Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Conference Object Citation - Scopus: 1De Novo Markup Language, a Standard To Represent De Novo Sequencing Results From Ms/Ms Data(Institute of Electrical and Electronics Engineers Inc., 2012) Takan, Savaş; Allmer, JensProteomics is the study of the proteins that can be derived from a genome. For the identification and sequencing of proteins, mass spectrometry has become the tool of choice. Within mass spectrometry-based proteomics, proteins can be identified or sequenced by either database search or de novo sequencing. Both methods have certain advantages and drawbacks but in the long run we envision de novo sequencing to become the predominant tool. Currently, de novo sequencing results are stored in arbitrary file formats, depending on the developers of the algorithms. We identified this as a large and unnecessary obstacle while integrating results from multiple de novo sequencing algorithms. Therefore, we designed a standard file format for the representation of de novo sequencing results. We further developed an application programming interface since we identified the lack of proper APIs as another obstacle, introducing a needlessly high learning curve for developers. © 2012 IEEE.Conference 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.Conference Object Citation - WoS: 5Citation - Scopus: 5Preparation of Ceramic Composite Membranes for Protein Separation(Trans Tech Publications, 2004) Erdem, İlker; Çiftçioğlu, Muhsin; Harsa, Hayriye ŞebnemCeramic supports were prepared from fine alumina and zirconia powders by dry-pressing and slip-casting. These supports were heat treated in the 1100° - 1200°C temperature range and dip-coated with ceramic sols prepared from alkoxides by using sol-gel methods. The average sol particle sizes were measured as 3-7 nm for zirconia and 30-40 nm for alumina by laser scattering technique. The optimum heat treatment temperature range was determined as 500°-600°C for dip-coated membranes by using TGA (thermo gravimetric analysis) results. The microstructure of the ceramic composite membranes was investigated by SEM (Scanning electron microscope). The clean water permeability (CWP) of the membranes was tested by using deionized water in a filtration set-up. Separation experiments were performed with bovine serum albumin (BSA, Stokes diameter: 7 nm) solution and whey to determine the protein separation capacity of the composite membranes. The CWP of the dry pressed alumina supports heat treated at 1100°C was found to be higher than the permeability of the slip-casted zirconia supports heat treated at 1200°C. The protein retention of the slip-casted zirconia support was determined as 60% by using UV-Vis spectrophotometer (Abs. at 280nm). A protein retention value of 96% was achieved for whey after the modification of the support with dip-coating. The permeate flux was 40 L/m2hour for dry-pressed alumina support dip-coated with zirconia sol calcined at 500°C.