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One name on the transition list comes unencumbered by potential conflicts but instead by bad luck.
Sherwood, C. A. et al. MaRiMba: a software application for spectral library-based MRM transition list assembly.
Skyline does not directly support crosslinking analysis, so the elemental composition of each crosslinked peptide species, precursor charge state, and retention time were imported as a small molecule transition list (generated in the R programming environment).
The final list consisted of 334 transitions (based on manual protein selection) and this transition list was divided among two method files for the final SRM analyses (Supplementary Table S2).
New C18 trap (2 cm) and C18 analytical columns (27.5 cm) were used and each sample was analyzed in two MS experiments to cover the entire peptide transition list (n = 334).
Fragmentation data was then used to develop a transition list for MRM (Additional file 2: Table S2).
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Additionally, as the available spectral library databases are growing, it is possible to find previous MS experiments that provide charge state, transition lists, and retention times38,39.
Though the résumé she submitted as part of the transition listed Yale University and Quinnipiac University School of Law under "education," when questioned by reporters, Patton admitted that she had not graduated from either institution.
The transition lists werecreated in Skyline v1.2 software (MacCoss Lab).
The best transitions (3 5 per precursor) were selected by manualinspection of the data in Skyline and scheduled transition lists were createdfor the final assays.
Transition lists were imported from SpectroDive™ into Skyline to generate.sky and.skyd files to place into PASSEL (ID PASS00633) [10] and provide access to SRM spectra in a publicly-available format.
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