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Tian M, Zhang N, Liu X, Guo L, Yang L. Sequential on-line C-terminal sequencing of peptides based on carboxypeptidase Y digestion and optically gated capillary electrophoresis with laser-induced fluorescence detection. J Chromatogr A 2016; 1459:152-159. [PMID: 27425760 DOI: 10.1016/j.chroma.2016.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 01/09/2023]
Abstract
We report a novel method for sequential on-line C-terminal sequencing of peptides, which combines carboxypeptidase Y (CPY) digestion with on-line derivatization and optically gated capillary electrophoresis with laser-induced fluorescence detection (OGCE-LIF). Various factors that may affect the C-terminal sequencing were investigated and optimized. High repeatability of on-line derivatization and the sequential OGCE-LIF assay of amino acids (AAs) was achieved with relative standard deviation (RSD) (n=20) less than 1.5% and 3.2% for migration time and peak height, respectively. A total of 13 AAs was efficiently separated in the present study, indicating that the method can be used for sequencing of peptides consisting of the 13 AAs studied. Using two synthesized N-terminally blocked peptides as test examples, we show that the present method can on-line monitor the released AAs with a temporal resolution of 50s during the entire CPY digestion process. The rates of AA release as a function of digestion time were easily measured; thus, the AA sequence of the peptide was determined with just one OGCE assay. Our study indicates the present approach is an effective, reliable, and convenient method for rapid analysis of the C-terminal sequence of peptides, with potential application in peptide analysis and proteome research.
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Affiliation(s)
- Miaomiao Tian
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, PR China
| | - Ning Zhang
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, PR China
| | - Xiaoxia Liu
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, PR China
| | - Liping Guo
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, PR China
| | - Li Yang
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, PR China.
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2
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Grundy H, Reece P, Buckley M, Solazzo C, Dowle A, Ashford D, Charlton A, Wadsley M, Collins M. A mass spectrometry method for the determination of the species of origin of gelatine in foods and pharmaceutical products. Food Chem 2016. [DOI: 10.1016/j.foodchem.2015.05.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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3
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Balizs G, Weise C, Rozycki C, Opialla T, Sawada S, Zagon J, Lampen A. Determination of osteocalcin in meat and bone meal of bovine and porcine origin using matrix-assisted laser desorption ionization/time-of-flight mass spectrometry and high-resolution hybrid mass spectrometry. Anal Chim Acta 2011; 693:89-99. [DOI: 10.1016/j.aca.2011.03.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 11/29/2022]
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4
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Sachon E, Clodic G, Blasco T, Jacquot Y, Bolbach G. In-Source Fragmentation of Very Labile Peptides in Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Anal Chem 2009; 81:8986-92. [DOI: 10.1021/ac901449d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuelle Sachon
- Laboratoire des Biomolécules, Ecole Normale Supérieure (ENS), Université P. et M. Curie, UMR-CNRS 7203, 4 Place Jussieu, Case Courrier 182, 75005 Paris, France, and Plateforme de Spectrométrie de Masse et Protéomique, IFR83, Université P. et M. Curie, 7-9 Quai Saint Bernard, Case Courrier 41, 75005 Paris, France
| | - Gilles Clodic
- Laboratoire des Biomolécules, Ecole Normale Supérieure (ENS), Université P. et M. Curie, UMR-CNRS 7203, 4 Place Jussieu, Case Courrier 182, 75005 Paris, France, and Plateforme de Spectrométrie de Masse et Protéomique, IFR83, Université P. et M. Curie, 7-9 Quai Saint Bernard, Case Courrier 41, 75005 Paris, France
| | - Thierry Blasco
- Laboratoire des Biomolécules, Ecole Normale Supérieure (ENS), Université P. et M. Curie, UMR-CNRS 7203, 4 Place Jussieu, Case Courrier 182, 75005 Paris, France, and Plateforme de Spectrométrie de Masse et Protéomique, IFR83, Université P. et M. Curie, 7-9 Quai Saint Bernard, Case Courrier 41, 75005 Paris, France
| | - Yves Jacquot
- Laboratoire des Biomolécules, Ecole Normale Supérieure (ENS), Université P. et M. Curie, UMR-CNRS 7203, 4 Place Jussieu, Case Courrier 182, 75005 Paris, France, and Plateforme de Spectrométrie de Masse et Protéomique, IFR83, Université P. et M. Curie, 7-9 Quai Saint Bernard, Case Courrier 41, 75005 Paris, France
| | - Gérard Bolbach
- Laboratoire des Biomolécules, Ecole Normale Supérieure (ENS), Université P. et M. Curie, UMR-CNRS 7203, 4 Place Jussieu, Case Courrier 182, 75005 Paris, France, and Plateforme de Spectrométrie de Masse et Protéomique, IFR83, Université P. et M. Curie, 7-9 Quai Saint Bernard, Case Courrier 41, 75005 Paris, France
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Sungurov YV, Eremeev NL, Lebedev AT, Maloshitskaya OA, Rudenskaya GN, Semenova SA. A mass-spectrometric approach to primary screening of collagenolytic enzymes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2008; 34:392-8. [DOI: 10.1134/s1068162008030175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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A method of isolating the collagen (I) α2 chain carboxytelopeptide for species identification in bone fragments. Anal Biochem 2008; 374:325-34. [DOI: 10.1016/j.ab.2007.12.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 11/30/2007] [Accepted: 12/01/2007] [Indexed: 11/16/2022]
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7
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Development of C-terminal Sequencing Analysis of Protein and Peptide. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2007. [DOI: 10.1016/s1872-2040(08)60011-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Unnithan AG, Myer MJ, Veale CJ, Danell AS. MS/MS of protonated polyproline peptides: the influence of N-terminal protonation on dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:2198-2203. [PMID: 17964801 DOI: 10.1016/j.jasms.2007.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 09/19/2007] [Accepted: 09/20/2007] [Indexed: 05/25/2023]
Abstract
A unique collision-induced dissociation pattern was observed for protonated polyproline peptides of length n in which y(n-2) and/or y(n-4) ions were formed in much higher abundance than any other product ions. Cleavage occurs only at every other amide bond, such that product ions are formed only from the losses of even numbers of proline residues. Exclusive losses of even numbers of proline residues were not observed from sodiated peptides. Further study of the tandem mass spectrometry (MS/MS) patterns of protonated proline-rich peptides showed that the substitution of alanine in the second position of polyproline peptides did not prevent the dominant formation of y(n-2) and y(n-4) ions. The loss of ProAla to form the y(8) ion from (ProAlaPro(8)NH(2)+H)(+) was as abundant as the loss of ProPro from (Pro(10)NH(2)+H)(+). However, modification of the peptides that presumably affected the location of the proton on the peptide did alter the MS/MS spectra. Pro(10) and Pro(5) with blocked N-termini or with arginine substituted for the first proline residue did not form abundant y(n-2) or y(n-4) ions. MS(3) and double resonance experiments showed that dissociation of intermediate y(n) product ions can produce y(n-2) ions, but are not necessary dissociation pathway intermediates. This analysis suggests that the ionizing proton must be located at the N-terminus for the peptide ion to dissociate in this manner.
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Affiliation(s)
- Anita G Unnithan
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27878, USA
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Armirotti A, Millo E, Damonte G. How to discriminate between leucine and isoleucine by low energy ESI-TRAP MSn. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:57-63. [PMID: 17010643 DOI: 10.1016/j.jasms.2006.08.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 08/18/2006] [Accepted: 08/19/2006] [Indexed: 05/12/2023]
Abstract
In peptide sequencing experiments involving a single step tandem mass acquisition, leucine and isoleucine are indistinguishable because both are characterized by a 113 Da mass difference from the other peptide fragments in the MS2 spectrum. In this work, we propose a new method to distinguish between these two amino acids in consecutive MSn experiments, exploiting a gas-phase fragmentation of isoleucine that leads to a diagnostic 69 Da ion. We used this method to assess the Leu/Ile residues of several synthetic peptides. The procedure was then tested on a tryptic digest of myoglobin, assigning the correct amino acid in the majority of the peptides. This work was performed with an old and low-resolution instrument, thus demonstrating that our method is suitable for a wide number of ion trap mass spectrometers, not necessarily expensive or up-to-date.
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Affiliation(s)
- Andrea Armirotti
- Department of Experimental Medicine-Biochemistry Section and Center of Excellence for Biomedical Research (DIMES), University of Genoa, Genoa, Italy.
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Xue X, Wu S, Wang Z, Zhu Y, He F. Protein probabilities in shotgun proteomics: Evaluating different estimation methods using a semi-random sampling model. Proteomics 2006; 6:6134-45. [PMID: 17133366 DOI: 10.1002/pmic.200600070] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The calculation of protein probabilities is one of the most intractable problems in large-scale proteomic research. Current available estimating methods, for example, ProteinProphet, PROT_PROBE, Poisson model and two-peptide hits, employ different models trying to resolve this problem. Until now, no efficient method is used for comparative evaluation of the above methods in large-scale datasets. In order to evaluate these various methods, we developed a semi-random sampling model to simulate large-scale proteomic data. In this model, the identified peptides were sampled from the designed proteins and their cross-correlation scores were simulated according to the results from reverse database searching. The simulated result of 18 control proteins was consistent with the experimental one, demonstrating the efficiency of our model. According to the simulated results of human liver sample, ProteinProphet returned slightly higher probabilities and lower specificity than real cases. PROT_PROBE was a more efficient method with higher specificity. Predicted results from a Poisson model roughly coincide with real datasets, and the method of two-peptide hits seems solid but imprecise. However, the probabilities of identified proteins are strongly correlated with several experimental factors including spectra number, database size and protein abundance distribution.
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Affiliation(s)
- Xiaofang Xue
- Beijing Institute of Radiation Medicine, Beijing, China
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Lammi MJ, Häyrinen J, Mahonen A. Proteomic analysis of cartilage- and bone-associated samples. Electrophoresis 2006; 27:2687-701. [PMID: 16739228 DOI: 10.1002/elps.200600004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The skeleton of the human body is built of cartilage and bone, which are tissues that contain extensive amounts of extracellular matrix (ECM). In bone, inorganic mineral hydroxyapatite forms 50-70% of the whole weight of the tissue. Although the organic matrix of bone consists of numerous proteins, 90% of it is composed of type I collagen. In cartilage, ECM forms a major fraction of the tissue, type II collagen and aggrecans being the most abundant macromolecules. It is obvious that the high content of ECM components causes analytical problems in the proteomic analysis of cartilage and bone, analogous to those in the analysis of low-abundance proteins present in serum. The massive contents of carbohydrates present in cartilage proteoglycans, and hydroxyapatite in bone, further complicate the situation. However, the development of proteomic tools makes them more and more tempting also for research of musculoskeletal tissues. Application of proteomic techniques to the research of chondrocytes, osteoblasts, osteocytes, and osteoclasts in cell cultures can immediately benefit from the present knowledge. Here we make an overview to previous proteomic research of cartilage- and bone-associated samples and evaluate the future prospects of applying proteomic techniques to investigate key events, such as cellular signal transduction, in cartilage- and bone-derived cells.
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Affiliation(s)
- Mikko J Lammi
- Department of Anatomy, Institute of Biomedicine, University of Kuopio, Finland.
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Lehmann WD, Wei J, Hung CW, Gabius HJ, Kirsch D, Spengler B, Kübler D. Effective solvation of alkaline earth ions by proline-rich proteolytic peptides of galectin-3 upon electrospray ionisation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:2404-10. [PMID: 16841364 DOI: 10.1002/rcm.2598] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In an analysis of a combined chymotrypsin/AspN digest of galectin-3 by positive ion nano-electrospray ionisation mass spectrometry (nanoESI-MS) several peptides were observed which showed metal adduct ions as their most abundant ion signals. The most prominent adduct ions were observed at m/z values corresponding to [M+40]2+, [M+41]3+, and [M+42]4+ ions. Detailed investigation of the [M+40]2+ ion of the peptide GAPAGPLIVPY showed that it was not, as originally expected, a [M+H+39K]2+ adduct ion but had the composition [M+40Ca]2+. This was verified by several approaches: (i) nanoESI-MS/MS of the [M+Ca]2+ adduct ions resulted in the virtually exclusive formation of doubly charged fragment ions; (ii) mass determination by quadrupole time-of-flight (QTOF)-MS provided a preliminary identification; and (iii) accurate mass measurement using nanoESI Fourier transform ion cyclotron resonance (FTICR)-MS at a mass resolving power of 500 000 allowed the specific detection and identification of the isobaric ion pairs [M+40Ca]2+/[M+H+39K]2+ and [M+24Mg]2+/[M+H+23Na]2+. All peptides in the chymotryptic galectin-3 digest without a basic residue (K or R) showed addition of calcium as the most prominent ionisation principle. A further common feature of these nonbasic peptides was the presence of several proline residues, which is assumed to be a factor promoting the intense addition of calcium. It was observed that the common trace levels of sodium and calcium in analytical grade solvents (about 1-10 microM) are sufficient to generate the [M+H+23Na]2+ and [M+40Ca]2+ ions as the most prominent species of the peptide GAPAGPLIVPY. We conclude that the sequence motifs P-XX-P and P-XXX-P favour the solvation of alkaline earth ions in ESI-MS. In view of the successful detection of physiological Ca/protein interactions by ESI-MS, this finding may point to a solvation of Ca2+ by galectin in solution. The findings open new routes of research in the study of metal/protein and metal/peptide interactions
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Affiliation(s)
- Wolf D Lehmann
- Central Spectroscopy, German Cancer Research Center, Heidelberg, Germany.
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1390-401. [PMID: 16237664 DOI: 10.1002/jms.811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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14
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447491 DOI: 10.1002/cfg.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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