Fig. 3: GlycoBinder enables streamlined MS3 data handling for advanced intact glycopeptide identification and accurate multiplexed quantification.
From: A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics
a The schematic workflow of GlycoBinder. b Different spectra-merging workflows produced different GPSM identification rates. TMT-labeled N-glycopeptides derived from DG75 cells were analyzed by Glyco-SPS-MS3 (48 raw files). All combined mgf files were searched using pGlyco 2 against a human database under 2% FDR. c Correlation of reporter ion intensities extracted by RawTools and PD. Each circle represents the extracted reporter ion intensity from a scan. A total of 14,081 reporter ions were compared. d Comparison of the two-step search with single searches using various databases (see main text). Sizes of the databases (light blue) and the resulting numbers of identified glycoforms (light brown) are shown. Source data are provided as a Source Data file.
