Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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COAR Access Rights: search.filters.coarAccessRights.open accessSubject: search.filters.subject.Tandem mass spectrometry

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  • Article
    Citation - WoS: 5
    Citation - Scopus: 5
    Non-Direct Sequence Ions in the Tandem Mass Spectrometry of Protonated Peptide Amides - an Energy-Resolved Study
    (American Chemical Society, 2013) Harrison, Alex G.; Taşoğlu, Çağdaş; Yalçın, Talat
    The fragmentation reactions of the MH+ ions of Leu-enkephalin amide and a variety of heptapeptide amides have been studied in detail as a function of collision energy using a QqToF beam type mass spectrometer. The initial fragmentation of the protonated amides involves primarily formation of bn ions, including significant loss of NH3 from the MH+ ions. Further fragmentation of these bn ions occurs following macrocyclization/ring opening leading in many cases to bn ions with permuted sequences and, thus, to formation of non-direct sequence ions. The importance of these non-direct sequence ions increases markedly with increasing collision energy, making peptide sequence determination difficult, if not impossible, at higher collision energies. [Figure not available: see fulltext.]
  • 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.