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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. | ||
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=== peakdb === | === peakdb === | ||
| - | *[[Technical Overview, MRM table | + | *[[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_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_mods table]]: the table of modification locations for the peptides in peakdb. | ||
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*[[Technical Overview, mem_pep_count table]]: the table of identification counts per peptide. | *[[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. | *[[Technical Overview, mem_peptides table]]: the table of details on each peptide in peakdb. | ||
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== Software == | == Software == | ||
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*[[Technical Overview, dblist_label_all.pl]]: to search by accession number, and display all results by pages. | *[[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.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_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, 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, 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, pgo.pl]]: to view the gene ontology of the proteins in a GPM result file. | ||
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=== peakdb === | === 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 == | ||
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*[[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, 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 |