Protein extraction and processing Cardiac proteins were extracted following subcellular fractionation by differential centrifugation over density gradients39. Excised cardiac tissues were homogenized in an extraction buffer composed of 250 mM sucrose, 10 mM HEPES, 10 mM Tris, 1 mM EGTA, 10 mM ...
3.2. Feature Vector Extraction Whether the encoded features are reliable or not can heavily affect the performance of PPIs prediction. The main challenge is how to effectively describe and represent an interacting protein pairs by a fixed length feature vector, in which the essential information conte...
acquisition lies within the possibility to interrogate a larger mass range in an LC/MS time frame because of the larger mass steps, yielding a more complex MS/MS spectrum at each step. The maintenance of high specificity can be achieved by the use of HR-MS/MS enabling tighter extraction ...
The extraction of 1 kg potassium phosphate in a phase system formed in the presence of ethanol costs approximately 6 to 7 DM. This is within the same order as for the cost resulting from the purchase price of 3 DM/kg salt and the additional costs for deposition of the primary bottom ...
For cytosolic soluble protein extraction, cells (equal number per replicate and per condition) were washed twice with phosphate-buffered saline (PBS) and incubated with a digitonin-based lysis buffer (50 mM tris pH 7.4, 0.01% digitonin, 5 mM EDTA, 150 mM NaCl, protease, and phosphatase...
In addition, the life cycle approach is selected due to its comprehensive nature, allowing for an all-encompassing evaluation of environmental impacts throughout the entire life cycle of the proteins, from raw material extraction, production, and supermarket gate. This method is crucial for ...
For the filter extraction, we used a protocol based on Kunert et al. [49] with some modifications. Briefly, each filter was cut into 16 segments. For TSP, three complete air filters (7 days sampling time) were pooled and extracted in different batches. In addition, one baked filter as ...
These distorting effects of the integration method are independent of the peak-picking method (centroid, gaussian peak detection etc.) that is applied by the data extraction software processing the raw data of the mass spectrometer. Quant itself uses MS/MS data extracted by other means and therefo...
The phenotypic profile of a gene, referred to as the gene-associated phenotype, can be obtained by large-scale text-mining of biomedical records using information extraction and retrieval techniques, and filtering the biomedical terms with specific vocabularies such as that from the Unified Medical ...
the cells were exposed to heavy SILAC medium and collected at different time points. After protein extraction, proteolysis with trypsin, sample preparation, and subsequent LC-MS/MS analysis, the peptides were identified by the Mascot database search engine and quantified using the isobarQuant softwar...