass spectrometry. Talanta 2011; 84:614-22. [DOI: 10.1016/j.talanta.2010.12.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 12/20/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022]
|
30
|
Jagannadham MV, Abou-Eladab EF, Kulkarni HM. Identification of outer membrane proteins from an Antarctic bacterium Pseudomonas syringae Lz4W. Mol Cell Proteomics 2011; 10:M110.004549. [PMID: 21447709 DOI: 10.1074/mcp.m110.004549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Subcellular fractionation of proteins is a preferred method of choice for detection and identification of proteins from complex mixtures such as bacterial cells. To characterize the membrane proteins of the Antarctic bacterium Pseudomonas syringae Lz4W, the membrane fractions were prepared using three different methods, namely Triton X-100 solubilization, sucrose density gradient, and carbonate extraction methods. The proteins were separated on one-dimensional polyacrylamide gels and analyzed using a combination of liquid chromatography-coupled electrospray ionization-MS. The membrane proteins that were prepared by carbonate extraction were separated on two-dimensional PAGE in different pI ranges using the detergent 2% amidosulfobetaine (ASB). The proteins were then subjected to matrix-assisted laser desorption ionization-time-of-flight/time-of-flight for analysis and identification. Because the genome sequence of P. syringae Lz4W is not known, the proteins were identified by using the relevant sequence databases of the Pseudomonas sp available at National Centre for Biotechnology Information (NCBI). The sequence identification of some tryptic peptides were validated by de novo sequencing and others by chemical modification and mass spectrometry. The peptide sequences of P. syringae Lz4W were then matched with the sequences of the peptides from different Pseudomonas sp. by similarity search of the proteins from different species using clustal W2 program. Thus by using a combination of the methods, we have been able to identify large number of proteins of this bacterial strain, which include most of the outer membrane proteins.
Collapse
Affiliation(s)
- M V Jagannadham
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India.
| | | | | |
Collapse
|
31
|
Cydzik M, Rudowska M, Stefanowicz P, Szewczuk Z. Derivatization of peptides as quaternary ammonium salts for sensitive detection by ESI-MS. J Pept Sci 2011; 17:445-53. [PMID: 21351320 DOI: 10.1002/psc.1342] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 10/19/2010] [Accepted: 11/11/2010] [Indexed: 01/19/2023]
Abstract
A series of model peptides in the form of quaternary ammonium salts at the N-terminus was efficiently prepared by the solid-phase synthesis. Tandem mass spectrometric analysis of the peptide quaternary ammonium derivatives was shown to provide sequence confirmation and enhanced detection. We designed the 2-(1,4-diazabicyclo[2.2.2] octylammonium)acetyl quaternary ammonium group which does not suffer from neutral losses during MS/MS experiments. The presented quaternization of 1,4-diazabicyclo[2.2.2]octane (DABCO) by iodoacetylated peptides is relatively easy and compatible with standard solid-phase peptide synthesis. This methodology offers a novel sensitive approach to analyze peptides and other compounds.
Collapse
Affiliation(s)
- Marzena Cydzik
- Faculty of Chemistry, University of Wrocław, Wrocław, Poland
| | | | | | | |
Collapse
|
32
|
Yan J, Gao J, Long DL, Miras HN, Cronin L. Self-Assembly of a Nanosized, Saddle-Shaped, Solution-Stable Polyoxometalate Anion Built from Pentagonal Building Blocks: [H34W119Se8Fe2O420]54−. J Am Chem Soc 2010; 132:11410-1. [DOI: 10.1021/ja104043s] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun Yan
- WestCHEM, Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Jing Gao
- WestCHEM, Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - De-Liang Long
- WestCHEM, Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Haralampos N. Miras
- WestCHEM, Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Leroy Cronin
- WestCHEM, Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| |
Collapse
|
33
|
Samgina TY, Gorshkov VA, Artemenko KA, Kovalev SV, Ogourtsov SV, Zubarev RA, Lebedev AT. Novel natural peptides from Hyla arborea schelkownikowi skin secretion. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:1749-1754. [PMID: 20499319 DOI: 10.1002/rcm.4571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Hyla arborea schelkownikowi is one of the leaf frog species inhabiting the southern territories of Russia and the former USSR. This frog species is a member of the Hylidae Rafinesque, 1815 batrachians family. The present study deals with the previously uninvestigated peptidome of the Hyla arborea schelkownikowi skin secretion. Nano-electrospray ionization Fourier transform mass spectrometry (nanoESI-FTMS) of the skin secretion, in the intact form and after acetylation, was selected as the general method of analysis. Electron-capture dissociation (ECD) and collision-induced dissociation (CID) fragmentation were both employed, while de novo sequencing was performed by manual interpretation of the MS data. The suppression of the cyclization of b-ions in the mass spectrometer by the acetylation reaction proved to be very efficient for the de novo sequencing of short peptides. Ten skin peptides were found and all of them, except for bradykinin, had not previously been reported. Six of the peptides belong to the tryptophyllins and related peptides, while three peptides are similar to the aureins.
Collapse
Affiliation(s)
- T Yu Samgina
- Organic Chemistry Department, Moscow State University, Leninskie gory 1/3, GSP-1, MSU, Moscow 119991, Russian Federation
| | | | | | | | | | | | | |
Collapse
|