LC-MS/MS data characterising cell surface glycoproteins from chondrogenic progenitor cells and mesenchymal stem cells

This dataset contains LC-MS/MS data generated from chondrogenic progenitor cell (CPC) and mesenchymal stem cell (MSC) surface glycoproteins, enriched with an aminooxy-biotin-based glycocapture technique. Together these results provide proteomic data on the surfaceome of two closely related cell types relevant to cartilage biology and osteoarthritis.
Data were generated with a Dionex Ultimate 3000 RSLCnano liquid chromatography (LC) system coupled with a Bruker Impact II QTOF mass spectroscopy (MS) instrument with CaptiveSpray nanoBooster source. MS acquisition rate was 5 Hz, followed by 10–20 Hz MS2 acquisition rate, depending on precursor intensity. The 20 most intense ions from each MS scan were selected for fragmentation. LC-MS/MS analysis was performed in 3 biological replicates for each sample.
For each replicate, 4 files are provided:
.baf file - A binary file in the Bruker proprietary data format, directly output from the MS instrument..xml file - Peak list in an XML-based format..mgf file - Peak list compiled in to the Mascot Generic Format (MGF)..mzid file - MZidentML search result file generated using Mascot 2.6.
The first 3 letters of each file name indicate the cell type from which the data was generated (CPC or MSC), each with three technical replicates.