Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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  • Article
    Citation - WoS: 4
    Citation - Scopus: 12
    Existing Bioinformatics Tools for the Quantitation of Post-Translational Modifications
    (Springer Verlag, 2012) Allmer, Jens
    Mass spectrometry (MS)-based proteomics, by itself, is a vast and complex area encompassing various mass spectrometers, different spectra, and search result representations. When the aim is quantitation performed in different scanning modes at different MS levels, matters become additionally complex. Quantitation of post-translational modifications (PTM) represents the greatest challenge among these endeavors. Many different approaches to quantitation have been described and some of these can be directly applied to the quantitation of PTMs. The amount of data produced via MS, however, makes manual data interpretation impractical. Therefore, specialized software tools meet this challenge. Any software currently able to quantitate differentially labeled samples may theoretically be adapted to quantitate differential PTM expression among samples as well. Due to the heterogeneity of mass spectrometry-based proteomics; this review will focus on quantitation of PTM using liquid chromatography followed by one or more stages of mass spectrometry. Currently available free software, which either allow analysis of PTM or are easily adaptable for this purpose, is briefly reviewed in this paper. Selected studies, especially those related to phosphoproteomics, shall be used to highlight the current ability to quantitate PTMs. © Springer-Verlag 2010
  • Article
    Citation - WoS: 1
    Citation - Scopus: 2
    Label-Free Quantitation, an Extension To 2db
    (Springer Verlag, 2010) Allmer, Jens
    Determining the differential expression of proteins under different conditions is of major importance in proteomics. Since mass spectrometry-based proteomics is often used to quantify proteins, several labelling strategies have been developed. While these are generally more precise than label-free quantitation approaches, they imply specifically designed experiments which also require knowledge about peptides that are expected to be measured and need to be modified. We recently designed the 2DB database which aids storage, analysis, and publication of data from mass spectrometric experiments to identify proteins. This database can aid identifying peptides which can be used for quantitation. Here an extension to the database application, named MSMAG, is presented which allows for more detailed analysis of the distribution of peptides and their associated proteins over the fractions of an experiment. Furthermore, given several biological samples in the database, label-free quantitation can be performed. Thus, interesting proteins, which may warrant further investigation, can be identified en passant while performing high-throughput proteomics studies. © 2009 Springer-Verlag.