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Bioinformatics Pipeline for Improving Identification of Modified Proteins by Neutral Loss Peak Filtering

Garcia, Krystine
http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1440157843

Abstract Details

2015, Master of Science (MS), Ohio University, Biomedical Engineering (Engineering and Technology).
Research has found that the central dogma of molecular biology is much more complex than making a gene into mRNA and then protein. One way that this has been found to be true is in post-translational modification (PTM) of proteins. PTMs are changes to specific side chains of amino acids after translation from mRNA. Unfortunately, only a few have been carefully studied meaning that most are not well understood. In turn, this has created problems for current methods of protein identification. Tandem mass spectrometry (MS/MS) is one common method of protein isolation and fragmentation that is usually followed by computational analysis for protein and peptide identification. The output from MS/MS is a spectrum of ion mass-to-charge ratios (m/z) versus their intensity, or a peak list, which is fed into the identification software for analysis. While these programs are generally good at identification, they were not created to incorporate large numbers of modifications. The problem is that spectra can include significant amounts of noise from modifications that can mask the y- and b- ion peaks used for identification. This has caused preprocessing to become both prevalent and necessary for identification of modified proteins. Through preprocessing and filtering of peaks from MS/MS data, we have enhanced the identification of proteins with modifications and specific phenotypes, presenting scientists with a more powerful tool for their protein research.
Lonnie Welch, Dr. (Advisor)
Jennifer Hines, Dr. (Committee Member)
Frank Drews, Dr. (Committee Member)
Frank Schwartz, Dr. (Committee Member)
43 p.
Biochemistry; Bioinformatics; Biomedical Engineering; Computer Science
post-translational modifications; mass spectrometry; bioinformatics; peptide peak filtering; proteins

Recommended Citations

Citations

  • Garcia, K. (2015). Bioinformatics Pipeline for Improving Identification of Modified Proteins by Neutral Loss Peak Filtering [Master's thesis, Ohio University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1440157843

    APA Style (7th edition)

  • Garcia, Krystine. Bioinformatics Pipeline for Improving Identification of Modified Proteins by Neutral Loss Peak Filtering. 2015. Ohio University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1440157843.

    MLA Style (8th edition)

  • Garcia, Krystine. "Bioinformatics Pipeline for Improving Identification of Modified Proteins by Neutral Loss Peak Filtering." Master's thesis, Ohio University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1440157843

    Chicago Manual of Style (17th edition)

ohiou1440157843
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© 2015, all rights reserved.
This open access ETD is published by Ohio University and OhioLINK.