Since the fragment ions containing no (zero), one, or two C-termini of the cross-linked peptides displayed a mass shift of 0, 4, and 8 Da, respectively, in the corresponding MS/MS spectra obtained from O- and O-water, the examination of mass shift of fragment ions can lend further support for the assignment of fragment ions.
The assignments of fragments a, b, d, and f were annotated as a bond cleavage and the formation of a new double bond (one proton loss plus two hydrogen losses), formulated as HR rules N2.
(Refer to Tables S1 S5 in the Supporting Information for the tabulations of mass assignments of fragment ions and abundances used for the calculations).
(See the diagram below for the detailed assignment of different fragments).
For the taxonomic assignment of metagenomic fragments, two methods were used.
Assignment of EST fragments by functional category and the percent representation of each category in the collection of the O. novo-ulmi yeast LMW library.
Second, specific categories within the themes were identified to check for interpreter consensus concerning the assignment of text fragments to major themes.
To try to bin fosmids within different phylogenetic groups, we analyzed tetranucleotide and pentanucleotide frequencies, which are often used for the assignment of genome fragments to distinct groups (Teeling, Meyerdierks, et al. 2004).
15 17 After having interviewed sufficient respondents, we (HMB and MLR) independently read through five interviews in each respondent group to identify general themes, and then to identify specific categories within the themes to check for interpreter consensus concerning the assignment of text fragments to major themes.
First, UVPD mass spectra derived from monoubiquitin and the unmodified Sic60-DHFR construct were compared to confirm that there was no significant fragment ion overlap that would prevent assignment of diagnostic fragment ions and that could not be overcome by the high mass accuracy used in this study (see Figure 6).
