The QoD constraints, referring to the maximum degree of data modifications, are specified along with standard Oozie XML schemas (version 0.2), and given to the F l u χ middleware with an associated dataflow description.
Only the initial shuttle vectors containing the modifications are specified.
The following variable modifications were specified: oxidation on methionine, SILAC heavy Arginine: C6-N4 (delta mass +10); SILAC heavy Lysine: C6-N2 (delta mass +8); SILAC medium Arginine: C6-N (delta mass +6); and SILAC medium Lysine: C6-N (delta mass +6).
Methionine oxidation was considered as a variable modification; trypsin was specified as the proteolytic enzyme, with one missed cleavage allowed.
The fixed modification of carbamidomethyl-C was specified, and the included variable modifications were acetylation of the N-terminus, deamidation of N, deamidation of Q and oxidation of M. Components were typically clustered with a 10ppm mass precision and a 0.25 min time tolerance against the database-generated theoretical peptide ion masses with a minimum of one matched peptide.
This was specified as modification with no objective medical reason, and this notion involves various social circumstances, transportation issues interfering patient's admission at scheduled date, and unmotivated doctor's decision to reduce recommended dose.
Carboxamidomethylation of Cys residues was specified as fixed modification and oxidation of Met residues as variable modifications.
Carboamidomethylation of cysteines was specified as fixed modification and oxidation of methionine was set as variable modifications; mass tolerance was set to 1 Da for precursor ion and ±0.4 Da for fragment ions and a maximum of two missed cleavages was allowed.
Carbamidomethyl on Cys was specified as fixed modification and acetylation on Lys and oxidation on Met were specified as variable modifications.
Carbamidomethyl on cysteine was specified as fixed modifications, oxidation of methionine was specified as variable modifications.
