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.
| Header | Description |
|---|---|
| prot_hit_num | Ordinal number of the protein hit (or protein family when grouping enabled) |
| prot_family_member | Ordinal number of the protein family member when grouping enabled |
| prot_acc | Protein accession string |
| prot_desc | Protein description taken from Fasta title line |
| prot_score | Protein Mascot score |
| prot_thresh | Threshold score for a significant protein match (PMF only) |
| prot_expect | Expectation value of the protein match (PMF only) |
| prot_mass | Protein mass |
| prot_matches | Count of PSMs |
| prot_matches_sig | Count of PSMs that have significant scores |
| prot_sequences | Count of distinct sequences |
| prot_sequences_sig | Count of distinct sequences that have significant scores |
| prot_cover | Protein sequence coverage |
| prot_len | Protein length in residues |
| prot_pi | Calculated protein isoelectric point |
| prot_tax_str | Protein taxonomy as string |
| prot_tax_id | Protein taxonomy as Tax ID |
| prot_seq | Protein sequence in 1 letter code |
| prot_empai | Protein emPAI value (spectral counting) |
| prot_acc_alpha | Protein accession of alpha peptide, or empty if not crosslinked match. Multiple accessions are separated by semicolons. |
| prot_acc_beta | Protein accession of beta peptide, or empty if not crosslinked match. Multiple accessions are separated by semicolons. |
| pep_query | Ordinal number of query after sorting by Mr |
| pep_rank | Peptide sequence match (PSM) rank. If two PSMs have same score they have the same rank. |
| pep_isbold | If grouping is enabled, then pep_isbold=1 when the PSM is significant and assigned to the first family member. For other family members, pep_isbold=0. If grouping is disabled, pep_isbold=1 indicates this is the highest scoring protein that contains a match to this query. |
| pep_isunique | Peptide sequence is unique to hit (grouping off) or family member (grouping on) |
| pep_exp_mz | Observed or experimental m/z value |
| pep_exp_mr | Molecular mass calculated from experimental m/z value |
| pep_exp_z | Observed or experimental charge |
| pep_calc_mr | Molecular mass calculated from matched peptide sequence |
| pep_delta | pep_exp_mr – pep_calc_mr |
| pep_start | Ordinal position of first peptide residue in protein sequence |
| pep_end | Ordinal position of last peptide residue in protein sequence |
| pep_miss | Count of missed cleavage sites in peptide |
| pep_score | Mascot score for PSM |
| pep_homol | Homology threshold score for PSM |
| pep_ident | Identity threshold score for PSM |
| pep_expect | Expectation value for PSM |
| pep_res_before | Flanking residue on N-term side of peptide |
| pep_seq | Peptide sequence in 1 letter code |
| pep_res_after | Flanking residue on C-term side of peptide |
| pep_frame | Translation frame number (only for NA sequence databases) |
| pep_var_mod | Variable modifications from all sources as list of names |
| pep_var_mod_pos | Variable 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_pos | When two variable modifications occur at the same site, a string of digits defining the second mod |
| pep_local_mod_pos | Query-level variable modifications as a string of digits. The names of the mods will be listed in pep_var_mod |
| pep_var_mod_conf | Percent confidence from site analysis for the variable modification sites |
| pep_num_match | Count of fragment ion matches in ion series used to calculate the score |
| pep_scan_title | Scan title taken from peak list |
| pep_source | Type of database (AA, NA, XA, or SL) |
| pep_linked_sites | Intact 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_beta | Beta peptide field analogous to pep_res_before |
| pep_seq_beta | Beta peptide field analogous to pep_seq |
| pep_res_after_beta | Beta peptide field analogous to pep_res_after |
| pep_frame_beta | Beta peptide field analogous to pep_frame |
| pep_var_mod_beta | Beta peptide field analogous to pep_var_mod |
| pep_var_mod_pos_beta | Beta peptide field analogous to pep_var_mod_pos |
| pep_summed_mod_pos_beta | Beta peptide field analogous to pep_summed_mod_pos |
| pep_local_mod_pos_beta | Beta peptide field analogous to pep_local_mod_pos |
| pep_monolink_mod_pos | Monolink 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_beta | Monolink positions in beta peptide. Identifiers are listed in the Linkers table. |
| pep_looplink_pos | Looplink 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_beta | Looplink 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