An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis

By Eugene A. Kapp, F. Schütz, L. Connolly, J. Chakel, J. Meza, Christine A. Miller, David Fenyo, Jimmy K. Eng, J. Adkins, Gilbert S. Omenn and 1 more. Proteomics, 2005

361 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/216a4107a4b1d0689f6fcffcb15221bbacb7e198

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Citations in the corpus

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, methodology): “depending on the type of instrument used to generate the data) [22-24].”
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2011, background): “of low identification rates (low sensitivity) (13) (14) and high”
The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra*S (2007, background): “Partly because of the challenges of large search space, current analyses typically only identify a fraction of the total MS/MS spectra acquired, roughly 5–20% for low resolution ion trap type instruments (3, 31) and 15–70% for quadrupole time-of-flight instruments (24, 32).”
Analysis and validation of proteomic data generated by tandem mass spectrometry (2007, background): “Although there is currently no theory on the optimality of the score, empirical evidence suggests that some scores perform better than others in different setting”
ProLuCID: an improved SEQUEST-like algorithm with enhanced sensitivity and specificity (2015, neutral): “Studies have shown that cross-correlation-based intensity-modeling methods have higher sensitivity while probability-based methods have higher speci ﬁ city [32,38].”
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics (2009, neutral): “, because of differences in the search engines themselves as well as different false discovery rate”
OpenMS – An open-source software framework for mass spectrometry (2008, background): “[41] showed that most of the correct identifications are found by various search engines.”