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When performing a decoy search, Mascot generates a randomized sequence of the same length for every sequence in the target database. The decoy sequence is generated such that it has the same average amino acid composition as the target database. The FDR is estimated as the ratio of decoy database matches to target database matches.
Structure of a typical L-alpha-amino acid in the "neutral" form. Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. [1] Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. [2]
Molecular weight (M.W.) (for molecular compounds) and formula weight (F.W.) (for non-molecular compounds), are older terms for what is now more correctly called the relative molar mass (M r). [8] This is a dimensionless quantity (i.e., a pure number, without units) equal to the molar mass divided by the molar mass constant .
The number average molar mass is a way of determining the molecular mass of a polymer.Polymer molecules, even ones of the same type, come in different sizes (chain lengths, for linear polymers), so the average molecular mass will depend on the method of averaging.
Mass of b 2-ions are listed in Table 2, as well as single amino acids that have equal mass to b 2-ions. [15] The mass of b 2-ion = mass of two amino acid residues + 1. Table 2. Mass of b2-ions in peptide fragmentation [16] Identify a sequence ion series by the same mass difference, which matches one of the amino acid residue masses (see Table 1).
It is the number of Nitrogens x 56.1 (Mwt of KOH) x 1000 (convert to milligrams) divided by molecular mass of the amine functional compound. So using Tetraethylenepentamine (TEPA) as an example: Mwt = 189, number of nitrogen atoms = 5 So 5 x 1000 x 56.1/189 = 1484. So the Amine Value of TEPA = 1484
The acid number is a measure of the number of carboxylic acid groups ... to calculate the free fatty acid value. [3] ... 204.23 g/mol is the molecular weight of KHP.
In computational biology, protein pK a calculations are used to estimate the pK a values of amino acids as they exist within proteins.These calculations complement the pK a values reported for amino acids in their free state, and are used frequently within the fields of molecular modeling, structural bioinformatics, and computational biology.