GetTransitionsAPI
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| - | GetTransitions is a CGI script that allows users to query the peptide and transition information stored in PABST. This list is defined by | + | GetTransitions is a CGI script that allows users to query the peptide and transition information stored in the Peptide Atlas/MRM Atlas. The transitions retrieved |
| + | are constrained by various parameters set by the user. In a web browser, these can be set interactively as needed, but the page can also be accessed in an automated | ||
| + | fashion using command-line utilities such as wget or curl, or directly from a program using an appropriate URL fetching mechanism. This page is meant to describe the | ||
| + | various parameters that a remote user can use to obtain transitions | ||
| - | action = 'QUERY' | ||
| - | pabst_build_id = '13' | ||
| - | pabst_build_id = '13' | ||
| - | protein_name_constraint = 'ENSP00000336829' | + | <PRE> |
| - | upload_file = '' | + | This section defines the parameters that can be used to refine the transitions retrieved from the Atlas, some required and some optional, with allowed values following |
| + | the field name where applicable. The following section shows the the descriptive text provided in the web UI to help further explain these options. | ||
| - | peptide_sequence_constraint = '' | + | ## Required parameters: |
| - | peptide_length = '' | + | ############################################ |
| - | empirical_proteotypic_constraint = '' | + | |
| - | n_protein_mappings_constraint = '' | + | |
| - | n_genome_locations_constraint = '' | + | |
| - | n_highest_intensity_fragment_ions = '3' | + | |
| - | n_peptides_per_protein = '3' | + | |
| + | action [ QUERY ] | ||
| + | # One of the following is required, typical remote use will involve specifying the organism. | ||
| + | organism_name [ yeast, mouse, human ] | ||
| + | pabst_build_id [ any accessible build_id ] | ||
| + | |||
| + | # One of the following must be set, upload file requires POST method and file encoding | ||
| + | protein_name_constraint | ||
| + | upload_file | ||
| + | |||
| + | # not strictly required, but page with return dense HTML otherwise. | ||
| + | output_mode [ tsv xml ] | ||
| + | |||
| + | ## Optional parameters | ||
| + | ############################################ | ||
| + | |||
| + | peptide_sequence_constraint | ||
| + | peptide_length | ||
| + | empirical_proteotypic_constraint | ||
| + | n_protein_mappings_constraint | ||
| + | n_genome_locations_constraint | ||
| + | n_highest_intensity_fragment_ions | ||
| + | n_peptides_per_protein | ||
| + | |||
| + | # Options below affect the PABST peptide scoring algorithm, explained here. Current default values are shown. | ||
| 4H = '1' | 4H = '1' | ||
| 5H = '1' | 5H = '1' | ||
| Line 46: | Line 66: | ||
| obs = '2' | obs = '2' | ||
| ssr_p = '0.5' | ssr_p = '0.5' | ||
| + | </PRE> | ||
| - | + | This section shows the help text for the various parameters. | |
| 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. | 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) | 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) | ||
| Line 61: | Line 82: | ||
| - | 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 | + | Example invocation using wget, and the resulting transitions. Output mode is 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 | + | 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&action=QUERY;output_mode=tsv;organism_name=Yeast' -O YAL003W_transitions.tsv |
| - | 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 | + | <PRE> |
| - | 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 | 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 2 994.52 1 y9 1 10000 33.2 | ||
| Line 81: | Line 97: | ||
| 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 2 669.37 1 y6 2 2955 22.9 | ||
| YAL003W R WFNHIASK A 1.43 IT 501.76 2 816.44 1 y7 3 827 22.9 | YAL003W R WFNHIASK A 1.43 IT 501.76 2 816.44 1 y7 3 827 22.9 | ||
| + | </PRE> | ||
Revision as of 19:51, 15 April 2010
GetTransitions is a CGI script that allows users to query the peptide and transition information stored in the Peptide Atlas/MRM Atlas. The transitions retrieved
are constrained by various parameters set by the user. In a web browser, these can be set interactively as needed, but the page can also be accessed in an automated fashion using command-line utilities such as wget or curl, or directly from a program using an appropriate URL fetching mechanism. This page is meant to describe the various parameters that a remote user can use to obtain transitions
This section defines the parameters that can be used to refine the transitions retrieved from the Atlas, some required and some optional, with allowed values following the field name where applicable. The following section shows the the descriptive text provided in the web UI to help further explain these options. ## Required parameters: ############################################ action [ QUERY ] # One of the following is required, typical remote use will involve specifying the organism. organism_name [ yeast, mouse, human ] pabst_build_id [ any accessible build_id ] # One of the following must be set, upload file requires POST method and file encoding protein_name_constraint upload_file # not strictly required, but page with return dense HTML otherwise. output_mode [ tsv xml ] ## Optional parameters ############################################ peptide_sequence_constraint peptide_length empirical_proteotypic_constraint n_protein_mappings_constraint n_genome_locations_constraint n_highest_intensity_fragment_ions n_peptides_per_protein # Options below affect the PABST peptide scoring algorithm, explained here. Current default values are shown. 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'
This section shows the help text for the various parameters.
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.
Example invocation using wget, and the resulting transitions. Output mode is tsv.
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&action=QUERY;output_mode=tsv;organism_name=Yeast' -O 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
