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. 2022 Apr 7;13:1900. doi: 10.1038/s41467-022-29530-y

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a Comparison of the performance between Glyco-Decipher, StrucGP, pGlyco 3.0, MSFragger-Glyco and Byonic using the dataset of mouse tissues. Top: Comparison between Glyco-Decipher and other software tools in the performance of glycopeptide-spectrum interpretation. Green: the spectra matched to identical peptide backbones in Glyco-Decipher and another tool. Orange: the spectra commonly identified in Glyco-Decipher and another tool but matched to different peptide backbones. Gray: spectra specifically matched by another tool. Bottom: Comparison between Glyco-Decipher and other software tools in peptide sequence identification. Green: the peptide sequence commonly identified by Glyco-Decipher and another tool in pair comparison. Gray: the peptide sequence specifically matched by another tool in pair comparison. b FDR analysis using the ¹³C/¹⁵N metabolically labeled yeast dataset. The isotope-based FDR was calculated by matching ¹³C/¹⁵N isotopic peak pairs in MS1 spectra (line). Red line: FDR analysis based on the total GPSM results of each tool; blue line: FDR analysis based on the GPSM results that overlapped with Glyco-Decipher; purple line: FDR analysis based on the GPSMs specifically identified by each tool. The proportions of GPSMs of oligo-mannose glycans with composition of Hex(n)HexNAc(2) (green pie), NeuAc (orange pie) or NeuGc (red pie) containing glycans identified by each tool are shown in the bottom table. Source data are provided as a Source Data file. c Distributions of GPSMs of ammonium-adducted glycans reported by Glyco-Decipher and pGlyco 3.0. d Number of ammonium adduction GPSMs with/without oligo-mannose glycan composition. e Comparison of glycopeptide identification results between Glyco-Decipher and StrucGP/pGlyco 3.0. The additional (gain), overlap and lost identifications of Glyco-Decipher compared to other software tools are indicated by blue, green and orange bars, respectively. f Distributions of mannose-6-phosphate (M6P) GPSMs (bars) and intact glycopeptides (dots) across mouse tissues reported by Glyco-Decipher and pGlyco 3.0. All M6P identifications were validated by the diagnostic oxonium ion (phosphorylated hexose, m/z = 243.0269) in the glycopeptide spectra.