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PeptideAtlas Tiered Human Integrated Search Proteome
In order to provide human proteomics MS/MS search databases that are well defined, comprehensive, and frequently updated,
we have developed an automated system that integrates all of major sources of human protein sequences into a set of
search databases. These databases are tiered into several levels of complexity from which researchers may choose depending on the
goal of the experiment and the data processing resources available.
Description of the Databases
On the first of every month, all protein lists are pulled down from their original sources. If any of them have changed,
they are integrated according to the description in Deutsch et al. (submitted) and released here. If none of the
source databases have changed, there is no new release. Briefly, the individual levels are as follows:
| Level 1 |
Includes only the core ~20,000 primary isoforms from
neXtProt (nP),
cRAP contaminants.
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| Level 2 |
Level 1 plus all ~22,000 "varplic" alternative splice isoforms from
neXtProt (nP), immunoglobulin variable region sequences from Swiss-Prot and IMGT.
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| Level 3 |
Level 2 plus UniProtKB "Complete Proteome" and additional non-redundant sequences from other small sources including microbes, external contributions, and additional RefSeq XP sequences.
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| Level 4 |
A "kitchen sink" database that includes Level 3 plus all other distinct sequences from UniProtKB/TrEMBL and RefSeq XP that are not already present in lower levels.
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Download THISP Databases
Below are the monthly releases of the THISP databases available for download. The "Base" is the set of Level 1-4 FASTA files (target and target-decoy). The "Components" is the set of all individual source components (from neXtProt, RefSeq, IMGT, cRAP, etc.) used to make the FASTA files in "Base", as described in the THISP article.
* What's a minid? A minid is a short "minimum identifier" for a digital object, typically either a single file,
or a zipped archive of multiple files. The minid server can resolve these minids into URLs that can be downloaded.
For more information on minids, see the introduction page and white paper. You can click on the little
clipboard icon to transfer the minid to your copy-paste clipboard.
THISP Changelog
Below is a list of changes that have been made to the building of THISP databases since publication.
| Date |
Changelog Comment |
| 2016-05-15 |
Submission of the manuscript to the JPR 2016 Human Proteome Project Special Issue. No changes to the build protocol have been made at this time. |
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