ABSTRACT: Dataset submission for journal publication:
Label-free quantification was performed using the software Progenesis LC-MS 3.0 (Nonlinear Dynamics, Germany). LC-MS runs were aligned to an automatically selected reference run. After peak picking, a list of the features was exported and analyzed using SearchGUI (Vaudel et al. 2011). Therefore, the list was divided 15 times and analyzed using the OMSSA and X!tandem search algorithm through the Uniprot/Trembel database (2013/07) of Canis familiaris entries. Established search parameters: tryptic digest with a maximum of one missed cleavage; fixed modification: carbamidomethylation of cysteine, variable modification: oxidation of methionine; peptide charge 2plus to 4plus; monoisotopic peptide masses; peptide tolerance of 0.3 Da; MS/MS tolerance of 0.5 Da. Data were imported into Peptide-Shaker (Version 0.22.5) and corrected with a false discovery rate of 0.05 (Barsnes et al. 2011; Vaudel et al. 2011). Afterwards, result files were imported to Progenesis and protein lists with calculated protein quantities were exported to Excel. For statistical analysis of the data a Students t-Test with a p-value less then 0.05 was performed with R (Team 2008).
Project description:Yeast was cultured in 2 parallel retentostats reaching near-zero growth. 5 time points were sampled from each reactor and labeled with 6-plex TMT. Pooled samples were fractionated with SCX. 2+ and 3+ fractions were run individually on a 3 h gradient of RP-UHPLC and sprayed into a Q-Exactive mass spectrometer. The raw data obtained, were initially processed with proteome discoverer 1.3 (Thermo Fisher, Bremen, Germany). The created peak lists were searched with Mascot (Matrix Science, Version 2.3) using the SGD database (containing 5779 entries) and the following parameters: 50 p.p.m. precursor mass tolerance and 0.05 Da fragment ion tolerance. Up to two missed cleavages were accepted, oxidation of methionine was set up as variable modification whereas cysteine carbamidomethylation and the TMT label on lysines and the N-terminus as fixed modifications. The resulting .dat files were exported and filtered for <1% false discovery rate at peptide level using in-house developed software Rockerbox (version 2.0.1) utilizing the percolator algorithm (van den Toorn et al, 2011). The filtering for significant changing proteins was done with the isobar software and a significance threshold of p ≤ 0.05. Isobar employs robust statistics that captures spectra and sample variability into a single statistical framework which is described in (Breitwieser et al, 2011).
Project description:Blood as connective tissue potentially contains evidence of all processes occurring within the organism, at least in trace amounts (Petricoin et al., 2006) . Because of their small size, peptides penetrate cell membranes and epithelial barriers more freely than proteins. Among the peptides found in blood, there are both fragments of proteins secreted by various tissues and performing their function in plasma and receptor ligands: hormones, cytokines and mediators of cellular response (Anderson et al., 2002) . In addition, in minor amounts, there are peptide disease markers (for example, oncomarkers) and even foreign peptides related to pathogenic organisms and infection agents. To propose an approach for detailed peptidome characterization, we carried out an LC-MS/MS analysis of blood serum and plasma samples taken from 20 healthy donors on a TripleTOF 5600+ mass-spectrometer. We prepared samples based on our previously developed method of peptide desorption from the surface of abundant blood plasma proteins followed by standard chromatographic steps (Ziganshin et al., 2011) . The mass-spectrometry peptidomics data presented in this article have been deposited to the ProteomeXchange Consortium (Deutsch et al., 2017)  via the PRIDE partner repository with the dataset identifier PXD008141 and 10.6019/PXD008141.
Project description:One of the dysbioses often observed in Crohn's disease (CD) patients is an increased abundance of Escherichia coli (10-100 fold compared to healthy individuals) (Gevers et al., 2014). The data reported is a large-scale proteome profile for E. coli isolates collected from CD patients and healthy individuals. 43 isolates were achieved from 30 CD patients (17 male, 12 female, median age 30) and 19 isolates from 7 healthy individuals (7 male, median age 19). Isolates were cultivated on LB medium at aerobic conditions up to medium log phase. Protein extraction was performed with sodium deoxycholate (DCNa) and urea, alcylation with tris(2-carboxyethyl)phosphine and iodacetamide. Protein trypsinolysis was performed as described in (Matyushkina et al., 2016). Total cell proteomes were analysed by shotgun proteomics with HPLC-MS/MS on a maXis qTOF mass-spectrometer. The data including HPLC-MS/MS raw files and exported Mascot search results was deposited to the PRIDE repository project accession: PXD010920, project https://doi.org/10.6019/PXD010920.
Project description:This paper summarises gas-chromatography (GC-MS) and preliminary UV-spectroscopy analyses data of fresh, unmodified venom of aculeate hymenopterans (ants, bees, wasps), mainly focusing on red imported fire ants. No solvents nor fractionation were used at any point, which is a novel approach to describing integral toxins cocktails as proposed by Fox et al. (2018a)  10.1016/j.toxicon.2018.02.050 where these results are discussed in deeper details. Herein we focus on further characterising the obtained venom extracted through a novel approach. Pertaining raw data is accessible from Fox et al. (2018b)  10.17632/cpnscw2gkc.1 including further relevant information regarding the used insects, machinery settings, chemical standards.
Project description:Sensing ability of caffeine interaction with Phe-Phe annotates (PNTs), is presented (Govindhan et al., 2017; Karthikeyan et al., 2014; Tavagnacco et al., 2013; Kennedy et al., 2011; Wang et al., 2017) [1-5] in this data set. Investigation of synthesized caffeine carrying peptide nanotubes are carried out by FT-Raman spectral analysis and high resolution transmission electron microscopy (HR-TEM). Particle size of the caffeine loaded PNTs is < 40 nm. The FT-Raman spectrum signals are enhanced in the region of 400-1700 cm-1. These data are ideal tool for the applications like biosensing and drug delivery research (DDS).
Project description:Mesenchymal stromal cells (MSCs), sometimes called mesenchymal stem cells, are cultured cells able to give rise to mature mesenchymal cells such as adipocytes, osteoblasts, and chondrocytes, and to secrete a wide range of trophic and immunomodulatory molecules. Evidence indicates that pericytes, cells that surround and maintain physical connections with endothelial cells in blood vessels, can give rise to MSCs (da Silva Meirelles et al., 2008 ; Caplan and Correa, 2011 ). We have compared the transcriptomes of highly purified, human adipose tissue pericytes subjected to culture-expansion in pericyte medium or MSC medium, with that of human adipose tissue MSCs isolated with traditional methods to test the hypothesis that their transcriptomes are similar (da Silva Meirelles et al., 2015 ). Here, we provide further information and analyses of microarray data from three pericyte populations cultured in pericyte medium, three pericyte populations cultured in MSC medium, and three adipose tissue MSC populations deposited in the Gene Expression Omnibus under accession number GSE67747.
Project description:The datasets presented in this article are related to the research articles entitled "Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies" (Bennike et al., 2015 ), and "Proteome Analysis of Rheumatoid Arthritis Gut Mucosa" (Bennike et al., 2017 ). The colon mucosa represents the main interacting surface of the gut microbiota and the immune system. Studies have found an altered composition of the gut microbiota in rheumatoid arthritis patients (Zhang et al., 2015; Vaahtovuo et al., 2008; Hazenberg et al., 1992) , ,  and inflammatory bowel disease patients (Morgan et al., 2012; Abraham and Medzhitov, 2011; Bennike, 2014) , , . Therefore, we characterized the proteome of colon mucosa biopsies from 10 inflammatory bowel disease ulcerative colitis (UC) patients, 11 gastrointestinal healthy rheumatoid arthritis (RA) patients, and 10 controls. We conducted the sample preparation and liquid chromatography mass spectrometry (LC-MS/MS) analysis of all samples in one batch, enabling label-free comparison between all biopsies. The datasets are made publicly available to enable critical or extended analyses. The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples.
Project description:PAHSAs are anti-diabetic and anti-inflammatory lipids. Syed et al. identify numerous experimental differences that likely account for the failure of Pflimlin et al. to observe PAHSA beneficial effects. The differences include different HFDs resulting in minimal/no glucose intolerance, different assay conditions, an LC-MS protocol that was not validated, and use of olive oil, a bioactive nutrient that improves glucose tolerance, as a vehicle.
Project description:1,2-Dibromoethane (DBE, ethylene dibromide) is a potent carcinogen due at least in part to its DNA cross-linking effects. DBE cross-links glutathione (GSH) to DNA, notably to sites on 2'-deoxyadenosine and 2'-deoxyguanosine ( Cmarik , J. L. , et al. ( 1991 ) J. Biol. Chem. 267 , 6672 - 6679 ). Adduction at the N6 position of 2'-deoxyadenosine (dA) had not been detected, but this is a site for the linkage of O6-alkylguanine DNA alkyltransferase ( Chowdhury , G. , et al. ( 2013 ) Angew. Chem. Int. Ed. 52 , 12879 - 12882 ). We identified and quantified a new adduct, S-[2-(N6-deoxyadenosinyl)ethyl]GSH, in calf thymus DNA using LC-MS/MS. Replication studies were performed in duplex oligonucleotides containing this adduct with human DNA polymerases (hPols) ?, ?, and ?, as well as with Sulfolobus solfataricus Dpo4, Escherichia coli polymerase I Klenow fragment, and bacteriophage T7 polymerase. hPols ? and ?, Dpo4, and Klenow fragment were able to bypass the adduct with only slight impedance; hPol ? and ? showed increased misincorporation opposite the adduct compared to that of unmodified 2'-deoxyadenosine. LC-MS/MS analysis of full-length primer extension products by hPol ? confirmed the incorporation of dC opposite S-[2-(N6-deoxyadenosinyl)ethyl]GSH and also showed the production of a -1 frameshift. These results reveal the significance of N6-dA GSH-DBE adducts in blocking replication, as well as producing mutations, by human translesion synthesis DNA polymerases.
Project description:Duplicate samples of bursal B- and stroma cells were isolated from four 21-day-old Ross 508 chickens as described (McCarthy, Burgess et al, 2005) except that we kept the stromal cells that do not pass through sterile gauze. Samples were analysed by DDF-MudPIT and the resulting spectra searched against an avian subset (AvDb; search term: gallus; 01/15/05) of the NRPD (NCBI) using Bioworks Browser 3.2 (ThermoElectron) as described (McCarthy, Burgess et al, 2005). The peptide (MS precursor ion) mass tolerance was set to 1.5 Da and the fragment ion (MS2) mass tolerance was set to 1.0 Da. Peptide matches were considered genuine if they had ÃƒÆ’Ã‚Â¢??Cn ÃƒÆ’Ã‚Â¢?Ãƒâ€šÃ‚Â¥ 0.1 and X correlation ÃƒÆ’Ã‚Â¢?Ãƒâ€šÃ‚Â¥ 1.9 (+1), 2.2 (+2), 3.75 (+3).