Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Conference Object Citation - Scopus: 1Ranking Tandem Mass Spectra: and the Impact of Database Size and Scoring Function on Peptide Spectrum Matches(Institute of Electrical and Electronics Engineers Inc., 2013) Has, Canan; Kundakçı, Cemal Ulaş; Altay, Aybuge; Allmer, JensProteomics is currently driven by mass spectrometry. For the analysis of tandem mass spectra many computational algorithms have been proposed. There are two approaches, one which assigns a peptide sequence to a tandem mass spectrum directly and one which employs a sequence database for looking up possible solutions. The former method needs high quality spectra while the latter can tolerate lower quality spectra. Since both methods are computationally expensive, it is sensible to establish spectral quality using an independent fast algorithm. In this study, we first establish proper settings for database search algorithms for the analysis of spectra in our gold benchmark dataset and then analyze the performance of ScanRanker, an algorithm for quality assessment of tandem MS spectra, on this ground truth data. We found that OMSSA and MSGFDB have limitations in their scoring functions but were able to form a proper consensus prediction using majority vote for our benchmark data. Unfortunately, ScanRanker's results do not correlate well with the consensus and ScanRanker is also too slow to be used in the capacity it is supposed to be used. © 2013 IEEEConference Object Relative Protein Quantitation With Post Translational Modifications in Mass Spectrometry Based Proteomics(Institute of Electrical and Electronics Engineers Inc., 2010) Allmer, JensMass spectrometry has become the tool of choice for most investigations in proteomics. Identification of proteins from complex mixtures has long been achieved and is now routinely used in countless high throughput studies. Quantitation by mass spectrometry is comparably newer and many different strategies have been proposed. One such strategy quantitates the difference in protein expression level among samples via extracted ion chromatograms, or spectral counts or a combination thereof. Another strategy involves mass modifications of the analytes in one or more of the samples under investigation. MSMAG has been developed as an extension to 2DB and it has been shown that it can aid in quantitation of data from experiments employing label-free quantitation. Recently, it has been extended to allow for analysis of data based on labelling strategies. This also makes it possible to quickly visualize and investigate inherent mass differences as presented by post translational modifications. ©2009 IEEE.