There is currently a significant demand for glycomic software which enables rapid and accurate data analysis. The advances over recent years in mass spectrometry instrumentation and throughput has resulted is researchers being able to produce very large amounts of data in relatively short time periods. Since informatics developments have not kept pace with the advances in analytical technologies, data analysis now represents a major bottleneck in glycomics-based discoveries. This is especially problematic in the search for glycomic markers of cancer because the biological samples are analyzed in multiple replicates, creating a considerable amount of data which must be compared and statistically analyzed to evaluate the significance of the results. Thus, there is a significant need for software which assists researchers in analyzing their complex glycomics data in a high-throughput manner. The research proposed in this application is to design an easy to use software application that will allow the automated assignment of MSn spectra obtained for O-linked and N-linked glycans. We have previously developed a prototype computer algorithm that can take an MS/MS spectrum and annotate it by identifying the O-glycan(s) or N-glycan(s) that are most likely to have generated it. The specific aims of this proposal are to evolve this prototype software into a more general software package that we hope will ultimately become widely used by researchers in the glycomics community and even the wider research community.
Public Health Relevance Statement: The proposed studies will provide a software package which will perform automated assignment of MSn spectra obtained for O-linked and N-linked glycans. Since the absence of bioinformatic tools for glycomics analysis has been a major impediment toward the discovery of new glycan biomarkers, it is believed that the software developed here will be a valuable resource to a diverse set of researchers. Making this software available to the scientific community will increase the throughput of glycomics research and speed the discovery process.
Project Terms: Algorithms; Alpha-1-Fetoprotein; Alpha-Fetoglobulin; Amino Acid Sequence; Analysis, Data; Annotation, Automated; Area; Automated Annotation; Bio-Informatics; Bioinformatics; Biological; Blood Serum; Breast; Cancer of the Ovary; Cancerous; Cancers; Carcinoma; Carcinoma of the Liver Cells; Cirrhosis; Collection; Communities; Complex; Computer Programs; Computer software; Computers; Data; Data Analyses; Deoxygalactose; Development; Diagnostic; Disease; Disorder; Drugs; Epithelial Neoplasms, Malignant; Epithelial Tumors, Malignant; European; Fetuins; Food; Foundations; Fucose; Future; Glycans; Glycobiology; Glycoproteins; Goals; HCC; Hand; Health; Hepatocellular Carcinoma; Hepatocellular cancer; Hepatoma; Human; Human Characteristics; Human Nature; Human, General; Informatics; Instrumentation, Other; Investigators; Killings; Laboratories; Link; Malignant Neoplasms; Malignant Ovarian Neoplasm; Malignant Ovarian Tumor; Malignant Tumor; Malignant Tumor of the Ovary; Malignant neoplasm of ovary; Man (Taxonomy); Man, Modern; Mass Spectrum; Mass Spectrum Analysis; Medication; Medicine; Metabolic Glycosylation; Methods; Molecular Biology, Protein Sequencing; NIH; National Institutes of Health; National Institutes of Health (U.S.); Patients; Pattern; Peptide Sequence Determination; Pharmaceutic Preparations; Pharmaceutical Preparations; Phase; Photometry/Spectrum Analysis, Mass; Policies; Polysaccharides; Primary carcinoma of the liver cells; Process; Protein Sequencing; Protein Structure, Primary; Proteomics; Research; Research Personnel; Research Resources; Researchers; Resources; Sampling; Science; Science of Medicine; Scientist; Screening procedure; Sequence Determinations, Amino Acid; Sequence Determinations, Protein; Serum; Software; Solutions; Specificity; Spectrometry, Mass; Spectroscopy, Mass; Spectrum Analyses, Mass; Spectrum Analysis, Mass; Speed; Speed (motion); Structure; TM-MKR; Technology; Testing; Time; Tumor Cell; Tumor Markers; United States National Institutes of Health; alpha-Fetoproteins; alpha-Fucose; annotation schema; automated annotation; base; biomarker; clinical applicability; clinical application; computer annotation; computer program/software; design; designing; develop software; developing computer software; disease/disorder; drug/agent; epithelial carcinoma; frontier; glycosylation; instrument; instrumentation; malignancy; meetings; neoplasm/cancer; neoplastic cell; ovarian cancer; prognostic; protein sequence; prototype; screening; screenings; software development; tandem mass spectrometry; tool; tumor; user-friendly
