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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.
Level 2 Level 1 plus all ~22,000 "varplic" alternative splice isoforms from neXtProt (nP), immunoglobulin variable region sequences from Swiss-Prot and IMGT.
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.
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.


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.

Release Base Minid* Components Minid* Download Link
2021-06-01 FTP Directory
2021-05-01 FTP Directory
2021-04-01 FTP Directory
2021-03-01 FTP Directory
2021-02-01 FTP Directory
2021-01-01 FTP Directory
2020-12-01 FTP Directory
2020-11-01 FTP Directory
2020-10-01 FTP Directory
2020-09-01 FTP Directory
2020-08-01 FTP Directory
2020-07-01 FTP Directory
2020-06-01 FTP Directory
2020-05-01 FTP Directory
2020-04-01 FTP Directory
2020-03-01 FTP Directory
2020-02-01 FTP Directory
2020-01-01 FTP Directory
2019-12-01 FTP Directory
2019-10-01 ark:/57799/b9p12c ark:/57799/b9j71t FTP Directory
2019-09-01 ark:/57799/b9m702 ark:/57799/b9gd9z FTP Directory
2019-08-01 ark:/57799/b9vm7p ark:/57799/b9qx5s FTP Directory
2019-07-01 ark:/57799/b94412 ark:/57799/b90f0j FTP Directory
2019-06-01 ark:/57799/b9cm6z ark:/57799/b97x42 FTP Directory
2019-05-01 ark:/57799/b9n41q ark:/57799/b9hf06 FTP Directory
2019-04-01 ark:/57799/b97410 ark:/57799/b93b0f FTP Directory
2019-03-01 ark:/57799/b9gm78 ark:/57799/b9bt6q FTP Directory
2019-02-01 ark:/57799/b9r13c ark:/57799/b9mb03 FTP Directory
2019-01-01 ark:/57799/b90h7w ark:/57799/b9vt6c FTP Directory
2018-12-01 ark:/57799/b98131 ark:/57799/b94b0r FTP Directory
2018-11-01 ark:/57799/b9hh7j ark:/57799/b9ct61 FTP Directory
2018-10-01 ark:/57799/b9b41x ark:/57799/b96f0d FTP Directory
2018-09-01 ark:/57799/b9km6t ark:/57799/b9fx59 FTP Directory
2018-08-01 ark:/57799/b9v41k ark:/57799/b9qf02 FTP Directory
2018-07-01 ark:/57799/b93m7v ark:/57799/b9zx4k FTP Directory
2018-06-01 ark:/57799/b9c42m ark:/57799/b97d8d FTP Directory
2018-05-01 ark:/57799/b9mm8w ark:/57799/b9gx3v FTP Directory
2018-04-01 ark:/57799/b9w43n ark:/57799/b9rb0b FTP Directory
2018-03-01 ark:/57799/b9912z ark:/57799/b9568q FTP Directory
2018-02-01 ark:/57799/b9f09h ark:/57799/b99967 FTP Directory
2018-01-01 ark:/57799/b98d5k ark:/57799/b94m3n FTP Directory
2017-12-01 ark:/57799/b9jt1p ark:/57799/b9f37s FTP Directory
2017-11-01 ark:/57799/b9v95t ark:/57799/b9qh3w FTP Directory
2017-10-01 ark:/57799/b9rk8s ark:/57799/b9ms77 FTP Directory
2017-09-01 ark:/57799/b92046 ark:/57799/b9x929 FTP Directory
2017-08-01 ark:/57799/b9bh0b ark:/57799/b96p97 FTP Directory
2017-07-01 ark:/57799/b9n04g ark:/57799/b9h62j FTP Directory
2017-06-01 ark:/57799/b9459f ark:/57799/b90c7h FTP Directory
2017-05-01 ark:/57799/b9w01h ark:/57799/b9r591 FTP Directory
2017-04-01 ark:/57799/b9fw2t ark:/57799/b9b599 FTP Directory
2017-03-01 ark:/57799/b9rc7b ark:/57799/b9mk5d FTP Directory
2017-02-01 ark:/57799/b90w2s ark:/57799/b9w305 FTP Directory
2017-01-01 ark:/57799/b9s880 ark:/57799/b9nk5q FTP Directory
2016-12-01 ark:/57799/b91s3f ark:/57799/b9x30g FTP Directory
2016-11-01 ark:/57799/b9988n ark:/57799/b95k5c FTP Directory
2016-10-01 ark:/57799/b96k5p ark:/57799/b92s3r FTP Directory
2016-09-01 ark:/57799/b9h013 ark:/57799/b9c888 FTP Directory
2016-08-01 ark:/57799/b9x59k ark:/57799/b9sg69 FTP Directory
2016-07-01 ark:/57799/b95p41 ark:/57799/b92012 FTP Directory
2016-06-01 ark:/57799/b9pp4p ark:/57799/b9k01q FTP Directory
2016-05-01 ark:/57799/b9rp49 ark:/57799/b9mw2c FTP Directory
2016-04-06 ark:/57799/b96p4b ark:/57799/b9301c FTP Directory
2016-03-01 ark:/57799/b9z59w ark:/57799/b9tg6m FTP Directory
2016-02-01 ark:/57799/b9h59v ark:/57799/b9cc7x FTP Directory
2016-01-01 ark:/57799/b97p4n ark:/57799/b93w2q FTP Directory
2015-12-01 ark:/57799/b90596 ark:/57799/b9vc78 FTP Directory
2015-11-01 ark:/57799/b9qp40 ark:/57799/b9kw22 FTP Directory
2015-10-01 ark:/57799/b9g59j ark:/57799/b9bc7m FTP Directory

* 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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