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Articles tagged: open search
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 [...]
Mass-tolerant vs Error tolerant
"A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides" in Nature Biotechnology is from Steven Gygi’s lab at Harvard Medical School. It describes the use of a very wide precursor mass tolerance, +/- 500 Da, to identify modified peptides in a Sequest search. How does this approach, which the authors call an [...]