Structured information parsed from a single Mascot search result file Information about the search Search title UTC date and time User name User email address URI for result report File path to MS input data URL to MS input data MS/MS peak list format Search type (from form) Mascot version Sequence database name Fasta file name Total number of entries in sequence database Total number of residues in sequence database Number of sequences after application of taxonomy filter Number of entries searched in error tolerant mode Number of queries Target false discovery rate (in percentage) Warning messages Decoy search statistics Number of matches above identity threshold in search of real database Number of matches above identity threshold in search of decoy database Number of matches above homology threshold in search of real database, (MS/MS only) Number of matches above homology threshold in search of decoy database, (MS/MS only) Highest protein score in search of real database, (PMF only) Highest protein score in search of decoy database, (PMF only) Summary of fixed modification info. modification name mass delta Neutral loss Summary of variable modification info. modification name mass delta Neutral loss Search parameters Taxonomy filter Enzyme Maximum number of missed cleavages Fixed modifications ICAT experiment Quantitation method Variable modifications Peptide mass tolerance Peptide mass tolerance units Peptide charge state Fragment mass tolerance Fragment mass tolerance units Monoisotopic or average Protein mass window Type of instrument Isotope error mode Decoy database also searched User defined parameters Report formatting parameters Significance threshold Max number of hits to report Use MudPIT protein scoring Ions score lower threshold Show all proteins that match the same set of peptides Show any proteins that match a sub-set of peptides Show peptide matches not assigned to protein hits Require proteins to include at least one bold, red match Cluster matches using the UniGene index for this species If false, use identity threshold for calculating expect values. If true, use homology threshold If true, group proteins into families If true, recalculate scores and expect values using Percolator Taxonomy to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences If true, peptide matches reported for a protein hit may contain duplicates (same sequence and modifications). Mass values for elements, residues, termini, and variable modifications Summary of quantitation normalisation bases if normalisation enabled. The search results Hits are numbered consecutively, but there may be no hits Each hit corresponds to one or more homologous proteins Description from Fasta title Mascot protein score Protein score significance threshold (PMF only) Expectation value corresponding to protein score (PMF only) Protein mass Number of peptide matches Number of peptide matches at or above significance threshold Number of distinct peptide sequences Number of distinct peptide sequences at or above significance threshold Percentage coverage Length in residues Calculated pI value Taxonomy Taxonomy ID Protein sequence emPAI value (MS/MS primary hit only) Protein quantitation ratio (MS/MS primary hit only) Peptide matches not assigned to proteins Query level information Supplied m/z Supplied charge (string that may contain a list of charges) Supplied precursor intensity Scan title Scan number range Retention time range peptol() qualifier seq() qualifier comp() qualifier tag() or etag() qualifier Peptide mass tolerance Peptide mass tolerance units Variable modifications Type of instrument Sum of all the ions intensities Total number of ions Peak list for ions 1 as a string (any series) Peak list for ions 2 as a string (N-term series) Peak list for ions 3 as a string (C-term series) Peptide match details Experimental m/z Experimental Mr Experimental charge Calculated Mr Mass error (calculated Mr - experimental Mr) 1 based residue count of peptide start position 1 based residue count of peptide end position Number of missed cleavages Mascot ions score Homology threshold (MS/MS only) Identity threshold (MS/MS only) Expectation value corresponding to ions score The preceding residue, - if peptide is N-term of protein Sequence The following residue, - if peptide is C-term of protein Frame number for translation of NA sequence Variable modification names as CSV Variable modifications encoded as string Summed modifications encoded as string Query-level modifications encoded as string Variable modification site analysis confidence (percentage between 0% and 100%) Number of fragment ion matches used for scoring Query level scan title Peptide quantitation ratio (MS/MS primary hit only) Peptide quantitation component intensity (MS/MS primary hit only) Peptide quantitation component assignment (metabolic quantitation only) 1-based query number Rank for this match, from 1 to 10 True if this is the highest scoring protein hit containing any match to this query True if this peptide sequence is unique to this protein hit (which may contain several same-set and sub-set proteins Schema minor version number Allowed values for the type attribute of normalisation_base element. Allowed values for the type attribute of TargetFDR. Allowed values for the count_type attribute of TargetFDR.