PARPST: a PARallel algorithm to find peptide sequence tags

Background: Protein identification is one of the most challenging problems in proteomics. Tandem mass spectrometry provides an important tool to handle the protein identification problem. Results: We developed a work-efficient parallel algorithm for the peptide sequence tag problem. The algorithm runs on the concurrent-read, exclusive-write PRAM in O(n) time using log n processors, where n is the number of mass peaks in the spectrum. The algorithm is able to find all the sequence tags having score greater than a parameter or all the sequence tags of maximum length. Our tests on 1507 spectra in the Open Proteomics Database shown that our algorithm is efficient and effective since achieves comparable results to other methods. Conclusions: The proposed algorithm can be used to speed up the database searching or to identify post-translational modifications, comparing the homology of the sequence tags found with the sequences in the biological database

A parallel algorithm for de novo peptide sequencing

Protein identification is a main problem in proteomics,the large-scale analysis of proteins. Tandem mass spec-trometry (MS/MS) provides an important tool to handleprotein identification problem. Indeed the spectrometeris capable of ionizing a mixture of peptides, essentiallyseveral copies of the same unknown peptide, dissociatingevery molecule into two fragments called complementaryions, and measuring the mass/charge ratios of the pep-tides and of their fragments. These measures are visualizedas mass peaks in a mass spectrum.There are two fundamental approaches to interpret thespectra. The first approach is to search in a database tofind the peptides that match the MS/MS spectra. This data-base search approach is effective for known proteins, butdoes not permit to detect novel proteins. This second taskcan be dealt with the de novo sequencing that computesthe amino acid sequence of the peptides directly fromtheir MS/MS spectra.In the de novo sequencing problem one knows the pep-tide mas

Metabolic Syndrome: Gender Differences

Metabolic syndrome is commonly defined as the association of multiple risk factors for the development of atherosclerotic disease. Despite the different definitions of diagnostic criteria, the presence of at least three of the following conditions defines the clinical presentation of the metabolic syndrome: atherogenic dyslipidemia (low levels of HDL cholesterol, high levels of triglycerides, apolipoprotein B and small and dense LDL), basically high levels of systolic and diastolic blood pressure, impaired fasting glycemia and abdominal obesity [1]. Primary pathogenic mechanisms underlying metabolic syndrome are mainly due to insulin resistance (or poor insulin sensitivity) and visceral obesity. Insulin resistance, a condition where insulin determines a lower biological effect than expected, is largely represented in patients with metabolic syndrome and it is associated with a high risk of developing type 2 diabetes in the short term. Obesity and physical inactivity represent predisposing conditions for the development of metabolic syndrome and perhaps represent the main mechanism underlying the epidemic of metabolic syndrome, as observed in recent years

Influence of Storage Temperature on Radiochemical Purity of 99mTc-Radiopharmaceuticals

The influence of effective room temperature on the radiochemical purity of 99mTc-radiopharmaceuticals was reported. This study was born from the observation that in the isolators used for the preparation of the 99mTc-radiopharmaceuticals the temperatures can be higher than those reported in the commercial illustrative leaflets of the kits. This is due, in particular, to the small size of the work area, the presence of instruments for heating, the continuous activation of air filtration, in addition to the fact that the environment of the isolator used for the 99mTc-radiopharmaceuticals preparation and storage is completely isolated and not conditioned. A total of 244 99mTc-radiopharmaceutical preparations (seven different types) have been tested and the radiochemical purity was checked at the end of preparation and until the expiry time. Moreover, we found that the mean temperature into the isolator was significantly higher than 25 C, the temperature, in general, required for the preparation and storage of 99mTc-radiopharmaceuticals. Results confirmed the radiochemical stability of radiopharmaceutical products. However, as required in the field of quality assurance, the impact that different conditions than those required by the manufacturer on the radiopharmaceuticals quality have to be verified before human administration