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Liu Y, Chen YN, Cheng J, Yan JX, Xue CY, Pan HY, Shen XY, Zhou J, Jiang P, Zhou YL, Zhang XX. Ultrasensitive HPLC-MS Quantification of S-(2-Succino) Cysteine Based on Ethanol/Acetyl Chloride Derivatization in Fumarate Accumulation Cells. Anal Chem 2023; 95:1817-1822. [PMID: 36625376 DOI: 10.1021/acs.analchem.2c03573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Succination is a nonenzymatic and irreversible post-translational modification (PTM) with important biological significance, yielding S-(2-succino) cysteine (2SC) residue. This PTM is low in abundance and often requires a large amount of protein samples for 2SC quantification. In this work, an efficient quantification method based on ethanol/acetyl chloride chemical derivatization was developed. The three carboxyl groups of 2SC were all esterified to increase hydrophobicity, greatly improving its ionization efficiency. The sensitivity was increased by 112 times; the limit of detection was reduced to 0.885 fmol, and the protein usage was reduced by at least 10 times. The established method was used to detect the overall concentration of 2SC in fumarate accumulation cells quantitatively.
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Affiliation(s)
- Ying Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu-Nan Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jie Cheng
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jin-Xin Yan
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chen-Yu Xue
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing 100038, China
| | - Hui-Yu Pan
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xu-Yang Shen
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng Jiang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Quantitation and sensory properties of three newly identified pyroglutamyl oligopeptides in sake. Biosci Biotechnol Biochem 2019; 83:357-364. [DOI: 10.1080/09168451.2018.1530095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
ABSTRACT
Three new peptides: (pGlu)L-ethyl, (pGlu)LFGP-ethyl and (pGlu)LFNP-ethyl, were identified in the search for pyroglutamyl oligopeptide ethyl esters in sake. The ethyl esterified peptides in sake were quantitated using stable isotope dilution analysis and additional quantitation of (pGlu)L was performed using an external standard method. The concentrations of (pGlu)L-ethyl and (pGlu)L in 33 commercial sake samples ranged from 0.16 to 1.57 mg/L and 1.49 to 7.55 mg/L, respectively. The sensory properties of the pyroglutamyl oligopeptide ethyl esters and corresponding non-esterified peptides were examined: the estimated difference threshold of (pGlu)L (2.0 mg/L) and (pGlu)L-ethyl (0.267 mg/L) was exceeded in 32 and 26 samples, respectively. Estimated thresholds of (pGlu)LFGP-ethyl and (pGlu)LFNP-ethyl were often lower than the levels in quantitated sake samples. The sensory effects of these pyroglutamyl dipeptides on a model sake quality may be negative because of their unpleasant taste, however, (pGlu)LFNP-ethyl may be positive because of its mild taste.
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Hashizume K, Ito T, Igarashi S. Quantitation using a stable isotope dilution assay (SIDA) and thresholds of taste-active pyroglutamyl decapeptide ethyl esters (PGDPEs) in sake. Biosci Biotechnol Biochem 2017; 81:426-430. [DOI: 10.1080/09168451.2016.1259554] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
A stable isotope dilution assay (SIDA) for two taste-active pyroglutamyl decapeptide ethyl esters (PGDPE1; (pGlu)LFGPNVNPWCOOC2H5, PGDPE2; (pGlu)LFNPSTNPWCOOC2H5) in sake was developed using deuterated isotopes and high-resolution mass spectrometry. Recognition thresholds of PGDPEs in sake were estimated as 3.8 μg/L for PGDPE1 and 8.1 μg/L for PGDPE2, evaluated using 11 student panelists aged in their twenties. Quantitated concentrations in 18 commercial sake samples ranged from 0 to 27 μg/L for PGDPE1 and from 0 to 202 μg/L for PGDPE2. The maximum levels of PGDPE1 and PGDPE2 in the sake samples were approximately 8 and 25 times higher than the estimated recognition thresholds, respectively. The results indicated that PGDPEs may play significant sensory roles in the sake. The level of PGDPEs in unpasteurized sake samples decreased during storage for 50 days at 6 °C, suggesting PGDPEs may be enzymatically decomposed.
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Affiliation(s)
- Katsumi Hashizume
- Department of Biological Resource Sciences, Akita Prefectural University, Akita, Japan
| | - Toshiko Ito
- Department of Biological Resource Sciences, Akita Prefectural University, Akita, Japan
| | - Shinya Igarashi
- Department of Biological Resource Sciences, Akita Prefectural University, Akita, Japan
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Paternoster V, Edhager AV, Sibbersen C, Nielsen AL, Børglum AD, Christensen JH, Palmfeldt J. Quantitative assessment of methyl-esterification and other side reactions in a standard propionylation protocol for detection of histone modifications. Proteomics 2016; 16:2059-63. [DOI: 10.1002/pmic.201500425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 03/18/2016] [Accepted: 04/08/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Veerle Paternoster
- Department of Biomedicine; Aarhus University; Aarhus Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research; i PSYCH, Aarhus and Copenhagen; Denmark
- Centre for Integrative Sequencing; i SEQ; Aarhus University; Denmark
| | | | - Christian Sibbersen
- Department of Chemistry; Aarhus University; Aarhus Denmark
- Department of Forensic Medicine; Bioanalytical Unit; Aarhus University; Aarhus Denmark
| | | | - Anders Dupont Børglum
- Department of Biomedicine; Aarhus University; Aarhus Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research; i PSYCH, Aarhus and Copenhagen; Denmark
- Centre for Integrative Sequencing; i SEQ; Aarhus University; Denmark
| | - Jane Hvarregaard Christensen
- Department of Biomedicine; Aarhus University; Aarhus Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research; i PSYCH, Aarhus and Copenhagen; Denmark
- Centre for Integrative Sequencing; i SEQ; Aarhus University; Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine; Aarhus University Hospital; Aarhus Denmark
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Vogel ER, Jackson W, Masterson DS. Efficient Esterification of Oxidized l-Glutathione and Other Small Peptides. Molecules 2015; 20:10487-95. [PMID: 26060914 PMCID: PMC6272753 DOI: 10.3390/molecules200610487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/30/2022] Open
Abstract
Oxidized l-glutathione was esterified to the tetra methyl ester using thionyl chloride in methanol solvent. Other alcohols were tested and the reaction progress was monitored via ESI-MS. This procedure proved to be compatible with other small peptides not containing serine and cysteine residues. In contrast to previously reported methods this procedure provided convenient access to esterified peptides requiring no purification, extended reaction times, or complicated reaction setups.
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Affiliation(s)
- Emily R Vogel
- Department of Chemistry and Biochemistry, the University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA.
| | - William Jackson
- Department of Chemistry and Biochemistry, the University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA.
| | - Douglas S Masterson
- Department of Chemistry and Biochemistry, the University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA.
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Couto N, Barber J, Gaskell SJ. Matrix-assisted laser desorption/ionisation mass spectrometric response factors of peptides generated using different proteolytic enzymes. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:1233-1240. [PMID: 22223413 DOI: 10.1002/jms.2009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Matrix-assisted laser desorption/ionisation (MALDI) mechanisms and the factors that influence the intensity of the ion signal in the mass spectrum remain imperfectly understood. In proteomics, it is often necessary to maximise the peptide response in the mass spectrum, especially for low abundant proteins or for proteolytic peptides of particular significance. We set out to determine which of the common proteolytic enzymes give rise to peptides with the best response factors under MALDI conditions. Standard proteins were enzymatically digested using four common proteases. We assessed relative response factors by coanalyzing the resulting digests. Thus, when tryptic peptides were added in equimolar quantities to their corresponding Asp-N, chymotrypsin and Glu-C digests, tryptic peptide signals were always predominant in the resulting MALDI mass spectra. Observable peaks attributable to non-tryptic peptides generally contained a terminal basic residue. It was proposed that a terminal basic residue has a disproportionate influence upon gas-phase basicity, and this hypothesis was supported by experiments with model isotopically labelled peptides. Experiments applying Cook's kinetic method showed that the peptide with a C-terminal arginine residue was more basic than the equivalent peptide with an N-terminal arginine, which was more basic than the peptide in which the arginine was mid-chain. Thus, the observation of the higher MALDI mass spectrometry response factors of tryptic peptides in comparison with peptides derived using other proteolytic enzymes corresponds with higher gas-phase basicities and may, along with other factors such as the complexity of the digest, influence the choice of enzyme in "bottom-up" proteomic experiments.
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Affiliation(s)
- Narciso Couto
- Michael Barber Centre for Mass Spectrometry, Manchester Interdisciplinary Biocentre, Princess Road, University of Manchester, Manchester, M1 7DN, UK
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Abstract
Chromatin proteins provide a scaffold for DNA packaging and a basis for epigenetic regulation and genomic maintenance. Despite understanding its functional roles, mapping the chromatin proteome (i.e. the "Chromatome") is still a continuing process. Here, we assess the biological specificity and proteomic extent of three distinct chromatin preparations by identifying proteins in selected chromatin-enriched fractions using mass spectrometry-based proteomics. These experiments allowed us to produce a chromatin catalog, including several proteins ranging from highly abundant histone proteins to less abundant members of different chromatin machinery complexes. Using a Normalized Spectral Abundance Factor approach, we quantified relative abundances of the proteins across the chromatin enriched fractions giving a glimpse into their chromosomal abundance. The large-scale data sets also allowed for the discovery of a variety of novel post-translational modifications on the identified chromatin proteins. With these comparisons, we find one of the probed methods to be qualitatively superior in specificity for chromatin proteins, but inferior in proteomic extent, evidencing a compromise that must be made between biological specificity and broadness of characterization. Additionally, we attempt to identify proteins in eu- and heterochromatin, verifying the enrichments by characterizing the post-translational modifications detected on histone proteins from these chromatin regions. In summary, our results provide insights into the value of different methods to extract chromatin-associated proteins and provide starting points to study the factors that may be involved in directing gene expression and other chromatin-related processes.
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Mandal AK, Ramasamy MRS, Sabareesh V, Openshaw ME, Krishnan KS, Balaram P. Sequencing of T-superfamily conotoxins from Conus virgo: pyroglutamic acid identification and disulfide arrangement by MALDI mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1396-404. [PMID: 17544293 DOI: 10.1016/j.jasms.2007.04.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 04/07/2007] [Accepted: 04/11/2007] [Indexed: 05/15/2023]
Abstract
De novo mass spectrometric sequencing of two Conus peptides, Vi1359 and Vi1361, from the vermivorous cone snail Conus virgo, found off the southern Indian coast, is presented. The peptides, whose masses differ only by 2 Da, possess two disulfide bonds and an amidated C-terminus. Simple chemical modifications and enzymatic cleavage coupled with matrix assisted laser desorption ionization (MALDI) mass spectrometric analysis aided in establishing the sequences of Vi1359, ZCCITIPECCRI-NH(2), and Vi1361, ZCCPTMPECCRI-NH(2), which differ only at residues 4 and 6 (Z = pyroglutamic acid). The presence of the pyroglutamyl residue at the N-terminus was unambiguously identified by chemical hydrolysis of the cyclic amide, followed by esterification. The presence of Ile residues in both the peptides was confirmed from high-energy collision induced dissociation (CID) studies, using the observation of w(n)- and d(n)-ions as a diagnostic. Differential cysteine labeling, in conjunction with MALDI-MS/MS, permitted establishment of disulfide connectivity in both peptides as Cys2-Cys9 and Cys3-Cys10. The cysteine pattern clearly reveals that the peptides belong to the class of T-superfamily conotoxins, in particular the T-1 superfamily.
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Affiliation(s)
- Amit Kumar Mandal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Brancia FL, Bereszczak JZ, Piatkowska E, Delneri D. Development of novel guanidino-labelling derivatisation (GLaD) reagents for liquid chromatography/matrix-assisted laser desorption/ionisation analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3069-76. [PMID: 17708507 DOI: 10.1002/rcm.3176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A new generation of guanidino-labelling (GLaD) reagents were developed for quantitative proteomics using offline microcapillary liquid chromatography (LC) matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS). In order to reduce the unwanted overlapping between the isotopic envelopes of the two differentially labelled peptide ions, a novel synthetic route was described for production of both (13)C- and (15)N-containing isotopomers of N,O-dimethylisourea. The use of these types of isotopes has no deleterious effect on the retention times of both differentially labelled peptides during offline microbore reversed-phase LC. In addition, the possibility to incorporate a mass difference of 4 Da can be exploited during post-source decay analysis to generate product ion spectra in which fragment ions containing the modifications appear as doublets in the corresponding product ion spectra, thus facilitating identification of the C-terminal fragment ions.
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Leitner A, Amon S, Rizzi A, Lindner W. Use of the arginine-specific butanedione/phenylboronic acid tag for analysis of peptides and protein digests using matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:1321-30. [PMID: 17340573 DOI: 10.1002/rcm.2967] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We have applied an arginine-specific labeling technique to the study of peptides by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The reaction converts the guanidine group of the arginine side chain by reacting it with 2,3-butanedione and an arylboronic acid. Despite the general chemical lability of the tag under acidic conditions, it was possible to employ acidic matrices like alpha-cyano-4-hydroxycinnamic acid without adverse effects, using the thin-layer technique for preparation. After optimizing the method using arginine-containing model peptides--for which sensitivity down to the low fmol range was demonstrated--the procedure was applied to enzymatic digests of several model proteins in solution and to protein spots in gels obtained by two-dimensional electrophoretic separation of cell lysate samples. Information on the presence of arginine in peptides can be easily obtained from the mass spectra by the characteristic mass shift and the isotope pattern resulting from the incorporation of boron. This information might serve as a valuable additional search constraint for achieving a higher degree of confidence for protein identification by peptide mass fingerprinting.
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Affiliation(s)
- Alexander Leitner
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria.
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:128-39. [PMID: 16402416 DOI: 10.1002/jms.948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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