Search results for "proteomics."
showing 10 items of 523 documents
Data-independent acquisition strategies for quantitative proteomics
2013
In shotgun proteomics, data-dependent precursor acquisition (DDA) is widely used to profile protein components in complex samples. Although very popular, there are some inherent limitations to the DDA approach, such as irreproducible precursor ion selection, under-sampling and long instrument cycle times. Unbiased ‘data-independent acquisition’ (DIA) strategies try to overcome those limitations. In MSE, which is supported by Waters Q-TOF instrument platforms, such as the Synapt G2-S, a wide band pass filter is used for precursor selection. During acquisition, alternating MS scans are collected at low and high collision energy (CE), providing precursor and fragment ion information, respectiv…
In-depth evaluation of software tools for data-independent acquisition based label-free quantification.
2015
Label-free quantification (LFQ) based on data-independent acquisition workflows currently experiences increasing popularity. Several software tools have been recently published or are commercially available. The present study focuses on the evaluation of three different software packages (Progenesis, synapter, and ISOQuant) supporting ion mobility enhanced data-independent acquisition data. In order to benchmark the LFQ performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, Escherichia coli). This model dataset simulates complex biological samples con…
Serum proteome profiling of primary breast cancer indicates a specific biomarker profile.
2011
Non-invasive biomarkers for early breast cancer detection are urgently needed, as the risk of recurrent morbidity and mortality is closely related to the stage of the disease at the time of primary surgery. Currently, there are no established clinical biomarkers for breast cancer. Evaluation of protein expression patterns in body fluids using proteomic technologies can be used to discover new biomarkers for the detection of breast cancer. The aim of this study was to identify a biomarker signature identifying primary non-metastatic breast cancer and healthy controls. We screened 91 serum samples including 45 breast cancer patients and 46 healthy women using a proteomic approach. We found 14…
Omics approaches to study the oral microbiome
2015
Introducción La visión clásica de los microorganismos como agentes infecciosos ha propiciado que se consideren como meros agentes causales de enfermedades. Sin embargo, la larga historia de coexistencia entre microorganismos y los seres humanos, ha hecho que ambos se hayan adaptado mutuamente y coevolucionen (Dubos et al. 1965, McFall-Ngai 2002). De hecho, en el cuerpo humano habitan 1014 células bacterianas, un orden de magnitud más que células humanas (Savage 1977). Entre los beneficios que la microbiota aporta, están su contribución a digerir alimentos y a aportar nutrientes, regulación del metabolismo, maduración del sistema inmune, etc. Por ello, hoy en día las enfermedades de origen…
Changes in Cardiac Proteome and Metabolome Following Exposure to the Pahs Retene and Fluoranthene and Their Mixture in Developing Rainbow Trout Alevi…
2022
Exposure to polycyclic aromatic hydrocarbons (PAHs) is known to affect developing organisms. Utilization of different omics-based technologies and approaches could therefore provide a base for the discovery of novel mechanisms of PAH induced development of toxicity. To this aim, we investigated how exposure towards two PAHs with different toxicity mechanisms: retene (an aryl hydrocarbon receptor 2 (Ahr2) agonist), and fluoranthene (a weak Ahr2 agonist and cytochrome P450 inhibitor (Cyp1a)), either alone or as a mixture, affected the cardiac proteome and metabolome in newly hatched rainbow trout alevins (Oncorhynchus mykiss). In total, we identified 65 and 82 differently expressed proteins (…
Proteomics of different tissues
2006
Livre publié sous forme électronique; International audience
Effects of Cyclooxygenase Inhibitors on Apoptotic Neuroretinal Cells
2008
Glaucoma is characterized by a loss of retinal ganglion cells (RGC) which is associated with a decrease of visual function. Neuroprotective agents as a new therapeutic strategy could prevent the remaining neurons from apoptotic cell death. Previous studies have shown the involvement of the Cyclooxygenase (COX)-2 signalling in the apoptotic death of neurons. Herein we investigated the neuroprotective effect of COX-1/COX-2- and selective COX-2- inhibitors on apoptotic. R28, a neuroretinal cell line and determined the PGE2 levels by ELISA. Furthermore we investigated differences in protein expression in the cells after exposure to elevated pressure compared to untreated cells by ProteinChip a…
Proteomic patterns of cultured breast cancer cells and epithelial mammary cells.
2002
: Breast cancer is one of the leading causes of death from cancer among women in western countries. The different types of breast cancer are grouped into invasive and noninvasive forms. Among the invasive types, ductal infiltrating carcinoma (DIC) is the most common and aggressive form. Using an in vitro model consisting of a DIC-derived cell line (8701-BC) and a nontumoral mammary epithelial cell line (HB2), we used the proteomics approach to search for homology and differences in protein expression patterns between tumoral and nontumoral phenotypes. Within an analysis window comprising 1,750 discernible spots we have currently catalogued 140 protein spots of potential interest. Fifty-eigh…
Biopharma business models in Canada.
2011
This article provides new insights into the different strategy paths or business models currently being implemented by Canadian biopharma companies. Through a case-study methodology, seven biopharma companies pertaining to three business models were analyzed, leading to a broad set of results emerging from the following areas: activity, business model and strategy; management and human resources; and RD, technology and innovation strategy. The three business models represented were: model 1 (conventional biotech oriented to new drug development, radical innovation and search for discoveries); model 2 (development of a technology platform, usually in proteomics and bioinformatics); and model…
The response ofAsterochloris erici(Ahmadjian) Skaloud et Peksa to desiccation: a proteomic approach
2013
The study of desiccation tolerance of lichens, and of their chlorobionts in particular, has frequently focused on the anti- oxidant system that protects the cell against photo-oxidative stress during dehydration/rehydration cycles. In this study, we used proteomic and transcript analyses to assess the changes associated with desiccation in the isolated phycobiont Aste- rochloris erici. Algae were dried either slowly (5-6 h) or rapidly (<60 min), and rehydrated after 24 h in the desiccated state. To identify proteins that accumulated during the drying or rehydration processes, we employed two-dimensional (2D) difference gel electrophoresis (DIGE) coupled with individual protein identificatio…