if a certain fragment fault-line has already been accounted for with another ion, we can skip further ions for that location. Read More

in MSMSFit, differenceThreshold could be a function of peak intensity. That is, there can be more leeway for greater intensity peaks. Read More

There’s something terrifying in chromosome 4… Read More

I’m experimenting with the MSMSFit scoring and am going down what looks like a very promising road. Interesting: When examining OutputFile2.pkl against chr4.fasta a peptide, GSWYSMRK, came up with a high MSMSFit score that HMM_Score somewhat overlooks (it gets an HMM score of about 60 depending on the peak cleaning method). What is interesting is [...] Read More

I suspect that some edge cases of MSMSFit (first, last fragments, peaks, etc.) may not be performing as desired. I especially suspect that searching for b-ions isn’t working nearly as well as it should. This has gone unnoticed until now because the way MSMSFit is written, close y-ion matches can pick up the slack for [...] Read More

Similar in principle to the various folding@home projects. It may seem that GFS may not be conducive to such segmentation as genomic data is quite large making download times prohibitive. This is not the case if a node “specializes” in a subset of the genome. A node only needs access to a spectrum file and [...] Read More

Lately GFS has been hanging during long tasks. It is a hang where processing drops to nothing (vs. high processing with zero progress). When running with two threads it hangs after about 35 minutes (counting 5 minutes of digestion) in single thread mode it goes for 55 minutes. When paused at the hang point and [...] Read More