Sequest, by Thermo Sciences, is a search engine that matches tandem mass spectra with peptide sequences. LabKey Server uses Sequest to search an mzXML file against a FASTA database and displays the results in the MS2 viewer for analysis.
This topic provides a reference list of parameters to accompany the configuration topic for Sequest. You can learn more about modifying Sequest settings in LabKey Server and using X!Tandem syntax for Sequest parameters in this topic:
LabKey Server provides additional parameters for Sequest where X!Tandem does not have an equivalent parameter, for working with the data pipeline and for performing quantitation, listed in the table on this page.
The Sequest parameters you see in a standard sequest.params file are defined here:
| sequest.params name | GROUP | NAME | Default | Notes | |
| first_database_name | pipeline | database | n.a. | Entered through the search form. | |
| peptide_mass_tolerance | spectrum | parent monoisotopic mass error plus parent monoisotopic mass error minus | 2.0f | They must be set to the same value | |
| use an indexed ("pre-digested") fasta file | pipeline | use_index | 0 (no) | If set, the SEQUEST pipeline will use a fasta file index to perform the search. If the index does not already exist, the pipeline will invoke makedb.exe to create the index. 1 means yes | |
| name of indexed fasta file | pipeline | index_name | empty | (Optional). Specifies the name of the index to generate and use. If no name is specified, the SEQUEST pipeline will create a name based on the values of the search parameters, in particular the enzyme_info. | |
| peptide_mass_units | spectrum | parent monoisotopic mass error units | Daltons | The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored | |
| ion_series | scoring | a ions b ions c ions x ions y ions z ions | no yes no no yes no | On is 1 and off is 0. No fractional values. | |
| sequest | d ions v ions w ions a neutral loss b neutral loss y neutral loss | no no no no yes yes | |||
| fragment_ion_tolerance | spectrum | fragment mass error | 1.0 | ||
| num_output_lines | sequest | num_output_lines | 10 | ||
| num_results | sequest | num_results | 500 | ||
| num_description_lines | sequest | num_description_lines | 5 | ||
| show_fragment_ions | sequest | show_fragment_ions | 0 | ||
| print_duplicate_references | sequest | print_duplicate_references | 40 | ||
| enzyme_info | protein | cleavage site | [RK]|{P} | ||
| max_num_differential_AA_per_mod | sequest | max_num_differential_AA_per_mod | 3 | ||
| max_num_differential_per_peptide | sequest | max_num_differential_per_peptide | 3 | ||
| diff_search_options | residue | potential modification mass | none | ||
| term_diff_search_options | refine | potential N-terminus modifications potential C-terminus modifications | none | ||
| nucleotide_reading_frame | n.a | n.a | 0 | Not settable. | |
| mass_type_parent | sequest | mass_type_parent | 0 | 0=average masses 1=monoisotopic masses | |
| mass_type_fragment | spectrum | fragment mass type | 1 | 0=average masses 1=monoisotopic masses | |
| normalize_xcorr | sequest | normalize_xcorr | 0 | ||
| remove_precursor_peak | sequest | remove_precursor_peak | 0 | 0=no 1=yes | |
| ion_cutoff_percentage | sequest | ion_cutoff_percentage | 0 | ||
| max_num_internal_cleavage_sites | scoring | maximum missed cleavage sites | 2 | ||
| protein_mass_filter | n.a. | n.a. | 0 0 | Not settable. | |
| match_peak_count | sequest | match_peak_count | 0 | ||
| match_peak_allowed_error | sequest | match_peak_allowed_error | 1 | ||
| match_peak_tolerance | sequest | match_peak_tolerance | 1 | ||
| create_output_files | n.a. | n.a. | 1 | Not settable. | |
| partial_sequence | n.a. | n.a. | none | Not settable. | |
| sequence_header_filter | n.a. | n.a. | none | Not settable. | |
| add_Cterm_peptide | protein | cleavage C-terminal mass change | 0 | ||
| add_Cterm_protein | protein | C-terminal residue modification mass | 0 | ||
| add_Nterm_peptide | protein | cleavage N-terminal mass change | 0 | ||
| add_Nterm_protein | protein | protein, N-terminal residue modification mass | 0 | ||
| add_G_Glycine add_A_Alanine add_S_Serine add_P_Proline add_V_Valine add_T_Threonine add_C_Cysteine add_L_Leucine add_I_Isoleucine add_X_LorI add_N_Asparagine add_O_Ornithine add_B_avg_NandD add_D_Aspartic_Acid add_Q_Glutamine add_K_Lysine add_Z_avg_QandE add_E_Glutamic_Acid add_M_Methionine add_H_Histidine add_F_Phenylalanine add_R_Arginine add_Y_Tyrosine add_W_Tryptophan | residue | modification mass | 0 |
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