WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 4Citation - Scopus: 4Protocol for Cell Surface Biotinylation of Magnetic Labeled and Captured Human Peripheral Blood Mononuclear Cells(Elsevier, 2022) Ayaz Güner, Şerife; Acar, Mustafa Burak; Boyvat, Dudu; Güner, Hüseyin; Bozalan, Habibe; Güzel, Melis; Yıldır, Selin Kübra; Altınsoy, Nilay; Fındık, Fatma; Karakükçü, Musa; Özcan, ServetAnalysis of the surfaceome of a blood cell subset requires cell sorting, followed by surface protein enrichment. Here, we present a protocol combining magnetically activated cell sorting (MACS) and surface biotinylation of the target cell subset from human peripheral blood mononuclear cells (PBMCs). We describe the steps for isolating target cells and their in-column surface biotinylation, followed by isolation and mass spectrometry analysis of biotinylated proteins. The protocol enables in-column surface biotinylation of specific cell subsets with minimal membrane disruption.Article Citation - WoS: 1Citation - Scopus: 1Dnmso; an Ontology for Representing De Novo Sequencing Results From Tandem-Ms Data(PeerJ Inc., 2020) Takan, Savaş; Allmer, JensFor the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.Article Citation - WoS: 47Citation - Scopus: 70Search for the X (5568) State Decaying Into B-s(0)pi(+/-) in Proton-Proton Collisions at Root S=8 Tev(American Physical Society, 2018) CMS Collaboration; Karapınar, GülerA search for resonancelike structures in the Bs0π± invariant mass spectrum is performed using proton-proton collision data collected by the CMS experiment at the LHC at s=8 TeV, corresponding to an integrated luminosity of 19.7 fb-1. The Bs0 mesons are reconstructed in the decay chain Bs0→J/ψφ, with J/ψ→μ+μ- and φ→K+K-. The Bs0π± invariant mass distribution shows no statistically significant peaks for different selection requirements on the reconstructed Bs0 and π± candidates. Upper limits are set on the relative production rates of the X(5568) and Bs0 states times the branching fraction of the decay X(5568)±→Bs0π±. In addition, upper limits are obtained as a function of the mass and the natural width of possible exotic states decaying into Bs0π±.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: 2Citation - Scopus: 2Changes in Protein Profiles of Multiple Myeloma Cells in Response To Bortezomib(Informa Healthcare, 2013) Turan, Taylan; Şanlı Mohamed, Gülşah; Baran, YusufThe objective of this study was to determine the changes in protein profiles of U-266 multiple myeloma cells in response to bortezomib. Bortezomib inhibited cell proliferation and increased the loss of mitochondrial membrane potential and caspase-3 activity in a dose-dependent manner. DECODON Delta2D Version 4.3 software demonstrated 37 differentially expressed protein spots: five proteins were newly formed, 10 proteins were lost, 12 proteins were up-regulated and 10 proteins were down-regulated in bortezomib-treated cells as compared to untreated cells. Some of the identified proteins after mass spectrometric analysis were as follows: apoptosis regulatory protein Siva (newly formed), caspase recruitment domain-containing protein 14 (lost), Ras-related protein Rab-25 (up-regulated), nuclear factor κB (NF-κB) p105 subunit (down-regulated). In summary, differentially expressed proteins of MM U-266 cells in response to bortezomib were analyzed and identified. The data obtained from this study may indicate the use of bortezomib for the treatment of various diseases.Article Citation - WoS: 10Citation - Scopus: 14Study of the Dijet Mass Spectrum in Pp›w+jets Events at ?s=7 Tev(American Physical Society, 2012) CMS Collaboration; Karapınar, GülerWe report an investigation of the invariant mass spectrum of the two jets with highest transverse momentum in pp→W+2-jet and W+3-jet events to look for resonant enhancement. The data sample corresponds to an integrated luminosity of 5.0 fb-1 collected with the CMS detector at √s=7 TeV. We find no evidence for the anomalous structure reported by the CDF Collaboration, and establish an upper limit of 5.0 pb at 95% confidence level on the production cross section for a generic Gaussian signal with mass near 150 GeV. Additionally, we exclude two theoretical models that predict a CDF-like dijet resonance near 150 GeV. © 2012 CERN.Article Citation - WoS: 215Citation - Scopus: 239Observation of Sequential Suppression in Pbpb Collisions(American Physical Society, 2012) CMS Collaboration; Karapınar, GülerThe suppression of the individual Υ(nS) states in PbPb collisions with respect to their yields in pp data has been measured. The PbPb and pp data sets used in the analysis correspond to integrated luminosities of 150μb -1 and 230nb-1, respectively, collected in 2011 by the CMS experiment at the LHC, at a center-of-mass energy per nucleon pair of 2.76TeV. The Υ(nS) yields are measured from the dimuon invariant mass spectra. The suppression of the Υ(nS) yields in PbPb relative to the yields in pp, scaled by the number of nucleon-nucleon collisions, RAA, is measured as a function of the collision centrality. Integrated over centrality, the RAA values are 0.56±0.08(stat)±0.07(syst), 0.12±0.04(stat)±0.02(syst), and lower than 0.10 (at 95% confidence level), for the Υ(1S), Υ(2S), and Υ(3S) states, respectively. The results demonstrate the sequential suppression of the Υ(nS) states in PbPb collisions at LHC energies. © 2012 CERN.Article Citation - WoS: 75Citation - Scopus: 80Search for Neutral Minimal Supersymmetric Standard Model Higgs Bosons Decaying To Tau Pairs in Pp Collisions at ?s=7tev(American Physical Society, 2011) Karapınar, Güler; Demir, Durmuş AliA search for neutral minimal supersymmetric standard model (MSSM) Higgs bosons in pp collisions at the LHC at a center-of-mass energy of 7 TeV is presented. The results are based on a data sample corresponding to an integrated luminosity of 36pb-1 recorded by the CMS experiment. The search uses decays of the Higgs bosons to tau pairs. No excess is observed in the tau-pair invariant-mass spectrum. The resulting upper limits on the Higgs boson production cross section times branching fraction to tau pairs, as a function of the pseudoscalar Higgs boson mass, yield stringent new bounds in the MSSM parameter space. © 2011 American Physical Society.Article Citation - WoS: 91Citation - Scopus: 106Algorithms for the De Novo Sequencing of Peptides From Tandem Mass Spectra(Taylor & Francis, 2011) Allmer, JensProteomics is the study of proteins, their time- and location-dependent expression profiles, as well as their modifications and interactions. Mass spectrometry is useful to investigate many of the questions asked in proteomics. Database search methods are typically employed to identify proteins from complex mixtures. However, databases are not often available or, despite their availability, some sequences are not readily found therein. To overcome this problem, de novo sequencing can be used to directly assign a peptide sequence to a tandem mass spectrometry spectrum. Many algorithms have been proposed for de novo sequencing and a selection of them are detailed in this article. Although a standard accuracy measure has not been agreed upon in the field, relative algorithm performance is discussed. The current state of the de novo sequencing is assessed thereafter and, finally, examples are used to construct possible future perspectives of the field. © 2011 Expert Reviews Ltd.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.