Technical Overview

Revision as of 17:53, 5 June 2009

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.

Database Tables

GPMDB

• Technical Overview, table relationships: how the tables of GPMDB work together.
• Technical Overview, result table: the table of GPM result files.
• Technical Overview, protein table: the table of identified proteins.
• Technical Overview, peptide table: the table of identified peptides.
• 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, peptide_word_index table: the table that drives tag searches of peptide sequences.
• 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, 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.

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.

peakdb

• Technical Overview, MRM table relationships: how the tables that make up the MRM information in peakdb work together.
• 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_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, 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, 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, ptissue.pl: to view proteins in a GPM result file in terms of BTO relationships.

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

• 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, 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.