GetTransitionsAPI

From SPCTools

 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