Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/27237
Full metadata record
DC FieldValueLanguage
dc.contributor.authorBoonen, Kurt-
dc.contributor.authorDe Haes, Wouter-
dc.contributor.authorVAN HOUTVEN, Joris-
dc.contributor.authorVERDONCK, Rik-
dc.contributor.authorBaggerman, Geert-
dc.contributor.authorVALKENBORG, Dirk-
dc.contributor.authorSchoofs, Liliane-
dc.date.accessioned2018-10-26T11:47:22Z-
dc.date.available2018-10-26T11:47:22Z-
dc.date.issued2018-
dc.identifier.citationSchrader, Michael; Fricker, Lloyd (Ed.). Peptidomics: Methods and Strategies, Humana Press, p. 141-159-
dc.identifier.isbn9781493975372-
dc.identifier.issn1940-6029-
dc.identifier.urihttp://hdl.handle.net/1942/27237-
dc.description.abstractIn differential peptidomics, peptide profiles are compared between biological samples and the resulting expression levels are correlated to a phenotype of interest. This, in turn, allows us insight into how peptides may affect the phenotype of interest. In quantitative differential peptidomics, both label-based and label-free techniques are often employed. Label-based techniques have several advantages over label-free methods, primarily that labels allow for various samples to be pooled prior to liquid chromatography-mass spectrometry (LC-MS) analysis, reducing between-run variation. Here, we detail a method for performing quantitative peptidomics using stable amine-binding isotopic and isobaric tags.-
dc.description.sponsorship1.Research Group of Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium 2.Research Group of Molecular and Functional Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium 3.Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven, Belgium 4.Research Group of Molecular Developmental Physiology and Signal Transduction, Department of Biology, KU Leuven, Leuven, Belgium 5.Center for Proteomics, University of Antwerp, Antwerp, Belgium 6.Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium-
dc.language.isoen-
dc.publisherHumana Press-
dc.relation.ispartofseriesMethods in Molecular Biology-
dc.rightsSpringer Science+Business Media, LLC 2018-
dc.subject.otherpeptidomics; isotopic tags; isobaric tags; mass spectrometry; protocols-
dc.titleQuantitative Peptidomics with Isotopic and Isobaric Tags-
dc.typeBook Section-
local.bibliographicCitation.authorsSchrader, Michael-
local.bibliographicCitation.authorsFricker, Lloyd-
dc.identifier.epage159-
dc.identifier.spage141-
local.bibliographicCitation.jcatB2-
local.publisher.placeNew York, NY, USA-
dc.relation.references1. Fricker LD (2007) Neuropeptidomics to study peptide processing in animal models of obesity. Endocrinology 148:4185–4190. https://doi.org/10.1210/en.2007-0123 CrossRefPubMedGoogle Scholar 2. Wardman JH, Zhang X, Gagnon S et al (2010) Analysis of peptides in prohormone convertase 1/3 null mouse brain using quantitative peptidomics. J Neurochem 114:215–225. https://doi.org/10.1111/j.1471-4159.2010.06760.x PubMedPubMedCentralGoogle Scholar 3. Miller LK, Hou X, Rodriguiz RM et al (2011) Mice deficient in endothelin-converting enzyme-2 exhibit abnormal responses to morphine and altered peptide levels in the spinal cord. J Neurochem 119:1074–1085. https://doi.org/10.1111/j.1471-4159.2011.07513.x CrossRefPubMedPubMedCentralGoogle Scholar 4. Brockmann A, Annangudi SP, T a R et al (2009) Quantitative peptidomics reveal brain peptide signatures of behavior. Proc Natl Acad Sci U S A 106:2383–2388. https://doi.org/10.1073/pnas.0813021106 CrossRefPubMedPubMedCentralGoogle Scholar 5. Chen R, Hui L, Cape SS et al (2010) Comparative neuropeptidomic analysis of food intake via a multi-faceted mass spectrometric approach. ACS Chem Neurosci 1:204–214. https://doi.org/10.1021/cn900028s CrossRefPubMedGoogle Scholar 6. Sterkel M, Urlaub H, Rivera-Pomar R, Ons S (2011) Functional proteomics of neuropeptidome dynamics during the feeding process of Rhodnius prolixus. J Proteome Res 10:3363–3371. https://doi.org/10.1021/pr2001012 CrossRefPubMedGoogle Scholar 7. Che F-Y, Fricker LD (2005) Quantitative peptidomics of mouse pituitary: comparison of different stable isotopic tags. J Mass Spectrom 40:238–249. https://doi.org/10.1002/jms.743 CrossRefPubMedGoogle Scholar 8. Thompson A, Schäfer J, Kuhn K et al (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75:1895–1904 CrossRefPubMedGoogle Scholar 9. Romanova EV, Dowd SE, Sweedler JV (2013) Quantitation of endogenous peptides using mass spectrometry based methods. Curr Opin Chem Biol 17:801–808. https://doi.org/10.1016/j.cbpa.2013.05.030 CrossRefPubMedGoogle Scholar 10. Fricker LD (2015) Limitations of mass spectrometry-based peptidomic approaches. J Am Soc Mass Spectrom 26:1981. https://doi.org/10.1007/s13361-015-1231-x CrossRefPubMedGoogle Scholar 11. Verdonck R, De Haes W, Cardoen D et al (2016) Fast and reliable quantitative peptidomics with labelpepmatch. J Proteome Res 15:1080–1089. https://doi.org/10.1021/acs.jproteome.5b00845 CrossRefPubMedGoogle Scholar 12. Maes E, Hadiwikarta WW, Mertens I et al (2016) CONSTANd: a normalization method for isobaric labeled spectra by constrained optimization. Mol Cell Proteomics 15(8):2779–2790 CrossRefPubMedPubMedCentralGoogle Scholar 13. Maes E, Valkenborg D, Baggerman G et al (2015) Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments. PLoS One 10:e0120115. https://doi.org/10.1371/journal.pone.0120115 CrossRefPubMedPubMedCentralGoogle Scholar 14. McAlister GC, Nusinow DP, Jedrychowski MP et al (2014) MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Anal Chem 86:7150–7158. https://doi.org/10.1021/ac502040v CrossRefPubMedPubMedCentralGoogle Scholar 15. Wühr M, Haas W, McAlister GC et al (2012) Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster. Anal Chem 84:9214–9221. https://doi.org/10.1021/ac301962s CrossRefPubMedPubMedCentralGoogle Scholar 16. Ma B, Zhang K, Hendrie C et al (2003) PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom 17:2337–2342. https://doi.org/10.1002/rcm.1196 CrossRefPubMedGoogle Scholar 17. Han X, He L, Xin L et al (2011) PeaksPTM: mass spectrometry-based identification of peptides with unspecified modifications. J Proteome Res 10:2930–2936. https://doi.org/10.1021/pr200153k CrossRefPubMedGoogle Scholar 18. Zhang J, Xin L, Shan B et al (2012) PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification. Mol Cell Proteomics 11:M111.010587. https://doi.org/10.1074/mcp.M111.010587 CrossRefPubMedGoogle Scholar 19. Han Y, Ma B, Zhang K (2005) SPIDER: software for protein identification from sequence tags with de novo sequencing error. J Bioinforma Comput Biol 3:697 CrossRefGoogle Scholar 20. R Core Team (2016) R: a language and environment for statistical computing. Vienna, Austria. http://www.r-project.org/. Accessed 24 Oct 2016 21. Shadforth IP, Dunkley TP, Lilley KS, Bessant C (2005) i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics 6:145. https://doi.org/10.1186/1471-2164-6-145 CrossRefPubMedPubMedCentralGoogle Scholar 22. Morano C, Zhang X, Fricker LD (2008) Multiple isotopic labels for quantitative mass spectrometry. Anal Bioanal Chem 80:9298–9309 CrossRefGoogle Scholar 23. Chiva C, Sabidó E (2014) HCD-only fragmentation method balances peptide identification and quantitation of TMT-labeled samples in hybrid linear ion trap/orbitrap mass spectrometers. J Proteome 96:263–270. https://doi.org/10.1016/j.jprot.2013.11.013 CrossRefGoogle Scholar 24. Gelman JS, Wardman J, Bhat VB et al (2012) Quantitative peptidomics to measure neuropeptide levels in animal models relevant to psychiatric disorders. In: Kobeissy FH (ed) Methods Mol Biol. Humana Press, pp 487–503 Google Scholar 25. Gelman JS, Dasgupta S, Berezniuk I, Fricker LD (2013) Analysis of peptides secreted from cultured mouse brain tissue. Biochim Biophys Acta 1834:2408–2417. https://doi.org/10.1016/j.bbapap.2013.01.043 CrossRefPubMedPubMedCentralGoogle Scholar 26. Wardman J, Fricker LD (2011) Quantitative peptidomics of mice lacking peptide-processing enzymes. In: Mbikay M, Seidah NG (eds) Methods Mol Biol. Humana Press, Totowa, pp 191–206 Google Scholar 27. Vaudel M, Burkhart JM, Zahedi RP et al (2015) PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol 33:22–24. https://doi.org/10.1038/nbt.3109 CrossRefPubMedGoogle Scholar 28. Rost HL, Sachsenberg T, Aiche S et al (2016) OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13:741–748. https://doi.org/10.1038/nmeth.3959 CrossRefPubMedGoogle Scholar-
local.type.refereedRefereed-
local.type.specifiedBook Section-
local.relation.ispartofseriesnr1719-
dc.identifier.doi10.1007/978-1-4939-7537-2_9-
local.bibliographicCitation.btitlePeptidomics: Methods and Strategies-
item.accessRightsRestricted Access-
item.contributorBoonen, Kurt-
item.contributorDe Haes, Wouter-
item.contributorVAN HOUTVEN, Joris-
item.contributorVERDONCK, Rik-
item.contributorBaggerman, Geert-
item.contributorVALKENBORG, Dirk-
item.contributorSchoofs, Liliane-
item.fullcitationBoonen, Kurt; De Haes, Wouter; VAN HOUTVEN, Joris; VERDONCK, Rik; Baggerman, Geert; VALKENBORG, Dirk & Schoofs, Liliane (2018) Quantitative Peptidomics with Isotopic and Isobaric Tags. In: Schrader, Michael; Fricker, Lloyd (Ed.). Peptidomics: Methods and Strategies, Humana Press, p. 141-159.-
item.validationvabb 2020-
item.fulltextWith Fulltext-
Appears in Collections:Research publications
Files in This Item:
File Description SizeFormat 
boonen2018.pdf
  Restricted Access		Published version742.18 kBAdobe PDFView/Open    Request a copy
Show simple item record

SCOPUSTM   
Citations

2
checked on Sep 2, 2020

WEB OF SCIENCETM
Citations

8
checked on Apr 15, 2024

Page view(s)

104
checked on Sep 7, 2022

Download(s)

84
checked on Sep 7, 2022

Google ScholarTM

Check

Altmetric


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.