ProteinProspector Input Variables

All ProteinProspector programs are implemented according to the Common Gateway Interface (CGI) standard. Hence the HTML form interface can be bypassed in automated settings as long as the programs receive their input in a manner which mimics the CGI format.

To facilitate such efforts this document provides a list of all the name-value pairs associated with the input variables for each program. Future development efforts will refrain from changing these parameters unless absolutely necessary.

MS-Fit MS-Tag MS-Seq MS-Edman Default Value Valid Values MS-Digest MS-Product MS-Comp DB-Stat MS-Isotope FA-Index

msparams_dir msparams_dir msparams_dir msparams_dir (UNIX)
\ (Windows) directory name msparams_dir msparams_dir msparams_dir msparams_dir msparams_dir msparams_dir

seqdb_dir seqdb_dir seqdb_dir seqdb_dir seqdb/ (UNIX)
seqdb\ (Windows) directory name seqdb_dir n/a n/a seqdb_dir n/a seqdb_dir

res_msfit_dir res_msfit_dir res_msfit_dir res_msfit_dir results_msfit/ (UNIX)
results_msfit\ (Windows) directory name n/a n/a n/a n/a n/a res_msfit_dir

n/a res_mstag_dir res_mstag_dir res_mstag_dir results_mstag/ (UNIX)
results_mstag\ (Windows) directory name n/a n/a n/a n/a n/a res_mstag_dir

n/a res_msseq_dir res_msseq_dir res_msseq_dir results_msseq/ (UNIX)
results_msseq\ (Windows) directory name n/a n/a n/a n/a n/a res_msseq_dir

res_msedman_dir res_msedman_dir res_msedman_dir res_msedman_dir results_msedman/ (UNIX)
results_msedman\ (Windows) directory name n/a n/a n/a n/a n/a res_msedman_dir

database database database database NCBInr.7.7.96 valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, NCBInr, nr, dbEST, dbest, DA, DN, PA, PN
Unknome in MS-Tag
database n/a n/a database n/a database

instrument_name instrument_name instrument_name n/a "" valid text strings defined in instrument.txt instrument_name instrument_name instrument_name n/a n/a n/a

dna_frame_translation dna_frame_translation dna_frame_translation dna_frame_translation 3 6, 3, -3, 1, -1 n/a n/a n/a n/a n/a n/a

results_from_file results_from_file results_from_file results_from_file 0 0, 1 n/a n/a n/a n/a n/a results_from_file

input_program_name input_program_name input_program_name input_program_name msfit msfit, mstag, msedman n/a n/a n/a n/a n/a input_program_name

input_filename input_filename input_filename input_filename "" text n/a n/a n/a n/a n/a input_filename

indicies indicies n/a indicies "" list of database indicies (integers) n/a n/a n/a n/a n/a indicies

accession_numbers accession_numbers n/a accession_numbers "" list of database accession numbers n/a n/a n/a n/a n/a accession_numbers

species species species species All valid text strings defined in *.sp.txt or All n/a n/a n/a species n/a species

prot_low_mass prot_low_mass prot_low_mass prot_low_mass 1000 integer n/a n/a n/a prot_low_mass n/a prot_low_mass

prot_high_mass prot_high_mass prot_high_mass prot_high_mass 100000 integer n/a n/a n/a prot_high_mass n/a prot_high_mass

full_mw_range full_mw_range full_mw_range full_mw_range 0 0, 1 n/a n/a n/a full_mw_range n/a full_mw_range

low_pi low_pi low_pi low_pi 3.0 double n/a n/a n/a low_pi n/a low_pi

high_pi high_pi high_pi high_pi 10.0 double n/a n/a n/a high_pi n/a high_pi

full_pi_range full_pi_range full_pi_range full_pi_range 0 0, 1 n/a n/a n/a full_pi_range n/a full_pi_range

enzyme enzyme enzyme enzyme Trypsin valid text strings defined in enzyme.txt and combinations of these separated by / characters enzyme n/a n/a enzyme n/a n/a

missed_cleavages missed_cleavages missed_cleavages n/a 1 integer missed_cleavages n/a n/a n/a n/a n/a

cys cys cys cys acrylamide valid text strings defined in cys.txt cys cys cys n/a cys n/a

comment comment comment comment "" text n/a n/a n/a n/a n/a n/a

results_to_file results_to_file results_to_file results_to_file 0 0, 1 n/a n/a n/a n/a n/a n/a

output_filename output_filename output_filename output_filename "" text n/a n/a n/a n/a n/a output_filename

nterm nterm nterm nterm Hydrogen valid text strings defined in n_terms.txt nterm nterm nterm n/a nterm n/a

cterm cterm cterm cterm Free Acid valid text strings defined in c_terms.txt cterm cterm cterm n/a cterm n/a

max_reported_hits max_reported_hits max_reported_hits max_reported_hits 50 integer n/a n/a max_reported_hits n/a n/a n/a

n/a max_hits max_hits n/a 200 integer n/a n/a n/a n/a n/a n/a

parent_mass_convert parent_mass_convert parent_mass_convert parent_mass_convert monoisotopic monoisotopic
average
Par(mi)Frag(av)
Par(av)Frag(mi) parent_mass_convert parent_mass_convert parent_mass_convert n/a n/a n/a

parent_mass_tolerance parent_mass_tolerance parent_mass_tolerance parent_mass_tolerance 0.5 double n/a n/a parent_mass_tolerance n/a n/a n/a

tolerance_units tolerance_units tolerance_units tolerance_units Da Da, %, ppm, mmu n/a n/a tolerance_units n/a n/a n/a

parent_shift_type parent_shift_type n/a n/a +/- +/-, =/+/-, =/+, =/- n/a n/a n/a n/a n/a n/a

parent_shift parent_shift n/a n/a 130.1 double n/a n/a n/a n/a n/a n/a

parent_masses n/a n/a parent_masses NULL 2 column table listing of doubles (mass-m/z) and integers (charge) n/a n/a n/a n/a n/a n/a

average_to_mono_convert n/a n/a n/a NULL list of 0's and 1's
0 = monoisotopic
1 = average n/a n/a n/a n/a n/a n/a

mod_AA n/a n/a n/a None Defined Peptide N-terminal Gln to pyroGlu
Oxidation of M
Protein N-terminus Acetylated
User Defined 1
Acrylamide Modified Cys mod_AA n/a n/a n/a n/a n/a

user1_name n/a n/a n/a "" valid text strings defined in usermod.txt user1_name n/a n/a n/a n/a n/a

min_parent_ion_matches n/a n/a n/a 1 integer n/a n/a n/a n/a n/a n/a

min_matches n/a n/a n/a 5 integer n/a n/a n/a n/a n/a n/a

mowse_on n/a n/a n/a 0 0, 1 n/a n/a n/a n/a n/a n/a

mowse_pfactor n/a n/a n/a 0.4 double n/a n/a n/a n/a n/a n/a

n/a fragment_masses fragment_masses n/a NULL 2 column table listing of doubles (mass-m/z) and integers (charge) n/a n/a n/a n/a n/a n/a

search_type search_type n/a n/a identity MS-Tag: identity or valid text strings
defined in homology.txt
MS-Seq: no errors, high mass error,
low mass error, middle masses error,
parent mass n/a n/a n/a n/a n/a n/a

params_at_end params_at_end params_at_end params_at_end 0 0, 1 n/a n/a n/a n/a n/a n/a

n/a n/a ion_type n/a b a,b,c,y n/a it n/a n/a n/a n/a

n/a it n/a n/a None Defined a,a-H2O,a-NH3,a-H3PO4,
b,b-H2O,b-NH3,b+H2O,
b-H3PO4,b-SOCH4,
y,y-H2O,y-NH3,y-H3PO4,y-SOCH4,
MH+,c,B,n,h,P,S,I,N,C n/a it n/a n/a n/a n/a

n/a max_num_unused_ions n/a n/a 0 integer n/a n/a n/a n/a n/a n/a

n/a fragment_mass_tolerance n/a n/a 1.0 double n/a n/a n/a n/a n/a n/a

n/a star_ions_off fragment_mass_tolerance n/a 0 0, 1 n/a n/a n/a n/a n/a n/a

n/a comp_ion comp_ion n/a None Defined regular expression n/a n/a comp_ion n/a n/a n/a

n/a parent_mass parent_mass n/a 1000.0 double n/a n/a parent_mass n/a n/a n/a

n/a parent_charge parent_charge n/a 1 integer n/a n/a parent_charge n/a n/a n/a

n/a mutation_matrix_off n/a n/a 0 0, 1 n/a n/a n/a n/a n/a n/a

n/a aa_exclude n/a n/a "" text string containing the following characters A,C,D,E,F,G,H,I,K,L,M, N,P,Q,R,S,T,V,W,Y n/a n/a aa_exclude n/a n/a n/a

n/a aa_add n/a n/a "" m,q,h,s,t,y,u n/a n/a aa_add n/a n/a n/a

n/a user_aa_c n/a n/a 2 integer user_aa_c user_aa_c user_aa_c n/a user_aa_c n/a

n/a user_aa_h n/a n/a 3 integer user_aa_h user_aa_h user_aa_h n/a user_aa_h n/a

n/a user_aa_n n/a n/a 1 integer user_aa_n user_aa_n user_aa_n n/a user_aa_n n/a

n/a user_aa_o n/a n/a 1 integer user_aa_o user_aa_o user_aa_o n/a user_aa_o n/a

n/a user_aa_s n/a n/a 0 integer user_aa_s user_aa_s user_aa_s n/a user_aa_s n/a

n/a user_aa_p n/a n/a 0 integer user_aa_p user_aa_p user_aa_p n/a user_aa_p n/a

n/a n/a n/a search_field Sequence and Mass Sequence Only
Sequence and Mass
Name
Accession number
Species
List of Sequences n/a n/a n/a n/a n/a n/a

n/a n/a composition_exclude n/a "" ACDEFGHIKLMNPQRSTVWY n/a n/a n/a n/a n/a n/a

n/a n/a n/a combo_output 0 0, 1 n/a n/a n/a n/a n/a n/a

n/a n/a regular_expression regular_expression . regular expression n/a n/a n/a n/a n/a n/a

n/a n/a n/a regular_expressions NULL list of regular expressions or text strings dependent on search_field parameter n/a n/a n/a n/a n/a n/a

n/a n/a n/a possible_sequences NULL list of peptides n/a n/a n/a n/a n/a n/a

n/a n/a n/a max_aa_substitutions 0 integer n/a n/a n/a n/a n/a n/a

n/a n/a n/a n/a 1 1, 2, 3, 4, 5, 6 dna_reading_frame n/a n/a dna_reading_frame n/a dna_reading_frame

n/a n/a n/a n/a "" protein as a text string user_protein_sequence n/a n/a n/a n/a user_protein_sequence

n/a n/a n/a n/a 0 0, 1 report_mult_charge n/a n/a n/a n/a n/a

n/a n/a n/a n/a 0 0, 1 hide_html_links n/a n/a n/a n/a n/a

n/a n/a n/a n/a 0 0, 1 hide_protein_sequence n/a n/a n/a n/a hide_protein_sequence

n/a n/a n/a n/a Index Number Index Number
Accession Number access_method n/a n/a n/a n/a n/a

n/a n/a n/a n/a 80707 integer index_num n/a n/a n/a n/a n/a

n/a n/a n/a n/a L39370 text accession_num n/a n/a n/a n/a accession_num

n/a n/a n/a n/a 500.0 double min_digest_fragment_mass n/a n/a n/a n/a n/a

n/a n/a n/a n/a 5 integer min_digest_fragment_length n/a n/a n/a n/a n/a

n/a use_instrument_ion_types n/a n/a 0 0,1 n/a use_instrument_ion_types n/a n/a n/a n/a

n/a n/a n/a n/a 1 positive integer or No Limit n/a max_ms_prod_charge n/a n/a n/a n/a

n/a n/a n/a n/a SAMPLER A,C,D,E,F,G,H,I,K,L,M,N,P,Q R,S,T,V,W,Y,m,q,h,s,t,y,u n/a sequence n/a n/a sequence n/a

n/a n/a n/a n/a Amino Acid Amino Acid
Peptide Elemental
Elemental n/a n/a combination_type n/a n/a n/a

n/a n/a n/a n/a Peptide Sequence Peptide Sequence
Elemental Composition n/a n/a n/a n/a distribution_type n/a

n/a n/a n/a n/a 60 integer n/a n/a n/a n/a elem_comp_c n/a

n/a n/a n/a n/a 86 integer n/a n/a n/a n/a elem_comp_h n/a

n/a n/a n/a n/a 13 integer n/a n/a n/a n/a elem_comp_n n/a

n/a n/a n/a n/a 13 integer n/a n/a n/a n/a elem_comp_o n/a

n/a n/a n/a n/a 2 integer n/a n/a n/a n/a elem_comp_s n/a

n/a n/a n/a n/a 0 integer n/a n/a n/a n/a elem_comp_p n/a

n/a n/a n/a n/a 0 0, 1 n/a n/a n/a n/a detailed_report n/a

n/a n/a n/a n/a 0 0, 1 n/a n/a n/a n/a n/a create_database_indicies

n/a n/a n/a n/a 0 0, 1 n/a n/a n/a n/a n/a create_sub_database

n/a n/a n/a n/a .sub text n/a n/a n/a n/a n/a sub_database_id

n/a n/a n/a n/a "" text n/a n/a n/a n/a n/a name_field

n/a n/a n/a n/a 0 0, 1 n/a n/a n/a n/a n/a create_user_database

n/a n/a n/a n/a 0 integer n/a n/a n/a n/a n/a start_index_number

n/a n/a n/a n/a 1 integer n/a n/a n/a n/a n/a end_index_number

n/a n/a n/a n/a 0 0, 1 n/a n/a n/a n/a n/a all_indicies

n/a n/a n/a n/a 0 0, 1 n/a n/a n/a n/a n/a dna_to_protein

n/a n/a n/a n/a 0 0, 1 n/a n/a n/a n/a n/a delete_dna_database

MS-Fit	MS-Tag	MS-Seq	MS-Edman	Default Value	Valid Values	MS-Digest	MS-Product	MS-Comp	DB-Stat	MS-Isotope	FA-Index

msparams_dir	msparams_dir	msparams_dir	msparams_dir	(UNIX) \ (Windows)	directory name	msparams_dir	msparams_dir	msparams_dir	msparams_dir	msparams_dir	msparams_dir
seqdb_dir	seqdb_dir	seqdb_dir	seqdb_dir	seqdb/ (UNIX) seqdb\ (Windows)	directory name	seqdb_dir	n/a	n/a	seqdb_dir	n/a	seqdb_dir
res_msfit_dir	res_msfit_dir	res_msfit_dir	res_msfit_dir	results_msfit/ (UNIX) results_msfit\ (Windows)	directory name	n/a	n/a	n/a	n/a	n/a	res_msfit_dir
n/a	res_mstag_dir	res_mstag_dir	res_mstag_dir	results_mstag/ (UNIX) results_mstag\ (Windows)	directory name	n/a	n/a	n/a	n/a	n/a	res_mstag_dir
n/a	res_msseq_dir	res_msseq_dir	res_msseq_dir	results_msseq/ (UNIX) results_msseq\ (Windows)	directory name	n/a	n/a	n/a	n/a	n/a	res_msseq_dir
res_msedman_dir	res_msedman_dir	res_msedman_dir	res_msedman_dir	results_msedman/ (UNIX) results_msedman\ (Windows)	directory name	n/a	n/a	n/a	n/a	n/a	res_msedman_dir
database	database	database	database	NCBInr.7.7.96	valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, NCBInr, nr, dbEST, dbest, DA, DN, PA, PN Unknome in MS-Tag	database	n/a	n/a	database	n/a	database
instrument_name	instrument_name	instrument_name	n/a	""	valid text strings defined in instrument.txt	instrument_name	instrument_name	instrument_name	n/a	n/a	n/a
dna_frame_translation	dna_frame_translation	dna_frame_translation	dna_frame_translation	3	6, 3, -3, 1, -1	n/a	n/a	n/a	n/a	n/a	n/a
results_from_file	results_from_file	results_from_file	results_from_file	0	0, 1	n/a	n/a	n/a	n/a	n/a	results_from_file
input_program_name	input_program_name	input_program_name	input_program_name	msfit	msfit, mstag, msedman	n/a	n/a	n/a	n/a	n/a	input_program_name
input_filename	input_filename	input_filename	input_filename	""	text	n/a	n/a	n/a	n/a	n/a	input_filename
indicies	indicies	n/a	indicies	""	list of database indicies (integers)	n/a	n/a	n/a	n/a	n/a	indicies
accession_numbers	accession_numbers	n/a	accession_numbers	""	list of database accession numbers	n/a	n/a	n/a	n/a	n/a	accession_numbers
species	species	species	species	All	valid text strings defined in *.sp.txt or All	n/a	n/a	n/a	species	n/a	species
prot_low_mass	prot_low_mass	prot_low_mass	prot_low_mass	1000	integer	n/a	n/a	n/a	prot_low_mass	n/a	prot_low_mass
prot_high_mass	prot_high_mass	prot_high_mass	prot_high_mass	100000	integer	n/a	n/a	n/a	prot_high_mass	n/a	prot_high_mass
full_mw_range	full_mw_range	full_mw_range	full_mw_range	0	0, 1	n/a	n/a	n/a	full_mw_range	n/a	full_mw_range
low_pi	low_pi	low_pi	low_pi	3.0	double	n/a	n/a	n/a	low_pi	n/a	low_pi
high_pi	high_pi	high_pi	high_pi	10.0	double	n/a	n/a	n/a	high_pi	n/a	high_pi
full_pi_range	full_pi_range	full_pi_range	full_pi_range	0	0, 1	n/a	n/a	n/a	full_pi_range	n/a	full_pi_range
enzyme	enzyme	enzyme	enzyme	Trypsin	valid text strings defined in enzyme.txt and combinations of these separated by / characters	enzyme	n/a	n/a	enzyme	n/a	n/a
missed_cleavages	missed_cleavages	missed_cleavages	n/a	1	integer	missed_cleavages	n/a	n/a	n/a	n/a	n/a
cys	cys	cys	cys	acrylamide	valid text strings defined in cys.txt	cys	cys	cys	n/a	cys	n/a
comment	comment	comment	comment	""	text	n/a	n/a	n/a	n/a	n/a	n/a
results_to_file	results_to_file	results_to_file	results_to_file	0	0, 1	n/a	n/a	n/a	n/a	n/a	n/a
output_filename	output_filename	output_filename	output_filename	""	text	n/a	n/a	n/a	n/a	n/a	output_filename
nterm	nterm	nterm	nterm	Hydrogen	valid text strings defined in n_terms.txt	nterm	nterm	nterm	n/a	nterm	n/a
cterm	cterm	cterm	cterm	Free Acid	valid text strings defined in c_terms.txt	cterm	cterm	cterm	n/a	cterm	n/a
max_reported_hits	max_reported_hits	max_reported_hits	max_reported_hits	50	integer	n/a	n/a	max_reported_hits	n/a	n/a	n/a
n/a	max_hits	max_hits	n/a	200	integer	n/a	n/a	n/a	n/a	n/a	n/a
parent_mass_convert	parent_mass_convert	parent_mass_convert	parent_mass_convert	monoisotopic	monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi)	parent_mass_convert	parent_mass_convert	parent_mass_convert	n/a	n/a	n/a
parent_mass_tolerance	parent_mass_tolerance	parent_mass_tolerance	parent_mass_tolerance	0.5	double	n/a	n/a	parent_mass_tolerance	n/a	n/a	n/a
tolerance_units	tolerance_units	tolerance_units	tolerance_units	Da	Da, %, ppm, mmu	n/a	n/a	tolerance_units	n/a	n/a	n/a
parent_shift_type	parent_shift_type	n/a	n/a	+/-	+/-, =/+/-, =/+, =/-	n/a	n/a	n/a	n/a	n/a	n/a
parent_shift	parent_shift	n/a	n/a	130.1	double	n/a	n/a	n/a	n/a	n/a	n/a
parent_masses	n/a	n/a	parent_masses	NULL	2 column table listing of doubles (mass-m/z) and integers (charge)	n/a	n/a	n/a	n/a	n/a	n/a
average_to_mono_convert	n/a	n/a	n/a	NULL	list of 0's and 1's 0 = monoisotopic 1 = average	n/a	n/a	n/a	n/a	n/a	n/a
mod_AA	n/a	n/a	n/a	None Defined	Peptide N-terminal Gln to pyroGlu Oxidation of M Protein N-terminus Acetylated User Defined 1 Acrylamide Modified Cys	mod_AA	n/a	n/a	n/a	n/a	n/a
user1_name	n/a	n/a	n/a	""	valid text strings defined in usermod.txt	user1_name	n/a	n/a	n/a	n/a	n/a
min_parent_ion_matches	n/a	n/a	n/a	1	integer	n/a	n/a	n/a	n/a	n/a	n/a
min_matches	n/a	n/a	n/a	5	integer	n/a	n/a	n/a	n/a	n/a	n/a
mowse_on	n/a	n/a	n/a	0	0, 1	n/a	n/a	n/a	n/a	n/a	n/a
mowse_pfactor	n/a	n/a	n/a	0.4	double	n/a	n/a	n/a	n/a	n/a	n/a
n/a	fragment_masses	fragment_masses	n/a	NULL	2 column table listing of doubles (mass-m/z) and integers (charge)	n/a	n/a	n/a	n/a	n/a	n/a
search_type	search_type	n/a	n/a	identity	MS-Tag: identity or valid text strings defined in homology.txt MS-Seq: no errors, high mass error, low mass error, middle masses error, parent mass	n/a	n/a	n/a	n/a	n/a	n/a
params_at_end	params_at_end	params_at_end	params_at_end	0	0, 1	n/a	n/a	n/a	n/a	n/a	n/a
n/a	n/a	ion_type	n/a	b	a,b,c,y	n/a	it	n/a	n/a	n/a	n/a
n/a	it	n/a	n/a	None Defined	a,a-H2O,a-NH3,a-H3PO4, b,b-H2O,b-NH3,b+H2O, b-H3PO4,b-SOCH4, y,y-H2O,y-NH3,y-H3PO4,y-SOCH4, MH+,c,B,n,h,P,S,I,N,C	n/a	it	n/a	n/a	n/a	n/a
n/a	max_num_unused_ions	n/a	n/a	0	integer	n/a	n/a	n/a	n/a	n/a	n/a
n/a	fragment_mass_tolerance	n/a	n/a	1.0	double	n/a	n/a	n/a	n/a	n/a	n/a
n/a	star_ions_off	fragment_mass_tolerance	n/a	0	0, 1	n/a	n/a	n/a	n/a	n/a	n/a
n/a	comp_ion	comp_ion	n/a	None Defined	regular expression	n/a	n/a	comp_ion	n/a	n/a	n/a
n/a	parent_mass	parent_mass	n/a	1000.0	double	n/a	n/a	parent_mass	n/a	n/a	n/a
n/a	parent_charge	parent_charge	n/a	1	integer	n/a	n/a	parent_charge	n/a	n/a	n/a
n/a	mutation_matrix_off	n/a	n/a	0	0, 1	n/a	n/a	n/a	n/a	n/a	n/a
n/a	aa_exclude	n/a	n/a	""	text string containing the following characters A,C,D,E,F,G,H,I,K,L,M, N,P,Q,R,S,T,V,W,Y	n/a	n/a	aa_exclude	n/a	n/a	n/a
n/a	aa_add	n/a	n/a	""	m,q,h,s,t,y,u	n/a	n/a	aa_add	n/a	n/a	n/a
n/a	user_aa_c	n/a	n/a	2	integer	user_aa_c	user_aa_c	user_aa_c	n/a	user_aa_c	n/a
n/a	user_aa_h	n/a	n/a	3	integer	user_aa_h	user_aa_h	user_aa_h	n/a	user_aa_h	n/a
n/a	user_aa_n	n/a	n/a	1	integer	user_aa_n	user_aa_n	user_aa_n	n/a	user_aa_n	n/a
n/a	user_aa_o	n/a	n/a	1	integer	user_aa_o	user_aa_o	user_aa_o	n/a	user_aa_o	n/a
n/a	user_aa_s	n/a	n/a	0	integer	user_aa_s	user_aa_s	user_aa_s	n/a	user_aa_s	n/a
n/a	user_aa_p	n/a	n/a	0	integer	user_aa_p	user_aa_p	user_aa_p	n/a	user_aa_p	n/a
n/a	n/a	n/a	search_field	Sequence and Mass	Sequence Only Sequence and Mass Name Accession number Species List of Sequences	n/a	n/a	n/a	n/a	n/a	n/a
n/a	n/a	composition_exclude	n/a	""	ACDEFGHIKLMNPQRSTVWY	n/a	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	combo_output	0	0, 1	n/a	n/a	n/a	n/a	n/a	n/a
n/a	n/a	regular_expression	regular_expression	.	regular expression	n/a	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	regular_expressions	NULL	list of regular expressions or text strings dependent on search_field parameter	n/a	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	possible_sequences	NULL	list of peptides	n/a	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	max_aa_substitutions	0	integer	n/a	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	n/a	1	1, 2, 3, 4, 5, 6	dna_reading_frame	n/a	n/a	dna_reading_frame	n/a	dna_reading_frame
n/a	n/a	n/a	n/a	""	protein as a text string	user_protein_sequence	n/a	n/a	n/a	n/a	user_protein_sequence
n/a	n/a	n/a	n/a	0	0, 1	report_mult_charge	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	n/a	0	0, 1	hide_html_links	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	n/a	0	0, 1	hide_protein_sequence	n/a	n/a	n/a	n/a	hide_protein_sequence
n/a	n/a	n/a	n/a	Index Number	Index Number Accession Number	access_method	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	n/a	80707	integer	index_num	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	n/a	L39370	text	accession_num	n/a	n/a	n/a	n/a	accession_num
n/a	n/a	n/a	n/a	500.0	double	min_digest_fragment_mass	n/a	n/a	n/a	n/a	n/a
n/a	n/a	n/a	n/a	5	integer	min_digest_fragment_length	n/a	n/a	n/a	n/a	n/a
n/a	use_instrument_ion_types	n/a	n/a	0	0,1	n/a	use_instrument_ion_types	n/a	n/a	n/a	n/a
n/a	n/a	n/a	n/a	1	positive integer or No Limit	n/a	max_ms_prod_charge	n/a	n/a	n/a	n/a
n/a	n/a	n/a	n/a	SAMPLER	A,C,D,E,F,G,H,I,K,L,M,N,P,Q R,S,T,V,W,Y,m,q,h,s,t,y,u	n/a	sequence	n/a	n/a	sequence	n/a
n/a	n/a	n/a	n/a	Amino Acid	Amino Acid Peptide Elemental Elemental	n/a	n/a	combination_type	n/a	n/a	n/a
n/a	n/a	n/a	n/a	Peptide Sequence	Peptide Sequence Elemental Composition	n/a	n/a	n/a	n/a	distribution_type	n/a
n/a	n/a	n/a	n/a	60	integer	n/a	n/a	n/a	n/a	elem_comp_c	n/a
n/a	n/a	n/a	n/a	86	integer	n/a	n/a	n/a	n/a	elem_comp_h	n/a
n/a	n/a	n/a	n/a	13	integer	n/a	n/a	n/a	n/a	elem_comp_n	n/a
n/a	n/a	n/a	n/a	13	integer	n/a	n/a	n/a	n/a	elem_comp_o	n/a
n/a	n/a	n/a	n/a	2	integer	n/a	n/a	n/a	n/a	elem_comp_s	n/a
n/a	n/a	n/a	n/a	0	integer	n/a	n/a	n/a	n/a	elem_comp_p	n/a
n/a	n/a	n/a	n/a	0	0, 1	n/a	n/a	n/a	n/a	detailed_report	n/a
n/a	n/a	n/a	n/a	0	0, 1	n/a	n/a	n/a	n/a	n/a	create_database_indicies
n/a	n/a	n/a	n/a	0	0, 1	n/a	n/a	n/a	n/a	n/a	create_sub_database
n/a	n/a	n/a	n/a	.sub	text	n/a	n/a	n/a	n/a	n/a	sub_database_id
n/a	n/a	n/a	n/a	""	text	n/a	n/a	n/a	n/a	n/a	name_field
n/a	n/a	n/a	n/a	0	0, 1	n/a	n/a	n/a	n/a	n/a	create_user_database
n/a	n/a	n/a	n/a	0	integer	n/a	n/a	n/a	n/a	n/a	start_index_number
n/a	n/a	n/a	n/a	1	integer	n/a	n/a	n/a	n/a	n/a	end_index_number
n/a	n/a	n/a	n/a	0	0, 1	n/a	n/a	n/a	n/a	n/a	all_indicies
n/a	n/a	n/a	n/a	0	0, 1	n/a	n/a	n/a	n/a	n/a	dna_to_protein
n/a	n/a	n/a	n/a	0	0, 1	n/a	n/a	n/a	n/a	n/a	delete_dna_database

ProteinProspector Input Variables byKarlAndPete ();

ProteinProspector Input Variables