Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

CSV export column headers

This table provides a key to the column headers in the configurable CSV export. (Elements and attributes in the configurable XML export are described in the schema annotations.)

In the descriptions, ‘grouping’ refers to protein family grouping as seen in the protein family summary.

prot_hit_numOrdinal number of the protein hit (or protein family when grouping enabled)
prot_family_memberOrdinal number of the protein family member when grouping enabled
prot_accProtein accession string
prot_descProtein description taken from Fasta title line
prot_scoreProtein Mascot score
prot_threshThreshold score for a significant protein match (PMF only)
prot_expectExpectation value of the protein match (PMF only)
prot_massProtein mass
prot_matchesCount of PSMs
prot_matches_sigCount of PSMs that have significant scores
prot_sequencesCount of distinct sequences
prot_sequences_sigCount of distinct sequences that have significant scores
prot_coverProtein sequence coverage
prot_lenProtein length in residues
prot_piCalculated protein isoelectric point
prot_tax_strProtein taxonomy as string
prot_tax_idProtein taxonomy as Tax ID
prot_seqProtein sequence in 1 letter code
prot_empaiProtein emPAI value (spectral counting)
prot_acc_alphaProtein accession of alpha peptide, or empty if not crosslinked match. Multiple accessions are separated by semicolons.
prot_acc_betaProtein accession of beta peptide, or empty if not crosslinked match. Multiple accessions are separated by semicolons.
pep_queryOrdinal number of query after sorting by Mr
pep_rankPeptide sequence match (PSM) rank. If two PSMs have same score they have the same rank.
pep_isboldIf grouping enabled, then a significant PSM. Otherwise, indicates this is the highest scoring protein that contains a match to this query.
pep_isuniquePeptide sequence is unique to hit (grouping off) or family member (grouping on)
pep_exp_mzObserved or experimental m/z value
pep_exp_mrMolecular mass calculated from experimental m/z value
pep_exp_zObserved or experimental charge
pep_calc_mrMolecular mass calculated from matched peptide sequence
pep_deltapep_exp_mr – pep_calc_mr
pep_startOrdinal position of first peptide residue in protein sequence
pep_endOrdinal position of last peptide residue in protein sequence
pep_missCount of missed cleavage sites in peptide
pep_scoreMascot score for PSM
pep_homolHomology threshold score for PSM
pep_identIdentity threshold score for PSM
pep_expectExpectation value for PSM
pep_res_beforeFlanking residue on N-term side of peptide
pep_seqPeptide sequence in 1 letter code
pep_res_afterFlanking residue on C-term side of peptide
pep_frameTranslation frame number (only for NA sequence databases)
pep_var_modVariable modifications from all sources as list of names
pep_var_mod_posVariable modifications as a string of digits, e.g. ’0.0001000.0′. Non-zero digits identify mods according to key in export header. First and last positions are for terminus mods.
pep_summed_mod_posWhen two variable modifications occur at the same site, a string of digits defining the second mod
pep_local_mod_posQuery-level variable modifications as a string of digits. The names of the mods will be listed in pep_var_mod
pep_var_mod_confPercent confidence from site analysis for the variable modification sites
pep_num_matchCount of fragment ion matches in ion series used to calculate the score
pep_scan_titleScan title taken from peak list
pep_sourceType of database (AA, NA, XA, or SL)
pep_linked_sitesIntact crosslinked sites as comma-separated list of integer triplets, e.g., 1:0:6,2:5:7. Numbers are alpha (= 1) site 0 (N-term) linker number 6 (from the Linkers table) and beta (= 2) site 5 linker number 7. (*)
pep_res_before_betaBeta peptide field analogous to pep_res_before
pep_seq_betaBeta peptide field analogous to pep_seq
pep_res_after_betaBeta peptide field analogous to pep_res_after
pep_frame_betaBeta peptide field analogous to pep_frame
pep_var_mod_betaBeta peptide field analogous to pep_var_mod
pep_var_mod_pos_betaBeta peptide field analogous to pep_var_mod_pos
pep_summed_mod_pos_betaBeta peptide field analogous to pep_summed_mod_pos
pep_local_mod_pos_betaBeta peptide field analogous to pep_local_mod_pos
pep_monolink_mod_posMonolink positions in alpha peptide. Identifiers are listed in the Linkers table. If not a crosslinked match, monolink positions in the peptide match.
pep_monolink_mod_pos_betaMonolink positions in beta peptide. Identifiers are listed in the Linkers table.
pep_looplink_posLooplink positions in alpha peptide, comma-separated list of integer pairs, e.g., 3:4. First number is looplink start position and second is looplink end position. If not a crosslinked match, looplink positions in the peptide match.
pep_looplink_pos_betaLooplink positions in beta peptide.

Results of quantitation using reporter or multiplex protocols appear to the right of the main table without column headers. Each row contains peptide quantitation data consisting of pairs of ratio names and ratio values followed by pairs of component names and component intensities.

The final peptide row for each protein contains additional protein quantitation data, on the right. This consists of 6 values for each ratio:
ratio name
ratio value
count of peptide values
geometric standard deviation, if available
an asterisk if the ratio is significant
p-values for the fold change, if available