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SEQUEST matches are, therefore, biased towards sequences where the phosphate is less labile, and ProPhosSI, in this current implementation, towards those where sites are labile.
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In the current implementation, this flexibility is maintained by integrating the catR library that offers different skill level estimation algorithms.
In the current implementation, this is achieved using a lookup table, but faster implementations are certainly possible (e.g., modeling the bone and soft tissue clusters as ellipsoids).
In the current implementation, this is realized by interfacing the catR-library (Magis & Raîche, 2012), that is also used in the Concerto platform.
In the current implementation, this parameter has to be specified by the user.
In the current implementation, this filter is deactivated when the number of errors exceeds 7. To complete this analysis, we measured the total time spent inside each filter.
We aimed to address this gap in the current implementation evidence-base through the application of a systematic, theory-based intervention modelling process (IMP) for the development and evaluation of interventions to change clinical practice [ 11].
Also, in the current implementation of this algorithm, little has been done ensure fast code or an efficient stopping rule.
Applied Biosystems (personal communication) confirmed that this reference bias exists in the current implementation of the Bioscope alignment algorithm, and efforts are underway to mitigate this isue in future implementations.
In the current implementation, thermomechanical package models have been implemented.
This functionality is not included in the current implementation of our algorithm.
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