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This page will serve as an index to the explanation pages for the entities that make up the GPM. | This page will serve as an index to the explanation pages for the entities that make up the GPM. | ||
| - | == | + | == Automatic Processes == |
*[[Technical Overview, GPMDB Updates]]: the steps taken to add new information to GPMDB. | *[[Technical Overview, GPMDB Updates]]: the steps taken to add new information to GPMDB. | ||
== Database Tables == | == Database Tables == | ||
| - | + | === GPMDB === | |
*[[Technical Overview, table relationships]]: how the tables of GPMDB work together. | *[[Technical Overview, table relationships]]: how the tables of GPMDB work together. | ||
*[[Technical Overview, result table]]: the table of GPM result files. | *[[Technical Overview, result table]]: the table of GPM result files. | ||
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*[[Technical Overview, aa table]]: the table of amino acid modifications and mutations. | *[[Technical Overview, aa table]]: the table of amino acid modifications and mutations. | ||
*[[Technical Overview, best_expect table]]: the table of the lowest (best) expect score and identification count for each protein. | *[[Technical Overview, best_expect table]]: the table of the lowest (best) expect score and identification count for each protein. | ||
| - | *[[Technical Overview, | + | *[[Technical Overview, peptide_index table]]: the table that drives tag searches of peptide sequences. |
*[[Technical Overview, paths table]]: the table of GPM file archive locations. | *[[Technical Overview, paths table]]: the table of GPM file archive locations. | ||
*[[Technical Overview, peptide_mut table]]: the table of peptides with known point mutations. | *[[Technical Overview, peptide_mut table]]: the table of peptides with known point mutations. | ||
| - | *[[Technical Overview, project table]]: the | + | *[[Technical Overview, project table]]: the table of information included with submittal of the original data file to the search software on the GPM. |
*[[Technical Overview, proseq table]]: the table of protein sequences dictated by RNA. | *[[Technical Overview, proseq table]]: the table of protein sequences dictated by RNA. | ||
| - | == | + | === EnspMapDB === |
| + | *[[Technical Overview, map table]]: the table of protein descriptions, found in the EnspMapDB database. | ||
| + | *[[Technical Overview, gpmnotes table]]: the table of notes included with the original data file submitted to the GPM search software, found in the EnspMapDB database. | ||
| - | *[[Technical Overview, | + | === peakdb === |
| - | *[[Technical Overview, dblist_gpmnum.pl]]: to search by GPM result file number. | + | *[[Technical Overview, MRM table relationships]]: how the tables that make up the MRM information in peakdb work together. |
| - | *[[Technical Overview, | + | *[[Technical Overview, mem_acc_nums table]]: the table of accession numbers and location on the protein for the peptides in peakdb. |
| + | *[[Technical Overview, mem_mods table]]: the table of modification locations for the peptides in peakdb. | ||
| + | *[[Technical Overview, mem_peak_info table]]: the table of mass and intensity pairs for each spectrum in peakdb. | ||
| + | *[[Technical Overview, mem_pep_count table]]: the table of identification counts per peptide. | ||
| + | *[[Technical Overview, mem_peptides table]]: the table of details on each peptide in peakdb. | ||
| + | |||
| + | == Software == | ||
| + | === GPMDB === | ||
| + | *[[Technical Overview, dblist_gpmnotes.pl]]: to search the project information stored in a GPM result file. | ||
| + | *[[Technical Overview, dblist_gpmnum.pl]]: to search by GPM result file number, and display the twenty most reliably identified proteins from it. | ||
| + | *[[Technical Overview, dblist_gpmnum_all.pl]]: to search by GPM result file number, and display all proteins identified from it by pages. | ||
*[[Technical Overview, dblist_keyword.pl]]: to search protein descriptions by keyword. | *[[Technical Overview, dblist_keyword.pl]]: to search protein descriptions by keyword. | ||
| + | *[[Technical Overview, dblist_label.pl]]: to search by accession number, and display the twenty best results. | ||
| + | *[[Technical Overview, dblist_label_all.pl]]: to search by accession number, and display all results by pages. | ||
| + | *[[Technical Overview, dblist_pep.pl]]: to search by residue sequence. | ||
| + | *[[Technical Overview, dblist_pep_modmass.pl]]: to search for protein identifications with specific residue modifications. | ||
| + | *[[Technical Overview, dblist_protein_mut.pl]]: to view peptides with known SNAPs. | ||
| + | *[[Technical Overview, dblist_pep_summary.pl]]: to view information on several peptides at a time. | ||
| + | *[[Technical Overview, dblist_v.pl]]: to view consensus peptide coverage information for a protein. | ||
| + | *[[Technical Overview, pepdelta.pl]]: to view displays about the parent ions identified in a GPM result file. | ||
| + | *[[Technical Overview, peptide.pl]]: to view a calculated spectrum of a specific peptide in a GPM result file. | ||
| + | *[[Technical Overview, peptide_xlib.pl]]: to define modifications to a peptide and view the resulting calculated spectrum. | ||
| + | *[[Technical Overview, pgel.pl]]: to view a simulated two-dimensional gel of the proteins in a GPM result file. | ||
| + | *[[Technical Overview, pgo.pl]]: to view the gene ontology of the proteins in a GPM result file. | ||
| + | *[[Technical Overview, phplctab.pl]]: to view calculated HPLC information about the peptides in a GPM result file. | ||
*[[Technical Overview, plist.pl]]: to view a summary of the protein identifications in a GPM result file. | *[[Technical Overview, plist.pl]]: to view a summary of the protein identifications in a GPM result file. | ||
| + | *[[Technical Overview, ppath.pl]]: to view proteins in a GPM result file in their KEGG pathways. | ||
*[[Technical Overview, protein.pl]]: to view all identifications of a protein. | *[[Technical Overview, protein.pl]]: to view all identifications of a protein. | ||
| - | *[[Technical Overview, | + | *[[Technical Overview, ptissue.pl]]: to view proteins in a GPM result file in terms of BTO relationships. |
| - | *[[Technical Overview, | + | |
| + | === peakdb === | ||
| + | *[[Technical Overview, peak_search.pl]]: to view MRM information at the protein level. | ||
| + | *[[Technical Overview, peak_details.pl]]: to view MRM information at the peptide level for a specific protein. | ||
== Display Elements == | == Display Elements == | ||
*[[Technical Overview, Coverage diagram]]: a graphical depiction of peptide coverage for both a specific protein identification and total peptide coverage for all identifications of a specific protein. | *[[Technical Overview, Coverage diagram]]: a graphical depiction of peptide coverage for both a specific protein identification and total peptide coverage for all identifications of a specific protein. | ||
*[[Technical Overview, AJAX content]]: asynchronously retrieved pieces of metadata about peptides and proteins. | *[[Technical Overview, AJAX content]]: asynchronously retrieved pieces of metadata about peptides and proteins. | ||
| + | *[[Technical Overview, protein information toolbar]]: a collection of internal and external links to further information regarding a protein accession number. | ||
| + | *[[Technical Overview, omega display]]: a metric of peptide coverage of a protein, with respect to charge state. | ||
This page will serve as an index to the explanation pages for the entities that make up the GPM.
Contents |