GetTransitionsAPI

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-[dcampbel@digdug virus_peptide_order]$ hgrep GetTransitions | grep tsv+ GetTransitions is a CGI script that allows users to query the peptide and transition information stored in PABST. This list is defined by
- 886 wget 'https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?pabst_build_id=13&protein_name_constraint=ENSP00000364321&upload_file=&peptide_sequence_constraint=&peptide_length=&empirical_proteotypic_constraint=&n_protein_mappings_constraint=&n_genome_locations_constraint=&n_highest_intensity_fragment_ions=3&n_peptides_per_protein=3&4H=1&5H=1&BA=1&C=0.95&D=1&DG=1&DP=1&Hper=1&M=0.95&NG=1&NxST=1&P=0.95&QG=1&R=1&S=1&W=1&Xc=1&max_l=25&max_p=0.2&min_l=7&min_p=0.2&nE=1&nGPG=1&nM=1&nQ=1&nX=1&nxxG=1&obs=2&ssr_p=0.5&set_current_work_group=&set_current_project_id=&QUERY_NAME=AT_GetPABSTList&apply_action_hidden=&action=QUERY;output_mode=tsv' -O foo.tsv+ 
- 889 wget 'https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?organism=human&protein_name_constraint=ENSP00000364321;n_highest_intensity_fragment_ions=3;n_peptides_per_protein=3;apply_action_hidden=&action=QUERY;output_mode=tsv' -O foo.tsv+action = 'QUERY'
- 890 wget 'https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?organism=human&protein_name_constraint=ENSP00000364321;n_highest_intensity_fragment_ions=30;n_peptides_per_protein=30;apply_action_hidden=&action=QUERY;output_mode=tsv' -O foo.tsv+pabst_build_id = '13'
- 892 wget 'https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?organism_name=human&protein_name_constraint=ENSP00000364321;n_highest_intensity_fragment_ions=30;n_peptides_per_protein=30;apply_action_hidden=&action=QUERY;output_mode=tsv' -O foo.tsv+pabst_build_id = '13'
- 1080 wget 'https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?organism_name=human&protein_name_constraint=ENSP00000364321;n_highest_intensity_fragment_ions=30;n_peptides_per_protein=30;apply_action_hidden=&action=QUERY;output_mode=tsv' -O foo.tsv+ 
- 1082 wget 'https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?organism_name=human&protein_name_constraint=ENSP00000364321;n_highest_intensity_fragment_ions=30;n_peptides_per_protein=30;apply_action_hidden=&action=QUERY;output_mode=tsv' -O foo.tsv+protein_name_constraint = 'ENSP00000336829'
 +upload_file = ''
 + 
 +peptide_sequence_constraint = ''
 +peptide_length = ''
 +empirical_proteotypic_constraint = ''
 +n_protein_mappings_constraint = ''
 +n_genome_locations_constraint = ''
 +n_highest_intensity_fragment_ions = '3'
 +n_peptides_per_protein = '3'
 + 
 + 
 +4H = '1'
 +5H = '1'
 +BA = '1'
 +C = '0.95'
 +D = '1'
 +DG = '1'
 +DP = '1'
 +Hper = '1'
 +M = '0.95'
 +NG = '1'
 +NxST = '1'
 +P = '0.95'
 +QG = '1'
 +R = '1'
 +S = '1'
 +W = '1'
 +Xc = '1'
 +max_l = '25'
 +max_p = '0.2'
 +min_l = '7'
 +min_p = '0.2'
 +nE = '1'
 +nGPG = '1'
 +nM = '1'
 +nQ = '1'
 +nX = '1'
 +nxxG = '1'
 +obs = '2'
 +ssr_p = '0.5'
 + 
 + 
 + 
 + protein_name_constraint Constraint for the Protein Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a semicolon; Use ! for NOT.
 + upload_file Path to file with list of Protein Names to be uploaded via the web interface (NOTE: if proteins are not found, search defaults to printing all proteins of the selected Atlas build)
 + peptide_sequence_constraint Constraint for the Peptide Sequence. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a semicolon; Use ! for NOT.
 + peptide_length Constraint for the num amino acids in seq Allowed syntax: "n", "> n", "< n", "between n and n", "n +- n"
 + empirical_proteotypic_constraint Constraint for the empirical proteotypic score for a peptide. Allowed syntax: "n.n", "> n.n", "< n.n", "between n.n and n.n", "n.n +- n.n"
 + n_protein_mappings_constraint Constraint for number of distinct proteins for this peptide ( >=0 )
 + n_genome_locations_constraint Constraint for number of genome locations for this peptide ( >=0 )
 + n_highest_intensity_fragment_ions Number highest inten frag ions per spec to keep, default 3
 + n_peptides_per_protein Number of peptides to return per protein, default 3
 + pabst_build_id Select desired PABST Build to search, required.
 + 
 + 
 +wget 'https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?protein_name_constraint=YAL003W;n_highest_intensity_fragment_ions=3;n_peptides_per_protein=3;apply_action_hidden=&action=QUERY;output_mode=tsv;organism_name=Yeast' -O YAL003W_transitions.tsv
 +--2010-04-15 12:31:18-- https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?protein_name_constraint=YAL003W;n_highest_intensity_fragment_ions=3;n_peptides_per_protein=3;apply_action_hidden=&action=QUERY;output_mode=tsv;organism_name=Yeast
 +Resolving db.systemsbiology.net... 10.0.176.130
 +Connecting to db.systemsbiology.net|10.0.176.130|:443... connected.
 +HTTP request sent, awaiting response... 200 OK
 +Length: unspecified [text/tab-separated-values]
 +Saving to: `YAL003W_transitions.tsv'
 + [ <=> ] 721 --.-K/s in 0.01s
 +2010-04-15 12:31:20 (54.6 KB/s) - `YAL003W_transitions.tsv' saved [721]
 +[dcampbel@digdug getTrans]$ cat YAL003W_transitions.tsv
 +Protein Pre Sequence Fol Score Src Q1_mz Q1_chg Q3_mz Q3_chg Label Rank RI SSR
 +YAL003W K SYIEGTAVSQADVTVFK A 1.60 IT 907.96 2 994.52 1 y9 1 10000 33.2
 +YAL003W K SYIEGTAVSQADVTVFK A 1.60 IT 907.96 2 1093.59 1 y10 2 4129 33.2
 +YAL003W K SYIEGTAVSQADVTVFK A 1.60 IT 907.96 2 494.30 1 y4 3 2497 33.2
 +YAL003W K SIVTLDVKPWDDETNLEEMVANVK A 1.56 IT 1373.19 2 1059.01 2 y18 1 3874 44.6
 +YAL003W K SIVTLDVKPWDDETNLEEMVANVK A 1.56 IT 1373.19 2 945.43 2 y16 2 1152 44.6
 +YAL003W K SIVTLDVKPWDDETNLEEMVANVK A 1.56 IT 1373.19 2 1009.48 2 y17 3 800 44.6
 +YAL003W R WFNHIASK A 1.43 IT 1002.52 1 555.32 1 y5 1 730 22.9
 +YAL003W R WFNHIASK A 1.43 IT 501.76 2 669.37 1 y6 2 2955 22.9
 +YAL003W R WFNHIASK A 1.43 IT 501.76 2 816.44 1 y7 3 827 22.9

Revision as of 19:32, 15 April 2010

 GetTransitions is a CGI script that allows users to query the peptide and transition information stored in PABST.  This list is defined by

action = 'QUERY' pabst_build_id = '13' pabst_build_id = '13'

protein_name_constraint = 'ENSP00000336829' upload_file =

peptide_sequence_constraint = peptide_length = empirical_proteotypic_constraint = n_protein_mappings_constraint = n_genome_locations_constraint = n_highest_intensity_fragment_ions = '3' n_peptides_per_protein = '3'


4H = '1' 5H = '1' BA = '1' C = '0.95' D = '1' DG = '1' DP = '1' Hper = '1' M = '0.95' NG = '1' NxST = '1' P = '0.95' QG = '1' R = '1' S = '1' W = '1' Xc = '1' max_l = '25' max_p = '0.2' min_l = '7' min_p = '0.2' nE = '1' nGPG = '1' nM = '1' nQ = '1' nX = '1' nxxG = '1' obs = '2' ssr_p = '0.5' 


protein_name_constraint            Constraint for the Protein Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a  semicolon; Use ! for NOT.     
upload_file                        Path to file with list of Protein Names to be uploaded via the web interface (NOTE: if proteins are not found, search defaults to printing all proteins of the selected Atlas build)                   
peptide_sequence_constraint        Constraint for the Peptide Sequence. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a  semicolon; Use ! for NOT. 
peptide_length                     Constraint for the num amino acids in seq Allowed syntax: "n", "> n", "< n", "between n and n", "n +- n"                                                                                               
empirical_proteotypic_constraint   Constraint for the empirical proteotypic score for a peptide.  Allowed syntax: "n.n", "> n.n", "< n.n", "between n.n and n.n", "n.n +- n.n"                                                            
n_protein_mappings_constraint      Constraint for number of distinct proteins for this peptide ( >=0 )                                                                                                                                    
n_genome_locations_constraint      Constraint for number of genome locations for this peptide ( >=0 )                                                                                                                                     
n_highest_intensity_fragment_ions  Number highest inten frag ions per spec to keep, default 3                                                                                                                 
n_peptides_per_protein             Number of peptides to return per protein, default 3                                                                                                                                           
pabst_build_id                     Select desired PABST Build to search, required.


wget 'https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?protein_name_constraint=YAL003W;n_highest_intensity_fragment_ions=3;n_peptides_per_protein=3;apply_action_hidden=&action=QUERY;output_mode=tsv;organism_name=Yeast' -O YAL003W_transitions.tsv --2010-04-15 12:31:18-- https://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/GetTransitions?protein_name_constraint=YAL003W;n_highest_intensity_fragment_ions=3;n_peptides_per_protein=3;apply_action_hidden=&action=QUERY;output_mode=tsv;organism_name=Yeast Resolving db.systemsbiology.net... 10.0.176.130 Connecting to db.systemsbiology.net|10.0.176.130|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/tab-separated-values] Saving to: `YAL003W_transitions.tsv' 

   [ <=>                                                                                                                                     ] 721         --.-K/s   in 0.01s

2010-04-15 12:31:20 (54.6 KB/s) - `YAL003W_transitions.tsv' saved [721] [dcampbel@digdug getTrans]$ cat YAL003W_transitions.tsv Protein Pre Sequence Fol Score Src Q1_mz Q1_chg Q3_mz Q3_chg Label Rank RI SSR YAL003W K SYIEGTAVSQADVTVFK A 1.60 IT 907.96 2 994.52 1 y9 1 10000 33.2 YAL003W K SYIEGTAVSQADVTVFK A 1.60 IT 907.96 2 1093.59 1 y10 2 4129 33.2 YAL003W K SYIEGTAVSQADVTVFK A 1.60 IT 907.96 2 494.30 1 y4 3 2497 33.2 YAL003W K SIVTLDVKPWDDETNLEEMVANVK A 1.56 IT 1373.19 2 1059.01 2 y18 1 3874 44.6 YAL003W K SIVTLDVKPWDDETNLEEMVANVK A 1.56 IT 1373.19 2 945.43 2 y16 2 1152 44.6 YAL003W K SIVTLDVKPWDDETNLEEMVANVK A 1.56 IT 1373.19 2 1009.48 2 y17 3 800 44.6 YAL003W R WFNHIASK A 1.43 IT 1002.52 1 555.32 1 y5 1 730 22.9 YAL003W R WFNHIASK A 1.43 IT 501.76 2 669.37 1 y6 2 2955 22.9 YAL003W R WFNHIASK A 1.43 IT 501.76 2 816.44 1 y7 3 827 22.9

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=GetTransitionsAPI"
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