It hit me today: What if the theoretical mass I’m calculating for ions is consistently off? Even if it is just a little (talking fractions of a proton), that would negatively impact a peptide matching algorithm’s performance. How can we measure this? Relatively easy. The somewhat challenging part is getting a set of spectra from [...] Read More

Here’s a kind of nifty animation of how TandemFit walks through each MS/MS peak twice (once forwards, once backwards) to find the matches to the theoretical ions of a peptide. Note that the ion being searched for is displayed. The animation! Read More

It looks like spectrum: T10475_Well_A13_2025.07_16898.mgf..pkl and spectrum: T10475_Well_A13_2025.07_17096.mgf..pkl are the same. This is bad news for me as TandemFit gets both of those “wrong”. The quotes because TandemFit’s match of QAGLQLQESLEPAVRLDR has 11 fragment alignments vs 2 produced by VPAPSIEDICHVLSTVCK which is the “correct” peptide. Update: other duplicates: T10475_Well_A12_1386.68_16898.mgf..pkl T10475_Well_A12_1386.68_17096.mgf..pkl T10475_Well_A03_1551.77_16898.mgf..pkl T10475_Well_A03_1551.77_17096.mgf..pkl T10475_Well_A11_1386.69_16898.mgf..pkl T10475_Well_A11_1386.69_17096.mgf..pkl T10475_Well_A10_1188.45_17096.mgf..pkl [...] Read More

To better peer into and inspect the code I have to calculate E values, I created a histogram visualizer. Here are two histograms for score distributions for two different spectra: (Note: The small green bars are were values are above zero, but wouldn’t normally be drawn as the bar would normally be less than one [...] Read More