Abstract
This data article describes serum glycoprotein biomarker discovery and qualification datasets generated using lectin magnetic bead array (LeMBA) – mass spectrometry techniques, “Serum glycoprotein biomarker discovery and qualification pipeline reveals novel diagnostic biomarker candidates for esophageal adenocarcinoma” [1]. Serum samples collected from healthy, metaplastic Barrett׳s esophagus (BE) and esophageal adenocarcinoma (EAC) individuals were profiled for glycoprotein subsets via differential lectin binding. The biomarker discovery proteomics dataset consisting of 20 individual lectin pull-downs for 29 serum samples with a spiked-in internal standard chicken ovalbumin protein has been deposited in the PRIDE partner repository of the ProteomeXchange Consortium with the data set identifier PRIDE: PXD002442. Annotated MS/MS spectra for the peptide identifications can be viewed using MS-Viewer (〈http://prospector2.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msviewer〉) using search key “jn7qafftux”. The qualification dataset contained 6-lectin pulldown-coupled multiple reaction monitoring-mass spectrometry (MRM-MS) data for 41 protein candidates, from 60 serum samples. This dataset is available as a supplemental files with the original publication [1].
Highlights
This data article describes serum glycoprotein biomarker discovery and qualification datasets generated using lectin magnetic bead array (LeMBA) – mass spectrometry techniques, “Serum glycoprotein biomarker discovery and qualification pipeline reveals novel diagnostic biomarker candidates for esophageal adenocarcinoma” [1]
Serum samples collected from healthy, metaplastic Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) individuals were profiled for glycoprotein subsets via differential lectin binding
Serum glycoprotein sub-fraction according to lectin binding to 20 different lectins, for 3 patient groups from healthy, Barrett's esophagus and esophageal adenocarcinoma
Summary
Glyco-centric proteomics analysis for serum biomarker discovery and qualification Table, Figure, Graph, Western-blot images The data for the biomarker discovery screen was acquired using an Agilent 6520 quadrupole time of flight (QTOF) coupled with a Chip Cube and 1200 HPLC. The lectin pulldowns were subjected to on-bead trypsin digestion followed by mass spectrometric analyses for protein identification and relative quantitation. Serum glycoprotein sub-fraction according to lectin binding to 20 different lectins, for 3 patient groups from healthy, Barrett's esophagus and esophageal adenocarcinoma. The data can be used to compare lectin-pulldown proteomes from different serum samples/. Raw QTOF spectra, searched peptide-spectrum matches and protein level quantitation for serum proteins isolated by binding to each of 20 lectins per serum sample for biomarker discovery. Peptide and protein level quantitation for serum proteins isolated by 6 individual lectin per serum sample for biomarker qualification. To profile differentially glycosylated serum proteins between disease conditions, each serum sample was subjected to parallel pulldown using 20 different lectins, prior to on-bead tryptic digest. The lectins used are: AAL, BPL, ConA, DSA, ECA, EPHA, GNL, HAA, HPA, JAC, LPHA, MAA, NPL, PSA, SBA, SNA, STL, UEA, WFA and WGA [2]
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