%0 Generic
%A Lin, Andy
%A Howbert, J. Jeffry
%A Noble, William Stafford
%D 2018
%T Combining High-Resolution and Exact Calibration To
Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution
MS2 Data
%U https://acs.figshare.com/articles/dataset/Combining_High-Resolution_and_Exact_Calibration_To_Boost_Statistical_Power_A_Well-Calibrated_Score_Function_for_High-Resolution_MS2_Data/7224158
%R 10.1021/acs.jproteome.8b00206.s007
%2 https://acs.figshare.com/ndownloader/files/13304198
%K shotgun proteomics database search tool
%K mass spectrometry data sets
%K Crux mass spectrometry toolkit
%K Tide search engine
%K High-Resolution MS 2 Data
%K value score functions
%K MS-GF
%K database search score function
%K p value
%X To
achieve accurate assignment of peptide sequences to observed
fragmentation spectra, a shotgun proteomics database search tool must
make good use of the very high-resolution information produced by
state-of-the-art mass spectrometers. However, making use of this information
while also ensuring that the search engine’s scores are well
calibrated, that is, that the score assigned to one spectrum can be
meaningfully compared to the score assigned to a different spectrum,
has proven to be challenging. Here we describe a database search score
function, the “residue evidence” (res-ev) score, that
achieves both of these goals simultaneously. We also demonstrate how
to combine calibrated res-ev scores with calibrated XCorr scores to
produce a “combined p value” score
function. We provide a benchmark consisting of four mass spectrometry
data sets, which we use to compare the combined p value to the score functions used by several existing search engines.
Our results suggest that the combined p value achieves
state-of-the-art performance, generally outperforming MS Amanda and
Morpheus and performing comparably to MS-GF+. The res-ev and combined p-value score functions are freely available as part of
the Tide search engine in the Crux mass spectrometry toolkit (http://crux.ms).
%I ACS Publications