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
[Obsolete] Target false discovery rate (in percentage)
[Obsolete] Protein false discovery rate (in percentage)
Warning messages
Decoy search statistics
[Obsolete] Number of matches above identity threshold in search of real databas
PSM count in target above identity threshold
[Obsolete] Number of matches above identity threshold in search of decoy database
PSM count in decoy above identity threshold
Sequence count in target above identity threshold
Sequence count in decoy above identity threshold
[Obsolete] Number of matches above homology threshold in search of real database, (MS/MS only)
PSM count in target above homology threshold
[Obsolete] Number of matches above homology threshold in search of decoy database, (MS/MS only)
PSM count in decoy above homology threshold
Sequence count in target above homology threshold
Sequence count in decoy above homology threshold
PSM FDR using homology threshold (%)
PSM FDR using identity threshold (%)
Sequence FDR using homology threshold (%)
Sequence FDR using identity threshold (%)
Protein family member count in target
Protein family member count in decoy
Protein family member FDR (%)
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
Summary of linkers info.
linker name
mass delta
Search parameters
Taxonomy filter
Enzyme
Maximum number of missed cleavages
Fixed modifications
ICAT experiment
Crosslinking method
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
Target FDR for PSMs (%)
User defined parameters
Report formatting parameters
Significance threshold
Target false discovery rate (absolute number)
Target false discovery rate type
Max number of hits to report
Minimum number of significant unique peptide sequences required for a protein hit
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
In a crosslink search, the protein family members of the alpha peptide
In a crosslink search, the protein family members of the beta peptide
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 beta peptide start position
1 based residue count of peptide end position
1 based residue count of beta 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
The preceding residue before beta peptide, - if peptide is N-term of protein
Sequence of beta peptide
The following residue after beta peptide, - if peptide is C-term of protein
Frame number for translation of NA sequence
Frame number for translation of NA sequence of beta peptide
Variable modification names as CSV
Variable modifications encoded as string
Summed modifications encoded as string
Query-level modifications encoded as string
Monolink information encoded as string
Variable modification names in beta peptides CSV
Variable modifications in beta peptide encoded as string
Summed modifications in beta peptide encoded as string
Query-level modifications in beta peptide encoded as string
Monolink information in beta peptide encoded as string
Looplinks information
Looplinks information in beta peptide
Linkage information
Variable modification site analysis confidence (percentage between 0% and 100%)
Number of fragment ion matches used for scoring
Query level scan title
Type of the source database or library, one of AA, NA or SL
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
0-based index 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.