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Vijayasarathy M, Kumar S, Das R, Balaram P. Cysteine-free cone snail venom peptides: Classification of precursor proteins and identification of mature peptides. J Pept Sci 2024; 30:e3554. [PMID: 38009400 DOI: 10.1002/psc.3554] [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: 09/02/2023] [Revised: 10/17/2023] [Accepted: 10/30/2023] [Indexed: 11/28/2023]
Abstract
The cysteine-free acyclic peptides present in marine cone snail venom have been much less investigated than their disulfide bonded counterparts. Precursor protein sequences derived from transcriptomic data, together with mass spectrometric fragmentation patterns for peptides present in venom duct tissue extracts, permit the identification of mature peptides. Twelve distinct gene superfamiles have been identified with precursor lengths between 64 and 158 residues. In the case of Conus monile, three distinct mature peptides have been identified, arising from two distinct protein precursors. Mature acyclic peptides are often post-translationally modified, with C-terminus amidation, a feature characteristic of neuropeptides. In the present study, 20 acyclic peptides from Conus monile and Conus betulinus were identified. The common modifications of C-terminus amidation, gamma carboxylation of glutamic acid (E to ϒ), N-terminus conversion of Gln (Q) to a pyroglutamyl residue (Z), and hydroxylation of Pro (P) to Hyp (O) are observed in one or more peptides identified in this study. Proteolytic trimming of sequences by cleavage at the C-terminus of Asn (N) residues is established. The presence of an asparagine endopeptidase is strengthened by the identification of legumain-like sequences in the transcriptome assemblies from diverse Conus species. Such sequences may be expected to have a cleavage specificity at Asn-Xxx peptide bonds.
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Affiliation(s)
- Marimuthu Vijayasarathy
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Sanjeev Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Rajdeep Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- Department of Biochemistry and Bioinformatics, GITAM School of Science, GITAM (Deemed to be) University, Visakhapatnam, India
| | - Padmanabhan Balaram
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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2
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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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3
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Edwards HM, Wu HT, Julian RR, Jackson GP. Differentiation of leucine and isoleucine residues in peptides using charge transfer dissociation mass spectrometry (CTD-MS). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9246. [PMID: 34927767 DOI: 10.1002/rcm.9246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
RATIONALE The function of a protein or the binding affinity of an antibody can be substantially altered by the replacement of leucine (Leu) with isoleucine (Ile), and vice versa, so the ability to identify the correct isomer using mass spectrometry can help resolve important biological questions. Tandem mass spectrometry approaches for Leu/Ile (Xle) discrimination have been developed, but they all have certain limitations. METHODS Four model peptides and two wild-type peptide sequences containing either Leu or Ile residues were subjected to charge transfer dissociation (CTD) mass spectrometry on a modified three-dimensional ion trap. The peptides were analyzed in both the 1+ and 2+ charge states, and the results were compared to conventional collision-induced dissociation spectra of the same peptides obtained using the same instrument. RESULTS CTD resulted in 100% sequence coverage for each of the studied peptides and provided a variety of side-chain cleavages, including d, w and v ions. Using CTD, reliable d and w ions of Xle residues were observed more than 80% of the time. When present, d ions are typically greater than 10% of the abundance of the corresponding a ions from which they derive, and w ions are typically more abundant than the z ions from which they derive. CONCLUSIONS CTD has the benefit of being applicable to both 1+ and 2+ precursor ions, and the overall performance is comparable to that of other high-energy activation techniques like hot electron capture dissociation and UV photodissociation. CTD does not require chemical modifications of the precursor peptides, nor does it require additional levels of isolation and fragmentation.
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Affiliation(s)
- Halle M Edwards
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, USA
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Pandeswari PB, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv 2018; 9:313-344. [PMID: 35521579 PMCID: PMC9059502 DOI: 10.1039/c8ra07200k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022] Open
Abstract
Owing to rapid growth in the elucidation of genome sequences of various organisms, deducing proteome sequences has become imperative, in order to have an improved understanding of biological processes. Since the traditional Edman method was unsuitable for high-throughput sequencing and also for N-terminus modified proteins, mass spectrometry (MS) based methods, mainly based on soft ionization modes: electrospray ionization and matrix-assisted laser desorption/ionization, began to gain significance. MS based methods were adaptable for high-throughput studies and applicable for sequencing N-terminus blocked proteins/peptides too. Consequently, over the last decade a new discipline called 'proteomics' has emerged, which encompasses the attributes necessary for high-throughput identification of proteins. 'Proteomics' may also be regarded as an offshoot of the classic field, 'biochemistry'. Many protein sequencing and proteomic investigations were successfully accomplished through MS dependent sequence elucidation of 'short proteolytic peptides (typically: 7-20 amino acid residues), which is called the 'shotgun' or 'bottom-up (BU)' approach. While the BU approach continues as a workhorse for proteomics/protein sequencing, attempts to sequence intact proteins without proteolysis, called the 'top-down (TD)' approach started, due to ambiguities in the BU approach, e.g., protein inference problem, identification of proteoforms and the discovery of posttranslational modifications (PTMs). The high-throughput TD approach (TD proteomics) is yet in its infancy. Nevertheless, TD characterization of purified intact proteins has been useful for detecting PTMs. With the hope to overcome the pitfalls of BU and TD strategies, another concept called the 'middle-down (MD)' approach was put forward. Similar to BU, the MD approach also involves proteolysis, but in a restricted manner, to produce 'longer' proteolytic peptides than the ones usually obtained in BU studies, thereby providing better sequence coverage. In this regard, special proteases (OmpT, Sap9, IdeS) have been used, which can cleave proteins to produce longer proteolytic peptides. By reviewing ample evidences currently existing in the literature that is predominantly on PTM characterization of histones and antibodies, herein we highlight salient features of the MD approach. Consequently, we are inclined to claim that the MD concept might have widespread applications in future for various research areas, such as clinical, biopharmaceuticals (including PTM analysis) and even for general/routine characterization of proteins including therapeutic proteins, but not just limited to analysis of histones or antibodies.
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Affiliation(s)
- P Boomathi Pandeswari
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
| | - Varatharajan Sabareesh
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
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Háda V, Bagdi A, Bihari Z, Timári SB, Fizil Á, Szántay C. Recent advancements, challenges, and practical considerations in the mass spectrometry-based analytics of protein biotherapeutics: A viewpoint from the biosimilar industry. J Pharm Biomed Anal 2018; 161:214-238. [PMID: 30205300 DOI: 10.1016/j.jpba.2018.08.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/22/2023]
Abstract
The extensive analytical characterization of protein biotherapeutics, especially of biosimilars, is a critical part of the product development and registration. High-resolution mass spectrometry became the primary analytical tool used for the structural characterization of biotherapeutics. Its high instrumental sensitivity and methodological versatility made it possible to use this technique to characterize both the primary and higher-order structure of these proteins. However, even by using high-end instrumentation, analysts face several challenges with regard to how to cope with industrial and regulatory requirements, that is, how to obtain accurate and reliable analytical data in a time- and cost-efficient way. New sample preparation approaches, measurement techniques and data evaluation strategies are available to meet those requirements. The practical considerations of these methods are discussed in the present review article focusing on hot topics, such as reliable and efficient sequencing strategies, minimization of artefact formation during sample preparation, quantitative peptide mapping, the potential of multi-attribute methodology, the increasing role of mass spectrometry in higher-order structure characterization and the challenges of MS-based identification of host cell proteins. On the basis of the opportunities in new instrumental techniques, methodological advancements and software-driven data evaluation approaches, for the future one can envision an even wider application area for mass spectrometry in the biopharmaceutical industry.
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Affiliation(s)
- Viktor Háda
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary.
| | - Attila Bagdi
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Zsolt Bihari
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | | | - Ádám Fizil
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Csaba Szántay
- Spectroscopic Research Department, Gedeon Richter Plc, Hungary.
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6
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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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7
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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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8
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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: 17] [Impact Index Per Article: 2.4] [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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9
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Schwob L, Lalande M, Egorov D, Rangama J, Hoekstra R, Vizcaino V, Schlathölter T, Poully JC. Radical-driven processes within a peptidic sequence of type I collagen upon single-photon ionisation in the gas phase. Phys Chem Chem Phys 2017; 19:22895-22904. [DOI: 10.1039/c7cp03376a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Radical creation after single-photon ionisation of collagen peptides induces the loss of molecules from amino-acid residue side-chains.
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Affiliation(s)
- Lucas Schwob
- CIMAP
- UMP 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Mathieu Lalande
- CIMAP
- UMP 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Dmitrii Egorov
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- The Netherlands
| | - Jimmy Rangama
- CIMAP
- UMP 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- The Netherlands
| | - Violaine Vizcaino
- CIMAP
- UMP 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- The Netherlands
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10
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Bagal D, Kast E, Cao P. Rapid Distinction of Leucine and Isoleucine in Monoclonal Antibodies Using Nanoflow LCMSn. Anal Chem 2016; 89:720-727. [DOI: 10.1021/acs.analchem.6b03261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dhanashri Bagal
- Discovery Attribute Sciences, Amgen, South San
Francisco, California 94080, United States
| | - Eddie Kast
- Discovery Attribute Sciences, Amgen, South San
Francisco, California 94080, United States
| | - Ping Cao
- Discovery Attribute Sciences, Amgen, South San
Francisco, California 94080, United States
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11
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Rathore D, Aboufazeli F, Dodds ED. Obtaining complementary polypeptide sequence information from a single precursor ion packet via sequential ion mobility-resolved electron transfer and vibrational activation. Analyst 2016; 140:7175-83. [PMID: 26357706 DOI: 10.1039/c5an01225b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tandem mass spectrometry (MS/MS) is now well-known as a powerful tool for characterizing the primary structures of peptides and proteins; however, in many cases the use of but a single dissociation method provides only a partial view of the amino acid sequences and post-translational modification patterns of polypeptides. While the application of multiple fragmentation methods can be more informative, this introduces the burden of acquiring multiple MS/MS spectra per analyte, thus reducing the effective duty cycle of such methods. In this work, initial proof-of-concept is provided for a method designed to overcome these barriers. This method relies on the complementary fragmentation information that can be provided by performing collision-induced dissociation (CID) and electron transfer dissociation (ETD) in concert, while also taking advantage of an ion mobility (IM) dimension to temporally resolve the occurrence of CID and ETD when applied to a single accumulated packet of precursor ions. In this way, the significant proportion of the precursor ion population that remains unreacted in ETD experiments is subjected to CID rather than being fruitlessly discarded. In addition, the two distinct fragmentation spectra can be extracted from their corresponding IM domains to render readily interpretable individual fragmentation spectra. This scheme was demonstrated for several polypeptides ranging from 1.3 to 8.6 kDa in molecular weight. In each case, IM-resolved CID and ETD events resulted in b/y and c/z ions, respectively, which each covered both unique and overlapping sequence information. These findings demonstrate that the combination of CID and ETD can be achieved with greater utilization of the available ion population and little or no loss of duty cycle.
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Affiliation(s)
- Deepali Rathore
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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12
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Nair D, Vanuopadath M, Nair BG, Pai JG, Nair SS. Identification and characterization of a library of surfactins and fengycins from a marine endophytic Bacillus sp. J Basic Microbiol 2016; 56:1159-1172. [PMID: 27160506 DOI: 10.1002/jobm.201600029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/24/2016] [Indexed: 11/05/2022]
Abstract
An endophytic bacterial strain from a marine green alga, Ulva lactuca, was isolated and identified by 16S rRNA gene sequencing method. The bacterial isolate was found to secrete two major families of cyclic depsilipopeptides, surfactins, and fengycins. Sequencing of the isolated lipopeptides was carried out using the MSn data obtained from an electrospray ionization (ESI) ion trap mass spectrometer coupled to an HPLC system. The assigned sequences were confirmed by a chemical derivatization approach involving esterification followed by mass spectrometric analysis. Distinction of leucine residues from isoleucine was established through a combined electron transfer dissociation-collision-induced dissociation (ETD-CID) method. The fengycins described in this study were found to cause significant delay of growth of two plants, Vigna radiata (mung bean) and Oryza sativa (rice). To the best of our knowledge, this is the first study describing identification and characterization of cyclic peptides from an endophytic Bacillus sp. isolated from marine algae.
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Affiliation(s)
- Divya Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana P.O. Kollam, Kerala, India
| | | | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana P.O. Kollam, Kerala, India
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Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:595-626. [PMID: 24737647 DOI: 10.1002/mas.21421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
This review describes some of the more interesting and imaginative ways in which mass spectrometry has been utilized to study a number of important post-translational modifications over the past two decades; from circa 1990 to 2013. A diverse range of modifications is covered, including citrullination, sulfation, hydroxylation and sumoylation. A summary of the biological role of each modification described, along with some brief mechanistic detail, is also included. Emphasis has been placed on strategies specifically aimed at detecting target modifications, as opposed to more serendipitous modification discovery approaches, which rely upon straightforward product ion scanning methods. The authors have intentionally excluded from this review both phosphorylation and glycosylation since these major modifications have been extensively reviewed elsewhere.
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Affiliation(s)
- Navin Chicooree
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
- School of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9SU, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - John R Griffiths
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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Godzien J, Armitage EG, Angulo S, Martinez-Alcazar MP, Alonso-Herranz V, Otero A, Lopez-Gonzalvez A, Barbas C. In-source fragmentation and correlation analysis as tools for metabolite identification exemplified with CE-TOF untargeted metabolomics. Electrophoresis 2015; 36:2188-2195. [DOI: 10.1002/elps.201500016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/08/2015] [Accepted: 02/08/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO); Facultad de Farmacia; Universidad CEU San Pablo, Campus Montepríncipe; Boadilla del Monte Madrid Spain
| | - Emily G. Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO); Facultad de Farmacia; Universidad CEU San Pablo, Campus Montepríncipe; Boadilla del Monte Madrid Spain
| | - Santiago Angulo
- Centre for Metabolomics and Bioanalysis (CEMBIO); Facultad de Farmacia; Universidad CEU San Pablo, Campus Montepríncipe; Boadilla del Monte Madrid Spain
| | - Mari Paz Martinez-Alcazar
- Centre for Metabolomics and Bioanalysis (CEMBIO); Facultad de Farmacia; Universidad CEU San Pablo, Campus Montepríncipe; Boadilla del Monte Madrid Spain
| | - Vanesa Alonso-Herranz
- Centre for Metabolomics and Bioanalysis (CEMBIO); Facultad de Farmacia; Universidad CEU San Pablo, Campus Montepríncipe; Boadilla del Monte Madrid Spain
| | - Abraham Otero
- Department of Information and Communications Systems Engineering; Universidad CEU San Pablo, Campus Montepríncipe; Boadilla del Monte Madrid Spain
| | - Angeles Lopez-Gonzalvez
- Centre for Metabolomics and Bioanalysis (CEMBIO); Facultad de Farmacia; Universidad CEU San Pablo, Campus Montepríncipe; Boadilla del Monte Madrid Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO); Facultad de Farmacia; Universidad CEU San Pablo, Campus Montepríncipe; Boadilla del Monte Madrid Spain
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15
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Li Z, Dilger JM, Pejaver V, Smiley D, Arnold RJ, Mooney SD, Mukhopadhyay S, Radivojac P, Clemmer DE. Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2014; 368:6-14. [PMID: 26023288 PMCID: PMC4443490 DOI: 10.1016/j.ijms.2014.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cross sections for 61 palmitoylated peptides and 73 cysteine-unmodified peptides are determined and used together with a previously obtained tryptic peptide library to derive a set of intrinsic size parameters (ISPs) for the palmitoyl (Pal) group (1.26 ± 0.04), carboxyamidomethyl (Am) group (0.92 ± 0.04), and the 20 amino acid residues to assess the influence of Pal- and Am-modification on cysteine and other amino acid residues. These values highlight the influence of the intrinsic hydrophobic and hydrophilic nature of these modifications on the overall cross sections. As a part of this analysis, we find that ISPs derived from a database of a modifier on one amino acid residue (CysPal) can be applied on the same modification group on different amino acid residues (SerPal and TyrPal). Using these ISP values, we are able to calculate peptide cross sections to within ± 2% of experimental values for 83% of Pal-modified peptide ions and 63% of Am-modified peptide ions. We propose that modification groups should be treated as individual contribution factors, instead of treating the combination of the particular group and the amino acid residue they are on as a whole when considering their effects on the peptide ion mobility features.
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Affiliation(s)
- Zhiyu Li
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | - Vikas Pejaver
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN 47405
| | - David Smiley
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Randy J Arnold
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Sean D Mooney
- Buck Institute for Research on Aging, Novato, CA 94945
| | | | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN 47405
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
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Poston CN, Higgs RE, You J, Gelfanova V, Hale JE, Knierman MD, Siegel R, Gutierrez JA. A quantitative tool to distinguish isobaric leucine and isoleucine residues for mass spectrometry-based de novo monoclonal antibody sequencing. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1228-1236. [PMID: 24845350 DOI: 10.1007/s13361-014-0892-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/05/2014] [Accepted: 03/10/2014] [Indexed: 06/03/2023]
Abstract
De novo sequencing by mass spectrometry (MS) allows for the determination of the complete amino acid (AA) sequence of a given protein based on the mass difference of detected ions from MS/MS fragmentation spectra. The technique relies on obtaining specific masses that can be attributed to characteristic theoretical masses of AAs. A major limitation of de novo sequencing by MS is the inability to distinguish between the isobaric residues leucine (Leu) and isoleucine (Ile). Incorrect identification of Ile as Leu or vice versa often results in loss of activity in recombinant antibodies. This functional ambiguity is commonly resolved with costly and time-consuming AA mutation and peptide sequencing experiments. Here, we describe a set of orthogonal biochemical protocols, which experimentally determine the identity of Ile or Leu residues in monoclonal antibodies (mAb) based on the selectivity that leucine aminopeptidase shows for n-terminal Leu residues and the cleavage preference for Leu by chymotrypsin. The resulting observations are combined with germline frequencies and incorporated into a logistic regression model, called Predictor for Xle Sites (PXleS) to provide a statistical likelihood for the identity of Leu at an ambiguous site. We demonstrate that PXleS can generate a probability for an Xle site in mAbs with 96% accuracy. The implementation of PXleS precludes the expression of several possible sequences and, therefore, reduces the overall time and resources required to go from spectra generation to a biologically active sequence for a mAb when an Ile or Leu residue is in question.
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Affiliation(s)
- Chloe N Poston
- Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, 46285, USA
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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
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Kaushik DK, Thounaojam MC, Mitra A, Basu A. Vespa tropica venom suppresses lipopolysaccharide-mediated secretion of pro-inflammatory cyto-chemokines by abrogating nuclear factor-κ B activation in microglia. Inflamm Res 2014; 63:657-65. [PMID: 24781802 DOI: 10.1007/s00011-014-0738-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/03/2014] [Accepted: 04/13/2014] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE AND DESIGN The present study was aimed to evaluate the anti-inflammatory potentials of Vespa tropica (VT) venom and its isolated peptides. Effects of whole venom and its two peptides (Vt1512 and Vt1386) on lipopolysaccharide (LPS) challenged BV-2 murine microglial cells was evaluated. MATERIALS Mouse microglial cell line, BV-2 and crude venom extract as well as purified peptides from VT along with LPS from Salmonella enterica were used for the studies. TREATMENT BV-2 cells were treated with 500 ng/ml of LPS and different doses of crude wasp venom as well as purified peptides. METHODS We used immunoblotting, cytokine bead arrays and fluorescence activated cell sorter (FACS) to evaluate the levels of various proteins, cytokines and reactive oxygen species (ROS). RESULTS Our studies suggest that treatment with whole venom significantly reduces oxidative stress and LPS-stimulated activation of microglia. Also, purified peptides from crude venom exhibited potential anti-inflammatory properties. Further, whole venom was found to be targeting Akt and p38 MAPK pathways, leading to suppressed NF-κB phosphorylation in LPS challenged BV-2 cells. CONCLUSIONS VT venom possesses anti-inflammatory properties and can be further explored for their therapeutic potential in treating various inflammatory conditions of the central nervous system (CNS).
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Affiliation(s)
- Deepak Kumar Kaushik
- National Brain Research Centre, Near NSG campus, Manesar-122050, Gurgaon, Haryana, 122051, India,
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Food Peptidomics: Large scale analysis of small bioactive peptides — A pilot study. J Proteomics 2013; 88:83-91. [DOI: 10.1016/j.jprot.2013.02.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 02/18/2013] [Accepted: 02/21/2013] [Indexed: 11/24/2022]
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Guthals A, Clauser KR, Frank AM, Bandeira N. Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides. J Proteome Res 2013; 12:2846-57. [PMID: 23679345 DOI: 10.1021/pr400173d] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Full-length de novo sequencing of unknown proteins remains a challenging open problem. Traditional methods that sequence spectra individually are limited by short peptide length, incomplete peptide fragmentation, and ambiguous de novo interpretations. We address these issues by determining consensus sequences for assembled tandem mass (MS/MS) spectra from overlapping peptides (e.g., by using multiple enzymatic digests). We have combined electron-transfer dissociation (ETD) with collision-induced dissociation (CID) and higher-energy collision-induced dissociation (HCD) fragmentation methods to boost interpretation of long, highly charged peptides and take advantage of corroborating b/y/c/z ions in CID/HCD/ETD. Using these strategies, we show that triplet CID/HCD/ETD MS/MS spectra from overlapping peptides yield de novo sequences of average length 70 AA and as long as 200 AA at up to 99% sequencing accuracy.
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Affiliation(s)
- Adrian Guthals
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
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Fully automated chip-based nanoelectrospray combined with electron transfer dissociation for high throughput top-down proteomics. OPEN CHEM 2013. [DOI: 10.2478/s11532-012-0130-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
AbstractThe conventional protocol for protein identification by electrospray ionization mass spectrometry (MS) is based on enzymatic digestion which renders peptides to be analyzed by liquid chromatography-MS and collision-induced dissociation (CID) multistage MS, in the so-called bottom-up approach. Though this method has brought a significant progress to the field, many limitations, among which, the low throughput and impossibility to characterize in detail posttranslational modifications in terms of site(s) and structure, were reported. Therefore, the research is presently focused on the development of procedures for efficient top-down fragmentation of intact protein ions. In this context, we developed here an approach combining fully automated chip-based-nanoelectrospray ionisation (nanoESI), performed on a NanoMate robot, with electron transfer dissociation (ETD) for peptide and top-down protein sequencing and identification. This advanced analytical platform, integrating robotics, microfluidics technology, ETD and alternate ETD/CID, was tested and found ideally suitable for structural investigation of peptides and modified/functionalized peptides as well as for top-down analysis of medium size proteins by tandem MS experiments of significantly increased throughput and sensitivity. The obtained results indicate that NanoMate-ETD and ETD/CID may represent a viable alternative to the current MS strategies, with potential to develop into a method of routine use for high throughput top-down proteomics.
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