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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
2023-02-01			FTP Directory
2023-01-01			FTP Directory
2022-12-01			FTP Directory
2022-11-01			FTP Directory
2022-10-01			FTP Directory
2022-09-01			FTP Directory
2022-08-01			FTP Directory
2022-07-01			FTP Directory
2022-06-01			FTP Directory
2022-05-01			FTP Directory
2022-04-01			FTP Directory
2022-03-01			FTP Directory
2022-02-01			FTP Directory
2022-01-01			FTP Directory
2021-12-01			FTP Directory
2021-10-01			FTP Directory
2021-09-01			FTP Directory
2021-08-01			FTP Directory
2021-07-01			FTP Directory
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.

Project funding: