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In order to gain sufficiently high fragment ion intensities, limited selectivity of precursor selection has to be addressed (e.g., isolation width = 2 or 3 u).
In our profile, fluorescence showed a decreasing intensity in high fragment lengths, except for the 318 bp peak containing 6 co-migrating fragments which exhibited much higher fluorescence intensity than the peaks of similar length.
Our fragment screening studies complement these findings by identifying relatively high fragment cross-reactivity between H4R and 5-HT3AR (Fig. 1b) and demonstrate that fragments are ideally suited to interrogate ligand binding sites.
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Protein identification results with statistically significant lower P and E values (<0.00005) and a satisfactorily higher fragment number (at least 10 fragments assigned) were manually validated.
Experimentally, higher fragment mass accuracy would significantly reduce the chances of spurious peak matches and should seamlessly increase the percentage of usable MS spectra.
For the horse genome we couldn't run CUDA-SW++ with higher fragment lengths of 4800 and so we selected 2400.
We choose 512 fragment length for E.coli because lower ones reduce the runtime marginally but the accuracy goes down considerably whereas higher fragment lengths don't yield higher accuracy and increase runtime.
This table demonstrates that FRazor with candidate list size 10 has higher fragment coverage than the fragment coverage of CBM with candidate list size 40, with scores 43.3% and 40.8%, respectively.
For each analyte and IS, two ions, i.e., the highest fragment (HF) for quantification and the nominal mass (NM) as a control, were selected in the SIM mode.
Vector fragments and high frequency fragments were identified by fragment frequency analysis and then removed in FPminer.
Fingerprint profile of each clone collected by the ABI data collection program was processed with the combination of software packages GenoProfiler [ 52] and FPMiner http://www.bioinforsoft.com/ to remove vector fragments, high frequency fragments, and cross-contaminated clones.
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