This is the Windows app named NOFI ranking whose latest release can be downloaded as NOFI-ranking_v1.zip. It can be run online in the free hosting provider OnWorks for workstations.
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Wine is a way to run Windows software on Linux, but with no Windows required. Wine is an open-source Windows compatibility layer that can run Windows programs directly on any Linux desktop. Essentially, Wine is trying to re-implement enough of Windows from scratch so that it can run all those Windows applications without actually needing Windows.
The NOFI ranking algorithm has been developed to assign low priority to fragment ions affected by interference. The implementation is an R script that can be customized. A future version will contain a modular version. The outline is as follows:
1) The input contains the list of SWATH fragment ion XICs from the identified and quantified peptides by software tools such as Skyline and OpenSWATH.
2) The first step in NOFI is the computation of the 4 attributes (RTd, FWHMd, IRd and IRrep) used to represent each fragment ion as a vector.
3) Multivariate outlier detection techniques are used to rank all the fragment ions from each peptide.
4) Several figures are generated (a pdf file) to visualize the effect of the Top-N fragment ions over different indicators.
5) The user can choose the number of top fragment ions per peptide, thereby utilizing the optimal subset of high priority Top-N NOFIs for quantification while excluding the impaired fragment ions.
This is an application that can also be fetched from https://sourceforge.net/projects/nofiranking/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.