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.

Sequest Parameters

The Sequest parameters you see in a standard sequest.params file are defined here:


sequest.params nameGROUPNAMEDefaultNotes
first_database_namepipelinedatabasen.a.Entered through the search form.
peptide_mass_tolerancespectrumparent monoisotopic mass error plus
parent monoisotopic mass error minus
2.0fThey must be set to the same value
use an indexed ("pre-digested") fasta filepipelineuse_index0 (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 filepipelineindex_nameempty(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_unitsspectrumparent monoisotopic mass error unitsDaltonsThe value for this parameter may be 'Daltons' or 'ppm': all other values are ignored
ion_seriesscoringa 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.

sequestd ions
v ions
w ions
a neutral loss
b neutral loss
y neutral loss
no
no
no
no
yes
yes
fragment_ion_tolerancespectrumfragment mass error1.0 
num_output_linessequestnum_output_lines10 
num_resultssequestnum_results500 
num_description_linessequestnum_description_lines5 
show_fragment_ionssequestshow_fragment_ions0 
print_duplicate_referencessequestprint_duplicate_references40 
enzyme_infoproteincleavage site[RK]|{P} 
max_num_differential_AA_per_modsequestmax_num_differential_AA_per_mod3 
max_num_differential_per_peptidesequestmax_num_differential_per_peptide3 
diff_search_optionsresiduepotential modification massnone 
term_diff_search_optionsrefinepotential N-terminus modifications
potential C-terminus modifications
none 
nucleotide_reading_framen.an.a0Not settable.
mass_type_parentsequestmass_type_parent00=average masses
1=monoisotopic masses
mass_type_fragmentspectrumfragment mass type10=average masses
1=monoisotopic masses
normalize_xcorrsequestnormalize_xcorr0 
remove_precursor_peaksequestremove_precursor_peak00=no
1=yes
ion_cutoff_percentagesequestion_cutoff_percentage0 
max_num_internal_cleavage_sitesscoringmaximum missed cleavage sites2 
protein_mass_filtern.a.n.a.0 0Not settable.
match_peak_countsequestmatch_peak_count0 
match_peak_allowed_errorsequestmatch_peak_allowed_error1 
match_peak_tolerancesequestmatch_peak_tolerance1 
create_output_filesn.a.n.a.1 Not settable.
partial_sequencen.a.n.a.noneNot settable.
sequence_header_filtern.a.n.a.noneNot settable.
add_Cterm_peptideproteincleavage C-terminal mass change0 
add_Cterm_proteinproteinC-terminal residue modification mass0 
add_Nterm_peptideproteincleavage N-terminal mass change0 
add_Nterm_proteinproteinprotein, N-terminal residue modification mass0 
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
residuemodification mass0 

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