Results of ASAPRatio pvalue analysis (adjusting ASAPRatio ratios for offset of dataset, and determining whether ratios are significantly different from chance values originating from 1:1 proteins) Ratio adjusted for dataset mean value Error adjusted for dataset mean value Heavy2light ratio adjusted for dataset mean value Heavy2light error adjusted for dataset mean value pvalue (probability of ratio due by chance to 1:1 protein) decimal representation of pvalue Results of ASAPRatio quantitation of protein Wildcard for summary info customized for a particular analysis used to infer protein identifications Name of analysis used for protein identifications Time of analysis full path database name windows full path database residues considered equivalent when comparing peptides sample organism (used for annotation purposes) input pepXML files windows pepXML file names file type (if not pepXML) minimum adjusted peptide probability contributing to protein probability minimum peptide weight contributing to protein probability total number of predicted correct protein ids (sum of probabilities) number of spectra from 1+ precursor ions number of spectra from 2+ precursor ions number of spectra from 3+ precursor ions number of spectra from 4+ precursor ions number of spectra from 5+ precursor ions minimum initial peptide probability to contribute to analysis total estimated number of correct peptide assignments in dataset enzyme applied to sample prior to MS/MS time of analysis name of protein-level analysis time of analysis unique id corresponding with analysis_result elements Source and filtering criteria used to generate dataset generation number (0 is root) File from which derived filtering criteria applied to data number preceding filter generations wildcard to be substituted with element storing analysis-specific result info name of protein level analysis unique identifier to analysis_summary element other protein sharing corresponding peptides protein description description unmodified aa sequence precursor ion charge prior to nsp adjustment after nsp adjustment after ni adjustment expected sibling ion instances expected sibling ion bin expected total instances link to spectra with other precursor ion charges assigned to same peptide confidence that peptide corresponds with this protein (rather than others in which it occurs) number of termini consistent with proteolytic cleavage estimated number of sibling peptides (other identified peptides corresponding to same protein) discretized nsp value number of times peptide assigned to spectrum of precursor ion charge in dataset database protein name confidence of protein id percent of protein sequence covered by corresponding peptides number of proteins with identical corresponding peptides protein group id total number of corresponding peptides that contributed to protein probability name of portein containing all corresponding peptides, and more fraction of correct dataset peptide identifications corresponding to protein can only have one analysis/id combination within each protein element index group probability (taking contributions from all group member proteins) Each group_sibling_id must be unique within a protein group analysis and id must correspond with those fields in an analysis_summary element Requires group numbers be unique for entire dataset ProteinProphet analysis details learned distributions of estimated number of sibling peptides histogram slice of estimated number of sibling peptides discretized bin number lower bound nsp value (inclusive) upper bound nsp value (exclusive) lower bound nsp value (exclusive) upper bound nsp value (inclusive) fraction of correct peptides in bin fraction of incorrect peptides in bin fraction of correct / fraction of incorrect pos_to_neg_ratio of preceding bin (if greater than that of current bin) learned distributions of estimated number of peptide instances ("number of instances") histogram slice of estimated number of sibling peptides discretized bin number lower bound nsp value (inclusive) upper bound nsp value (exclusive) lower bound nsp value (exclusive) upper bound nsp value (inclusive) fraction of correct peptides in bin fraction of incorrect peptides in bin fraction of correct / fraction of incorrect pos_to_neg_ratio of preceding bin (if greater than that of current bin) predicted error/sensitivity for filtering at minimum probability filter setting predicted sensitivity (fraction of correct results passing filter) predicted error rate (fraction of results passing filter than are incorrect) predicted number of correct results passing filter predicted number of incorrect results passing filter whether or not occams razor was used to apportion peptides corresponding to multiple proteins whether or not related proteins are organized together in common protein groups whether or not all proteins corresponding to each identified peptide were used in analysis whether or not peptide probabilities were adjusted for estimated number of sibling peptides proteinprophet number of initial iterations to compute peptide weights proteinprophet number of interations used to compute nsp distributions proteinprophet number of final interations used to compute final peptide weights special run options