Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures

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An insight into iTRAQ: where do we stand now? (2012, methodology): “The mass spectrometers used were similar (although the study is weakened due to difference in sensitivity of the MS platforms) but also the data were necessarily acquired in different modes: iTRAQ data were obtained on an older QToF MS (Global Ultima, Waters Corporation) operating in data-dependent ”
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, background): “New search tools are also being developed in support of data independent acquisition schemes [41], in which multiple precursor ions are purposely fragmented simultaneously (i.”
DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics (2015, methodology): “18 ).”
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!”