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.

An alternative to using the CGI method is to run the programs from the command line. To do this each name value pair needs to be a separate argument. For example to run FA-Index from the command line on a Windows NT system you can use something like this:

ucsfbin3.4\faindex.cgi - msparams_dir=msparams3.4\ seqdb_dir=d:\seqdb\ output_filename=ucsfhtml3.4\js create_database_indicies=1 database=SwissProt.02.99

Note that the first argument has to be a dash character.

When doing this you need to be careful that any characters in the command line are not interpreted by the command line interpreter. For example if a value contains a space the interpreter needs some way of knowing that this isn't the next argument. To get round this any "special characters" have to be encoded. One way of doing this is to use the same encoding as that used in the CGI method.

A useful book explaining CGI programming is:

CGI Programming on the World Wide Web, Shishir Gundavaram, O'Reilly, 1996

MS-Fit MS-Tag MS-Seq MS-Pattern 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_mspattern_dir res_mspattern_dir res_mspattern_dir res_mspattern_dir results_mspattern/ (UNIX)
results_mspattern\ (Windows)		 directory name n/a n/a n/a n/a n/a res_mspattern_dir
database database database database "" valid prefixes: Genpept, gen, SwissProt, swp, Owl, owl, Ludwignr, NCBInr, nr, dbEST, dbest, pdbEST, pdbest, DA, DN, PA, PN, pDA, pDN, Pdefault, Ddefault, pDdefault.

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, mspattern 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
names names names names None Defined list of text strings n/a n/a n/a names n/a names
accession_nums accession_nums accession_nums accession_nums None Defined list of text strings n/a n/a n/a accession_nums n/a accession_nums
species_names species_names species_names species_names None Defined list of text strings n/a n/a n/a species_names n/a species_names
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
sort_type n/a n/a n/a Score Sort Score Sort
MW Sort
pI Sort
 n/a n/a n/a n/a n/a n/a
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
n/a n/a n/a n/a 0 0, 1 end_terminus n/a n/a n/a n/a n/a
n/a n/a n/a n/a N N, C stripping_terminus n/a n/a n/a n/a n/a
n/a n/a n/a n/a 2 integer start_strip n/a n/a n/a n/a n/a
n/a n/a n/a n/a 4 integer end_strip n/a n/a n/a n/a 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
parent_contaminant_masses n/a n/a n/a NULL list of singly charged masses 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
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 ion_unmatched_type n/a n/a Max. % Unmatched Ions Max. % Unmatched Ions
Max. Num Unmatched Ions
Min. Num Matched Ions		 n/a n/a n/a n/a n/a n/a
n/a max_percent_ions_unused n/a n/a 0 double n/a n/a 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 min_num_used_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 exclude_flag 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 MassSequence 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 1 non-zero positive integeropen_reading_frame n/a n/a n/a n/a n/a
n/a n/a n/a n/a "" protein as a text stringuser_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_typesn/a n/a 0 0,1 n/a use_instrument_ion_typesn/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 "" Elemental formula of the form Cx Hy Oz etc where x, y and z are integers. Elements defined in elements.txt can be used. n/a n/a n/a n/a elemental_compositionn/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