GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis

Abstract

Identification evaluation and result dissemination are essential components in mass spectrometry-based proteomics analysis. The visualization of fragment ions in mass spectrum provides strong evidence for peptide identification and modification localization. Here, we present an easy-to-use tool, named GP-Plotter, for ion annotation of tandem mass spectra and corresponding image output. Identification result files of common searching tools in the community and user-customized files are supported as input of GP-Plotter. Multiple display modes and parameter customization can be achieved in GP-Plotter to present annotated spectra of interest. Different image formats, especially vector graphic formats, are available for image generation which is favorable for data publication. Notably, GP-Plotter is also well-suited for the visualization and evaluation of glycopeptide spectrum assignments with comprehensive annotation of glycan fragment ions. With a user-friendly graphical interface, GP-Plotter is expected to be a universal visualization tool for the community. GP-Plotter has been implemented in the latest version of Glyco-Decipher (v1.0.4) and the standalone GP-Plotter software is also freely available at https://github.com/DICP-1809.

Keywords: Glycoproteomics; Glycosylation; Proteomics; Software; Visualization.

Figure 1

The overall design of GP-Plotter A. Overview of GP-Plotter. B. Main graphic interface of GP-Plotter for users. The main panel of GP-Plotter contains four parts. (1) List of peptide identifications and corresponding mass spectra which are indexed with spectrum scan number. (2) Visualization pane of the selected spectrum in the spectrum identification list. (3) Table of candidate mass spectra to be saved as image. (4) Parameter setting pane for image generation.

Figure 2

The enumeration algorithm for theoretical glycan Y fragment ions in glycopeptide spectrum annotation H: Hex, hexose; N: HexNAc, N-acetylhexosamine; A: NeuAc, N-acetyl-neuraminic acid; F: Fuc, fucose.

Figure 3

Close inspection of chimeric spectra identified by different software tools with ion annotation of GP-Plotter A. Spectrum annotation based on the result of Glyco-Decipher. B. Spectrum annotation based on the result of Byonic. C. Spectrum annotation based on the result of pGlyco 3.0. In the glycopeptide spectrum, the identical peptide sequence of “TPASDPHGDNLTYSVFYTK” was identified by Glyco-Decipher, Byonic, and pGlyco3, but different glycan compositions were matched due to the isotopic shift in precursor correction: Hex(4)HexNAc(5)Fuc(2) was matched by Glyco-Decipher and pGlyco3, but Hex(4)HexNAc(5)NeuAc(1) was matched by Byonic.

Figure 4

Spectral visualization in GP-Plotter assists modification site localization on peptide sequences Diagnostic fragment ions, including neutral loss ions, for different phosphorylation sites (S6 and S7) on the peptide “GNAEGSSDEEGKLVIDEPAK” can be easily detected in the mirrored spectrum mode provided by GP-Plotter.