Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 2Citation - Scopus: 5Pgminer: Complete Proteogenomics Workflow; From Data Acquisition To Result Visualization(Elsevier Ltd., 2017) Has, Canan; Allmer, JensIn parallel with the development of nucleotide sequencing an equally important interest in further describing the sequence in terms of function arose and the latter represents the current bottleneck in the overall research question. Sequencing the transcriptome allows determination of expressed nucleotide sequences and using mass spectrometry allows sequencing on the protein level. Both approaches can only sequence a subset of the existing transcripts. Moreover, for example post translational modification events can only be determined on the proteomics level. Therefore, it is essential to combine proteomics and genomics. For that purpose, proteogenomics data analysis pipelines have been described. Here, we describe a novel proteogenomics workflow which encompasses everything from the acquisition of data to result visualization in the Konstanz Information Miner (KNIME), a state of the art workflow management and data analytics platform. We amended KNIME with a number of processes like peptide consensus prediction, peptide mapping, and database equalizing, as well as result visualization. This enabled construction of our new workflow, entitled PGMiner, which not only includes all data analysis steps, but is highly customizable which is rather cumbersome for most existing pipelines. Furthermore, no burdensome installation processes have to be performed making PGMiner the most user friendly tool available.Article Citation - WoS: 81Citation - Scopus: 102Effects of Equivalence Ratio on Species and Soot Concentrations in Premixed N-Heptane Flames(Elsevier Ltd., 2002) İnal, Fikret; Senkan, Selim M.The micro-structure of laminar premixed, atmospheric-pressure, fuel-rich flames of n-heptane/oxygen/argon has been studied at two equivalence ratios (C/O = 0.63 and C/O = 0.67). A heated quartz microprobe coupled to an online gas chromatography/mass spectrometry (HP 5890 Series II/HP 5972) has been used to establish the identities and absolute concentrations of stable major, minor, and trace species by the direct analysis of samples withdrawn from the flames. Benzene was the most abundant aromatic compound identified. The largest PAH detected were the family of C18H10 (molecular weight of 226) that include cyclopenta[cd]pyrene and benzo[ghi]fluoranthene, with peak concentrations reaching 8 ppm and 6 ppm, respectively. Soot particle diameters, number densities, and volume fractions were determined using classical light scattering and extinction measurements. The largest soot particle diameter measured was about 18 nm and the soot volume fraction reached the amount of 4.9 × 10-7.