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The major drawback of sound processing may be the higher false identification rate.
For single spectral evidence hits, a similar calculation leads to only 4.9% false identification rate.
For this threshold, the estimated false identification rate is less than 1%.
The false identification rate for the non-pressure extracted tissue surrogates was 42% (pH 4) and 100% (pH 8).
Only proteins with expression probabilities corresponding to a false identification rate of less than 0.01 (1%) were reported (1863 proteins).
Using this strategy, we identified 1100 S. coelicolor proteins with less than 2% false identification rate and quantification variances comparable to, if not better than, other proteomic approaches.
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Protein identity, sequence coverage, and false identification rates were evaluated by liquid chromatography-MS (LC/MS).
The false identification rates for the pressure extracted multi-protein surrogate samples were 5.7% (pH 8) and 7.8% (pH 4), which was comparable to the native, unfixed protein mixture, with a false identification percentage of 3.3%.
LC/MS/MS of surrogates extracted with heat and elevated pressure identified a number of full-length tryptic peptides with false identification rates comparable to that of the unfixed protein mixture.
The software library 'mspire' developed in the Ruby programming language offers quick and memory-efficient readers for standard xml proteomics formats, converters for intermediate file types in typical proteomics spectral-identification work flows (including the Bioworks.srf format), and modules for the calculation of peptide false identification rates.
Spectra were queried against the curated entries of the NCBI RefSeq database and Xcorr values adjusted for an empiric false positive identification rate of 1% for forward-sequence proteins as determined by the inclusion of reversed protein sequences[60].
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