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Using the Paragon method [ 20], the peak lists were compared against the Uniprot mouse database.
Paragon method was used in Thorough ID search effort with Biological modifications selected in ID Focus.
MS/MS spectra generated from nanoLC/ESI-based IDA analyses were interrogated using ProteinPilot™ software 2.0 (Applied Biosystems, Foster City, CA) for database search against the FlyBase FB2008_06 D. virilis peptides database by Paragon method.
Analysis of the resulting LC-MS/MS files in ProteinPilot using the Paragon method [ 20] identified and quantified a total of 898 proteins common between 5, 12, and 24 month old mouse synaptic mitochondria.
ProteinPilot Software v2.0 (an updated and integrated version of ProQuant and ProGroup Viewer software applications) and the Paragon method [ 38] (Applied Biosystems MDS SCIEX) were used to analyze the MS data (.wiff files) to identify and quantify proteins resolved by LC-MS/MS [ 25].
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The confidence level for protein identification was set up to 1.3 (95%), which is the default setting for the detected protein threshold in a Paragon™ method.
MS/MS spectra were extracted and searched against the SwissProt database using ProteinPilot™ software (Applied Biosystems, Foster City, CA) with Paragon™ method and the following parameters: all species, trypsin as enzyme (one missed cleavage allowed), cysteine static modification with methylmethanethiosulfate and iTRAQ (peptide labeled at N-terminal and lysine) as sample type.
Post-translational modification analysis (using the ProteinPilot and special factors: phosphorylation emphasis, paragon search method) revealed that the cofilin form decreased by lovastatin was phosphorylated at S3, S8 and T16.
Two-thirds of the specimens with positive findings for paraprotein(s) were also confirmed by a conventional manual immunofixation electrophoresis method involving the use of Paragon Blue stain (Paragon; Beckman-Coulter, Brea, CA, USA).
It astonishes me that the country that touts itself as the beacon of democracy and fairness in the world, the paragon of justice and equality, does not have a uniform method of voting.
In his haste to portray the French as paragons of balance in food attitudes, Pollan overlooks French fad diets like the Montignac Method, a low-carb, Atkins-esque program run through a Gallic filter.
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