Dataset Information

Accurate LC peak boundary detection for ¹⁶O/¹⁸O labeled LC-MS data.

ABSTRACT: In liquid chromatography-mass spectrometry (LC-MS), parts of LC peaks are often corrupted by their co-eluting peptides, which results in increased quantification variance. In this paper, we propose to apply accurate LC peak boundary detection to remove the corrupted part of LC peaks. Accurate LC peak boundary detection is achieved by checking the consistency of intensity patterns within peptide elution time ranges. In addition, we remove peptides with erroneous mass assignment through model fitness check, which compares observed intensity patterns to theoretically constructed ones. The proposed algorithm can significantly improve the accuracy and precision of peptide ratio measurements.

SUBMITTER: Cui J

PROVIDER: S-EPMC3792097 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Accurate LC peak boundary detection for ¹⁶O/¹⁸O labeled LC-MS data.

Cui Jian J Petritis Konstantinos K Tegeler Tony T Petritis Brianne B Ma Xuepo X Jin Yufang Y Gao Shou-Jiang S J SJ Zhang Jianqiu Michelle JM

PloS one 20131007 10

In liquid chromatography-mass spectrometry (LC-MS), parts of LC peaks are often corrupted by their co-eluting peptides, which results in increased quantification variance. In this paper, we propose to apply accurate LC peak boundary detection to remove the corrupted part of LC peaks. Accurate LC peak boundary detection is achieved by checking the consistency of intensity patterns within peptide elution time ranges. In addition, we remove peptides with erroneous mass assignment through model fitn ...[more]

PMID: 24115998

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Project description:BackgroundGlycosylation 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.ResultsHere, 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.ConclusionsThe 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.

Dataset Information

Accurate LC peak boundary detection for ¹⁶O/¹⁸O labeled LC-MS data.

Publications

Accurate LC peak boundary detection for ¹⁶O/¹⁸O labeled LC-MS data.

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