A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identification
Abstract Background Glycosylation is an important modification to proteins that plays a significant role in biological processes. Glycan structures are characterized by liquid chromatography (LC) combined with mass spectrometry (MS), but data interpretation of LC/MS and MS/MS data can be time-consum...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-06-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05346-5 |
| _version_ | 1797801256937324544 |
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| author | Ashna Dhingra Zayla Schaeffer Natalia I. Majewska Nepomuceno Jennifer Au Joomi Ahn |
| author_facet | Ashna Dhingra Zayla Schaeffer Natalia I. Majewska Nepomuceno Jennifer Au Joomi Ahn |
| author_sort | Ashna Dhingra |
| collection | DOAJ |
| description | Abstract Background Glycosylation is an important modification to proteins that plays a significant role in biological processes. Glycan structures are characterized by liquid chromatography (LC) combined with mass spectrometry (MS), but data interpretation of LC/MS and MS/MS data can be time-consuming and arduous when analyzed manually. Most of glycan analysis requires dedicated glycobioinformatics tools to process MS data, identify glycan structure, and display the results. However, software tools currently available are either too costly or heavily focused on academic applications, limiting their use within the biopharmaceutical industry for implementing the standardized LC/MS glycan analysis in high-throughput manner. Additionally, few tools provide the capability to generate report-ready annotated MS/MS glycan spectra. Results Here, we present a MATLAB-based app, GlyKAn AZ, which can automate data processing, glycan identification, and customizable result displays in a streamlined workflow. MS1 and MS2 mass search algorithms along with glycan databases were developed to confirm the fluorescent labeled N-linked glycan species based on accurate mass. A user-friendly graphical user interface (GUI) streamlines the data analysis process, making it easy to implement the software tool in biopharmaceutical analytical laboratories. The databases provided with the app can be expanded through the Fragment Generator functionality which automatically identifies fragmentation patterns for new glycans. The GlyKAn AZ app can automatically annotate the MS/MS spectra, yet this data display feature remains flexible and customizable by users, saving analysts’ time in generating individual report-ready spectra figures. This app accepts both OrbiTrap and matrix-assisted laser desorption/ionization–time of flight (MALDI–TOF) MS data and was successfully validated by identifying all glycan species that were previously identified manually. Conclusions The GlyKAn AZ app was developed to expedite glycan analysis while maintaining a high level of accuracy in positive identifications. The app’s customizable user inputs, polished figures and tables, and unique calculated outputs set it apart from similar software and greatly improve the current manual analysis workflow. Overall, this app serves as a tool for streamlining glycan identification for both academic and industrial needs. |
| first_indexed | 2024-03-13T04:47:42Z |
| format | Article |
| id | doaj.art-a54c50223a8c4704aee364f0496806c2 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-03-13T04:47:42Z |
| publishDate | 2023-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-a54c50223a8c4704aee364f0496806c22023-06-18T11:26:26ZengBMCBMC Bioinformatics1471-21052023-06-0124111710.1186/s12859-023-05346-5A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identificationAshna Dhingra0Zayla Schaeffer1Natalia I. Majewska Nepomuceno2Jennifer Au3Joomi Ahn4Bioprocess Technologies and Engineering, BioPharmaceuticals R&D, AstraZenecaBioprocess Technologies and Engineering, BioPharmaceuticals R&D, AstraZenecaDepartment of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins UniversityCell Culture and Fermentation Sciences, BioPharmaceuticals R&D, AstraZenecaAnalytical Sciences, BioPharmaceuticals R&D, AstraZenecaAbstract Background Glycosylation is an important modification to proteins that plays a significant role in biological processes. Glycan structures are characterized by liquid chromatography (LC) combined with mass spectrometry (MS), but data interpretation of LC/MS and MS/MS data can be time-consuming and arduous when analyzed manually. Most of glycan analysis requires dedicated glycobioinformatics tools to process MS data, identify glycan structure, and display the results. However, software tools currently available are either too costly or heavily focused on academic applications, limiting their use within the biopharmaceutical industry for implementing the standardized LC/MS glycan analysis in high-throughput manner. Additionally, few tools provide the capability to generate report-ready annotated MS/MS glycan spectra. Results Here, we present a MATLAB-based app, GlyKAn AZ, which can automate data processing, glycan identification, and customizable result displays in a streamlined workflow. MS1 and MS2 mass search algorithms along with glycan databases were developed to confirm the fluorescent labeled N-linked glycan species based on accurate mass. A user-friendly graphical user interface (GUI) streamlines the data analysis process, making it easy to implement the software tool in biopharmaceutical analytical laboratories. The databases provided with the app can be expanded through the Fragment Generator functionality which automatically identifies fragmentation patterns for new glycans. The GlyKAn AZ app can automatically annotate the MS/MS spectra, yet this data display feature remains flexible and customizable by users, saving analysts’ time in generating individual report-ready spectra figures. This app accepts both OrbiTrap and matrix-assisted laser desorption/ionization–time of flight (MALDI–TOF) MS data and was successfully validated by identifying all glycan species that were previously identified manually. Conclusions The GlyKAn AZ app was developed to expedite glycan analysis while maintaining a high level of accuracy in positive identifications. The app’s customizable user inputs, polished figures and tables, and unique calculated outputs set it apart from similar software and greatly improve the current manual analysis workflow. Overall, this app serves as a tool for streamlining glycan identification for both academic and industrial needs.https://doi.org/10.1186/s12859-023-05346-5GlycosylationGlycansTandem mass spectrometryMatrix-assisted laser desorption/ionizationMATLABLiquid chromatography |
| spellingShingle | Ashna Dhingra Zayla Schaeffer Natalia I. Majewska Nepomuceno Jennifer Au Joomi Ahn A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identification BMC Bioinformatics Glycosylation Glycans Tandem mass spectrometry Matrix-assisted laser desorption/ionization MATLAB Liquid chromatography |
| title | A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identification |
| title_full | A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identification |
| title_fullStr | A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identification |
| title_full_unstemmed | A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identification |
| title_short | A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identification |
| title_sort | matlab based app to improve lc ms ms data analysis for n linked glycan peak identification |
| topic | Glycosylation Glycans Tandem mass spectrometry Matrix-assisted laser desorption/ionization MATLAB Liquid chromatography |
| url | https://doi.org/10.1186/s12859-023-05346-5 |
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