Glycopeptide variable window SWATH for improved Data Independent Acquisition glycoprotein analysis.

Glycopeptide variable window SWATH for improved Data Independent Acquisition glycoprotein analysis.
Anal Biochem. 2020 Feb 28;:113667
Authors: Zhou C, Schulz BL
Abstract
N-glycosylation plays an essential role in regulating protein folding and function in eukaryotic cells. Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH) has proven useful as a data independent acquisition (DIA) MS method for analysis of glycoproteins and their glycan modifications. By separating the entire m/z range into consecutive isolation windows, DIA-MS allows comprehensive MS data acquisition and high-sensitivity detection of molecules of interest. Variable width DIA windows allow optimal analyte measurement, as peptide ions are not evenly distributed across the full m/z range. However, the m/z distribution of glycopeptides is different to that of unmodified peptides because of their large glycan structures. Here, we improved the performance of DIA glycoproteomics by using variable width windows optimized for glycopeptides. This method allocates narrow windows at m/z ranges rich in glycopeptides, improving analytical specificity and performance. We show that related glycoforms must fall in separate windows to allow accurate glycopeptide measurement. We demonstrate the utility of the method by comparing the cell wall glycoproteomes of wild-type and N-glycan biosynthesis deficient yeast and showing improved measureme...

Source: Analytical Biochemistry - February 27, 2020 Category: Biochemistry Authors: Zhou C, Schulz BL Tags: Anal Biochem Source Type: research