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Articles tagged: delta mass
Error tolerant searches now show statistical significance
The latest release of Mascot Server introduces some important changes to error tolerant searches. Matches from the second pass search now have expect values attached, indicating confidence levels. These are either estimates based on counting trials or empirical values derived from searching a decoy database. If you are not familiar with the error tolerant search, now is the time to [...]
Results round-up for the ‘dark matter’ challenge
In June, we tried to harness the power of crowd-sourcing to explain some of the unidentified modifications found in open database searches. We selected 20 abundant and unassigned mass deltas from Supplementary Table 3 of the recent MSFragger paper from Alexey Nesvizhskii’s group at U. Michigan and offered prizes for the first credible explanations. There were 35 unannotated deltas in [...]
Trying to illuminate proteomics ‘dark matter’
The May 2017 issue of Nature Methods has a paper from Alexey Nesvizhskii’s group at U. Michigan describing a new open database search program called MSFragger. Strikingly, they also observed the two highly abundant but unidentified mass deltas reported in Steven Gygi’s 2015 mass tolerant paper: 301.9864 and 249.9803. The challenges of open searching were discussed in an earlier blog [...]