DOI: 10.20350/digitalcsic/12683
title: Experimental data files of manuscript Peptidomic pipeline for biomarker hunting of defective pre-slaughter stress bovine meat assisted by liquid chromatography-mass spectrometry analysis and chemometrics

description: The dataset is made available under the Open Database License. Any rights in individual contents of the database are licensed under the Database Contents License. Please, read the full ODbL 1.0 license text for the exact terms that apply. Users of the dataset are free to: Share: copy, distribute and use the database, either commercially or non-commercially. Create: produce derivative works from the database. Adapt: modify, transform and build upon the database. Under the following conditions: Attribution: You must attribute any public use of the database, or works produced from the database. For any use or redistribution of the database, or works produced from it, you must make clear to others the license of the original database. Share-Alike: If you publicly use any adapted version of this database, or works produced from an adapted database, you must also offer that adapted database under the ODbL.
description: List of experimental data: A- mgf files_OFFGEL fractions HIGH 2_ddMS2 Mascot generic format (mgf) files from OFFGEL fractions (12) of HIGH 2 replicate as an example of identifications achieved in preliminary full-MS/dd-MS2 analysis. 1-Fraction 1 2-Fraction 2 3-Fraction 3 4-Fraction 4 5-Fraction 6 6-Fraction 6 7-Fraction 7 8-Fraction 8 9-Fraction 9 10-Fraction 10 11-Fraction 11 12-Fraction 12 NOTE: Files with .mgf extension are adequate for MS/MS interrogation in Mascot Search Engine (www.matrixscience.com) B-Preliminary MS1-potential peptide biomarkers_OFGL-CAL batch Full-MS1 analyses (mzML files) of highest calibration step of curves from OFGL-batch (NORMAL and HIGH pHu replicates, n=4) to perform the preliminary approach of potential peptide biomarkers. Calibration curves were from isolated replicates pooling their respective OFFGEL fractions considered (12). Statistical analysis of results will lead to the obtaining of candidates further studied by SRM assays. 1-E_CAL HIGH 1 2-E_CAL HIGH 2 3-E_CAL HIGH 3 4-E_CAL HIGH 4 5-E_CAL HIGH 1 6-E_CAL HIGH 2 7-E_CAL HIGH 3 8-E_CAL HIGH 4 NOTE: inspection of full-MS1 mzML extension is featured by open-source viewers and data processing solutions (i.e. MZmine 2; http://mzmine.github.io/download.html). C-SRM_OFGL-CAL batch SRM1 assay (RAW and mzML files) of calibration curves from NORMAL AND HIGH pHu replicates (n=4) submitted to OFFGEL fractionation/enrichment. Calibration curves were made from pooled fractions (12) of isolated replicates. OFGL-CAL HIGH 1 1-A 2-B 3-C 4-D 5-E_HIGH 1 OFGL-CAL HIGH 2 1-A 2-B 3-C 4-D 5-E_HIGH 2 OFGL-CAL HIGH 3 1-A 2-B 3-C 4-D 5-E_HIGH 3 OFGL-CAL HIGH 4 1-A 2-B 3-C 4-D 5-E_HIGH 4 OFGL-CAL NORMAL 1 1-A 2-B 3-C 4-D 5-E_NORMAL 1 OFGL-CAL NORMAL 2 1-A 2-B 3-C 4-D 5-E_NORMAL 2 OFGL-CAL NORMAL 3 1-A 2-B 3-C 4-D 5-E_NORMAL 3 OFGL-CAL NORMAL 4 1-A 2-B 3-C 4-D 5-E_NORMAL 4 NOTE: inspection of RAW extensions is enabled by freely available ThermoScientific Xcalibur and FreeStyle applications (https://thermo.flexnetoperations.com). Inspection of SRM mzML files can be featured by freeware solutions (i.e. Skyline, https://skyline.ms/wiki/home/software/Skyline/). D-SRM_Direct Extraction_Replicates Batch SRM 1 and 2 assays (RAW and mzML files) of biomarkers suggested by the preliminary full-MS1 approach. Protein extracts from replicates of meat groups assayed (n=6) were directly analyzed without a previous purification step. Replicates were separately analyzed. SRM 1-REPLICATES 1-HIGH 1 2-HIGH 2 3-HIGH 3 4-HIGH 4 5-HIGH 5 6-HIGH 6 7-Normal 1 8-Normal 2 9-Normal 3 10-Normal 4 11-Normal 5 12-Normal 6 SRM 2-REPLICATES 1-HIGH 1 2-HIGH 2 3-HIGH 3 4-HIGH 4 5-HIGH 5 6-HIGH 6 7-Normal 1 8-Normal 2 9-Normal 3 10-Normal 4 11-Normal 5 12-Normal 6 NOTE: inspection of RAW and mzML SRM files described above. E-SRM_Direct Extraction-CAL batch SRM 1 and 2 analyses (RAW and mzML files) of calibration curves from pooled NORMAL and HIGH pHu replicates, respectively. Protein extracts of replicates assayed were obtained without any previous purification step. SRM1-CAL HIGH-CAL 1-A 2-B 3-C 4-D 5-E NORMAL-CAL 1-A 2-B 3-C 4-D 5-E SRM2-CAL HIGH-CAL 1-A 2-B 3-C 4-D 5-E NORMAL-CAL 1-A 2-B 3-C 4-D 5-E NOTE: inspection of RAW and mzML SRM files described above. END