the analysis results are applied to improve the search engine X!
Tandem [3] at present. Therefore, data repositories play a very
important role not only in collecting the data but also in developing
and disseminating the scientific methodologies globally.
The data stored in the repositories are not limited to the raw
data. For example, in an isobaric tag experiment such as tandem
mass tag (TMT), the meaning of the data cannot be understood,
and the analysis results cannot be interpreted unless there is an
appropriately labeled result file added to the repository. Therefore,
in addition to the raw data itself, other information such as the
experimental conditions for acquiring the data, the settings of the
equipment, the software used for the analysis, and its parameters are
also required to be submitted. Generally, this information is called
“meta-information” and is required to be stored in the repository
in an appropriate form associated with the data file or the entire
data set.
The ProteomeXchange (PX) Consortium [4] was established in
2008 to facilitate the cooperation among multiple repositories that
have been involved in proper gathering of these datasets and information in response to HUPO (Human Proteome Organization)
analysis guidelines. PX Consortium provides the collected information to the PX system that assigns a unique PX ID to each dataset
and provides a web page to link the corresponding data repository.
This allows the users to seamlessly use the data stored in different
repositories. As of 2019, PX Consortium has six repositories as the
official members: PRIDE [5], PeptideAtlas (PASSEL) [6], MassIVE (https://massive.ucsd.edu/), jPOST [7], iProX [8], and Panorama Public [9].
Among these repositories, PASSEL and Panorama Public are
the repositories dedicated for SRM data acquired from the target
proteomics studies, and the other four are the repositories dedicated for the shotgun proteomics data, and one of these four is
covered in this chapter.
The jPOST repository (https://repository.jpostdb.org/) was
developed in Japan and was established for the purpose of serving as
a proteome data repository in the Asia-Oceania region. Actually,
there have been many data submissions from the areas other than
Asia and Oceania. The jPOST repository has organized its functions such that the users can complete all the procedures of data
registration within a single web browser and has also developed and
implemented a PRESTO system that facilitates high-speed data
transfer by parallelizing data transfer without the need of additional
software. The jPOST repository is an official data repository
certified by the Japan Proteome Society (JPrOS) and also cooperates with the proteome data journal, Journal of Proteome Data
and Methods (JPDM), which describes the details of metainformation of the proteome data, launched by JPrOS in 2019. In
the data descriptor article categorized by JPDM, it is essential to
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Yu Watanabe et al.
Tandem [3] at present. Therefore, data repositories play a very
important role not only in collecting the data but also in developing
and disseminating the scientific methodologies globally.
The data stored in the repositories are not limited to the raw
data. For example, in an isobaric tag experiment such as tandem
mass tag (TMT), the meaning of the data cannot be understood,
and the analysis results cannot be interpreted unless there is an
appropriately labeled result file added to the repository. Therefore,
in addition to the raw data itself, other information such as the
experimental conditions for acquiring the data, the settings of the
equipment, the software used for the analysis, and its parameters are
also required to be submitted. Generally, this information is called
“meta-information” and is required to be stored in the repository
in an appropriate form associated with the data file or the entire
data set.
The ProteomeXchange (PX) Consortium [4] was established in
2008 to facilitate the cooperation among multiple repositories that
have been involved in proper gathering of these datasets and information in response to HUPO (Human Proteome Organization)
analysis guidelines. PX Consortium provides the collected information to the PX system that assigns a unique PX ID to each dataset
and provides a web page to link the corresponding data repository.
This allows the users to seamlessly use the data stored in different
repositories. As of 2019, PX Consortium has six repositories as the
official members: PRIDE [5], PeptideAtlas (PASSEL) [6], MassIVE (https://massive.ucsd.edu/), jPOST [7], iProX [8], and Panorama Public [9].
Among these repositories, PASSEL and Panorama Public are
the repositories dedicated for SRM data acquired from the target
proteomics studies, and the other four are the repositories dedicated for the shotgun proteomics data, and one of these four is
covered in this chapter.
The jPOST repository (https://repository.jpostdb.org/) was
developed in Japan and was established for the purpose of serving as
a proteome data repository in the Asia-Oceania region. Actually,
there have been many data submissions from the areas other than
Asia and Oceania. The jPOST repository has organized its functions such that the users can complete all the procedures of data
registration within a single web browser and has also developed and
implemented a PRESTO system that facilitates high-speed data
transfer by parallelizing data transfer without the need of additional
software. The jPOST repository is an official data repository
certified by the Japan Proteome Society (JPrOS) and also cooperates with the proteome data journal, Journal of Proteome Data
and Methods (JPDM), which describes the details of metainformation of the proteome data, launched by JPrOS in 2019. In
the data descriptor article categorized by JPDM, it is essential to
310
Yu Watanabe et al.