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 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

Related Topics

Configure Sequest Parameters