2026-06-11T13:01:20+02:00 https://library.wur.nl/oai

oai:library.wur.nl:wurpubs/342047 2026-03-31

urn:nbn:nl:ui:32-342047 2026-03-31 urn:nbn:nl:ui:32-342047/mods Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS America A.H.P. 125023022 0000-0002-0167-1194 0000000390072042 aut Cordewener J.H.G. 072809353 000000039570466X aut van Geffen M.H.A. aut Lommen A. 074967665 0000000388490931 aut Vissers J.P.C. aut Bino R.J. 071872353 0000000389715987 aut Hall R.D. 183190696 0000-0002-5786-768X 0000000118742043 aut text info:eu-repo/semantics/article 2006 10.1002/pmic.200500034 2-s2.0-32144446968 000235207700027 en A method for high-resolution proteomics analyses of complex protein mixtures is presented using multidimensional HPLC coupled to MS (MDLC-MS). The method was applied to identify proteins that are differentially expressed during fruit ripening of tomato. Protein extracts from red and green tomato fruits were digested by trypsin. The resulting highly complex peptide mixtures were separated by strong cation exchange chromatography (SCX), and subsequently analyzed by RP nano-LC coupled to quadrupole-TOF MS. For detailed quantitative comparison, triplicate RP-LC-MS runs were performed for each SCX fraction. The resulting data sets were analyzed using MetAlign software for noise and data reduction, multiple alignment and statistical variance analysis. For each RP-LC-MS chromatogram, up to 7000 mass components were detected. Peak intensity data were compared by multivariate and statistical analysis. This revealed a clear separation between the green and red tomato samples, and a clear separation of the different SCX fractions. MS/MS spectra were collected using the data-dependent acquisition mode from a selected set of differentially detected peptide masses, enabling the identification of proteins that were differentially expressed during ripening of tomato fruits. Our approach is a highly sensitive method to analyze proteins in complex mixtures without the need of isotope labeling. EPS-3 RIKILT - Business Unit Safety & Health PRI Bioscience Plant Physiology (PPH) comparative proteomics gel-electrophoresis liquid-chromatography mass-spectrometry membrane-proteins metabolites mixtures protein expression technology EPS-3 RIKILT - Business Unit Veiligheid & Gezondheid PRI Bioscience Plant Physiology (PPH) Proteomics 6 2 641 653 16159853 urn:nbn:nl:ui:32-342047/obj 2026-03-31 http://purl.org/eprint/accessRights/RestrictedAccess