OLAV: Towards high‐throughput tandem mass spectrometry data identification

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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): “The Mascot error-tolerant search (37) allows the selection of only a handful of proteins that are assumed to be correct after the first pass, whereas Phenyx (23) can be applied to a full list of proteins identified in a first round.”
Scaffold: A bioinformatic tool for validating MS/MS‐based proteomic studies (2010, background): “Database-search results can be used from a variety of search engines, including several commercial engines (MASCOT [7], SEQUEST [8], Phenyx [9], SpectrumMill [10] and IdentityE [11]) and open-source engines (X! Tandem [12] and OMSSA [13]).”
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, background): “[275] Colinge J, Masselot A, Giron M, Dessingy T, Magnin J.”
Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures (2009, methodology): “The accuracy of the peptide assignments can be improved in a number of ways, including additional MS/MS data processing [29], improved charge-state determination [30], low quality MS/MS data removal [31], redundant MS/ MS spectra clustering [32, 33], and the use of more sophisticated scoring schemes”