To the Editor:
Your editorial “Credit where credit is overdue”
aptly summarized the existing situation in the proteomics field, where full data disclosure
remains very much a work in progress. Importantly, it also correctly pointed out that
‘the software provided by the public repositories for searching and analysing proteomics
data is not as efficient and as user friendly as it could be’. We therefore here introduce
PRIDE Inspector (http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector), a
user-friendly, freely available open source software tool that allows the user to
efficiently browse and visualize mass spectrometry (MS) proteomics data. One of the
key features of PRIDE Inspector is that it allows the user to perform an initial assessment
on data quality and reliability. PRIDE Inspector can thus be used by researchers before
their data submission is performed, by journal editors and peer reviewers during the
manuscript review process, and by any interested user in the field after public release
of the data in PRIDE (Figure 1).
Despite the increasing popularity of MS based proteomics, and the overall tendency
in the life sciences towards open sharing of biological data, relatively little proteomics
data is currently available in the public domain. This situation is however changing
thanks to stricter data sharing guidelines by scientific journals and funding agencies.
Some proteomics journals (for instance, Proteomics and Molecular and Cellular Proteomics,
MCP) recommend, and in some concrete cases mandate public deposition of MS data in
support of manuscripts. Journals from the Nature group also strongly recommend submission
of proteomics data to repositories like PRIDE
Nevertheless, in practical terms, this public data-sharing policy can only succeed
if reliable and user-friendly software tools exist to streamline the submission task.
Therefore, the PRIDE Converter
application (http://code.google.com/p/pride-converter) was developed for data submissions
to the PRIDE database
. Not only has PRIDE Converter rapidly become the most popular data submission path
for PRIDE (accounting for 77% of all PRIDE experiments submitted since January 2009),
its release also corresponded to the start of a very significant increase in the amount
of deposited data in PRIDE (Supplementary Figure 1). Of course, the availability of
data in public repositories is only a first step. The interpretation and validation
of proteomics data remains controversial, especially for cases where proteins have
been identified on the basis of one unique peptide-to-spectrum match, or if post-translational
modifications (PTMs) are reported. The ability to inspect and validate reported results
during the review process, as well as after publication, is therefore of paramount
importance. Because of the amount of data involved, such inspections can only be undertaken
efficiently with the help of suitable software tools that combine ease of access with
effective visualizations. While viewers for MS proteomics data are already available
, they tend to suffer from different types of limitations. They may have been developed
around a single proprietary and/or unique data format, fail to properly handle the
very large files that are routinely produced, have only limited visualization and
analysis functionality or be costly to license for smaller groups or individuals.
We therefore developed PRIDE Inspector as a very user friendly, freely available tool
to browse, inspect and analyse proteomics data from the PRIDE repository, or presented
in standard formats.
PRIDE Inspector is a stand-alone Graphical User Interface (GUI) written in Java, released
under the Apache2 open source license, which can be freely downloaded from http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector.
Furthermore, PRIDE Inspector can also be started through a direct web link from the
PRIDE homepage (http://www.ebi.ac.uk/pride). The main features of PRIDE Inspector
are listed in the Supplementary Information, along with a description of its overall
software architecture and other technical details.
PRIDE Inspector supports fast loading of PRIDE XML and mzML
(the community data standard for MS data) files, and provides direct access to all
public PRIDE data through a direct MySQL database connection. Moreover, it includes
an automated data download capability for private PRIDE experiments that allows journal
editors and peer reviewers with the correct login credentials to assess the relevant
experiment(s) during peer review. The Web Start version available at the PRIDE homepage
furthermore adds the ability to start the application and access a particular dataset
through a simple URL.
PRIDE Inspector presents different views to the users, each focusing on a specific
aspect of the data (Figure 2). Depending on the type of information available for
a file format or PRIDE dataset, some views can remain inactive (Supp. Figure 2). For
that reason, an ‘Experiment Summary’ overview window is available in the bottom left
part of the GUI. A context-sensitive ‘Help’ function is also included, providing tailored
documentation for the current view. Currently, there are six views available in PRIDE
Inspector. Firstly, the ‘Overview’ tab, which includes easily readable, uniform experimental
metadata. The precise information displayed can vary slightly depending on the file
format used and is split in three different views: ‘Experiment General’, ‘Sample and
Protocol’, and ‘Instrument and Processing’ (Supp. Figures 3-6). The second view concerns
proteins (Supp. Figures 7-8), and is possibly the most interesting view for biologists.
For each identified protein, peptides, PTMs and corresponding spectra are displayed
in a concise manner. Metadata related to protein identification (such as search engine
or search database) are also provided here. A powerful spectrum viewer is available
as well, including an automatic annotation of the spectra based on submitted fragment
ions. Combinations of up to three amino acids are indicated next to the mass differences
between consecutive peaks (Supp. Figures 7 and 9). PRIDE Inspector also accesses some
of the most popular protein databases (UniProtKB, UniParc, IPI, Ensembl and NCBI nr
database) via a web service to retrieve the most up-to-date protein sequences and
names for the reported identifiers. Using the PRIDE Inspector sequence viewer (Supp.
Figures 8 and 11) it is possible to highlight different features in the protein sequence
such as identified peptides and PTMs. The updated status of the protein identifier
in the database (active, deleted, changed, unknown, merged or demerged, see Supp Information)
is also provided, which can affect the reliability of the protein identification.
In fact, it is then possible to find peptides that originally matched the sequence
of the identified protein, but that no longer match the most recent version of the
sequence in the database, The third view then focuses on the peptide identifications
themselves. Metadata such as peptide score (adapted for the search engine used) and
observed PTMs are displayed for each peptide (Supp. Figures 10-11). In both protein
and peptide views, the difference between experimental and theoretical mass-over-charge
ratio (delta m/z) is calculated for each peptide precursor and highlighted in the
application, which can be useful as an indication for errors or inconsistencies. For
both views, it is also possible to filter out the decoy matches and, as such, a straightforward
estimation of the peptide FDR is also provided. The fourth view is aimed at accessing
and visualizing all spectra in the data set, not only the identified ones (Supp. Figure
12). For mzML files, chromatograms are displayed here as well (Supp. Figure 13). Submitted
metadata (e.g. precursor m/z and intensity) is shown for each entry, along with calculated
information such as the number of peaks or the total peak intensity. Manual annotation
of spectra is supported as well for quick de novo sequencing. The fifth view provides
a collection of summary charts for assessing the overall properties of the dataset.
At the time of writing, up to eight different charts can be generated per dataset,
depending on the information available (Supp. Figures 14-18). These simple and easily
understandable charts can provide a quick overview on data quality and reliability.
Importantly, information in the spectrum-related charts can be shown for identified,
unidentified or all spectra. Each chart is documented thoroughly in the supplementary
information. Finally, a sixth tab focuses on the quantification information, where
available (Supp. Figure 19). This kind of data is currently only present in a small
number of PRIDE submissions but it is expected to become more and more popular. Apart
from visualizing the quantification values for both protein and peptides, it is also
possible to generate histograms where the expression values of up to ten proteins
can be compared. Sample metatada for each reagent can also be easily visualized. Ratios
can always be recalculated if the user decides to change the control sample.
Apart from the six main tabs, the ‘Search PRIDE’ panel gives access to all public
data in PRIDE. It is then easy to search for particular experiments filtering by different
types of metadata (Supp. Figures 20-21). In addition to data visualization and analysis
functionality, PRIDE Inspector also provides various data export options (Supp. Figure
22). First of all, all spectra can be exported to Mascot Generic Format (mgf) files.
In addition, details for all protein and/or peptide identifications (including PTMs),
and the peptide to protein mappings can be output as tables in tab-delimited format.
Finally, spectra and chromatograms (including annotations) can be saved as images
in various formats.
PRIDE Inspector is fully supported and maintained by the PRIDE team. Moreover, it
provides extra APIs/libraries, which can be reused independently by the scientific
community: the PRIDE XML JAXB library (for rapid and memory-efficient reading of PRIDE
XML files), and the PRIDE mzGraph Browser library (for the visualization and annotation
of spectra and chromatograms). These libraries are described in the supplementary
information. In addition, new features can be easily added to PRIDE Inspector thanks
to its modular software architecture and permissive open source licensing. Currently
ongoing extensions include full support of the version 1.1 of the mzIdentML community
standard for peptide and protein identifications
, since this format has only just reached stability (v1.1 was released on September
2011). Once mzIdentML is fully supported, it will also be possible to check thoroughly
the issues related to protein inference
. This means that researchers need to be aware of this limitation when interpreting
protein identifications reported by non-ambiguous (or shared) peptides. The PRIDE
XML format is limited for that aim in the sense that only one of the possible peptide-protein
mappings is usually reported.
PRIDE Inspector thus provides a user-friendly, comprehensive tool for the browsing,
inspection, and evaluation of data in the PRIDE database, or in a compatible standard
file format. As such, we believe that PRIDE Inspector will substantially increase
the ability of researchers, editors and peer-reviewers to explore, review, evaluate,
and reuse proteomics data.