biology

Proteomics Identifications Database

Proteomics Identifications Database is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Proteomics Identifications Database rather than just read about it. In short: The PRIDE (PRoteomics IDEntifications database) is a public data repository of mass spectrometry-based proteomics data, and is maintained by the European Bioinformatics Institute as part of the Proteomics Team. Originally designed by Lennart Martens in 2003 during a stay at the European Bioinformatics Institute as a Marie Curie fellow of the European Commission in the "Quality of Life" Programme (Contract number: QL…

Key takeaways

Proteomics Identifications Database belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Proteomics Identifications Database to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Proteomics Identifications Database from memory before moving on to harder problems.

Reference excerpt

The PRIDE (PRoteomics IDEntifications database) is a public data repository of mass spectrometry-based proteomics data, and is maintained by the European Bioinformatics Institute as part of the Proteomics Team. Originally designed by Lennart Martens in 2003 during a stay at the European Bioinformatics Institute as a Marie Curie fellow of the European Commission in the "Quality of Life" Programme (Contract number: QLRI-1999-50595), PRIDE was established as a production service in 2005. The original grant application document from June 2013 to start construction of PRIDE has since been published in a viewpoint article. Several similar proteomics databases have been built, including the GPMDB, PeptideAtlas, Proteinpedia and the NCBI Peptidome. The PRIDE database constitutes a structured data repository, and stores the original experimental data from the researchers without editorial control over the submitted data. In total, PRIDE contains data from about 60 species, the biggest fraction of it coming from human samples (including the data from the two draft human proteomes) followed by the fruit fly Drosophila melanogaster and mouse.

Formats and the submission process Since detailed proteomics data currently cannot be curated from the existing literature, the source of PRIDE data is solely submissions by academic researchers. PRIDE is a standards-compliant public repository, meaning that its own XML-based data exchange format for submissions, PRIDE XML, was built around the Proteomics Standards Initiative mzData standard for mass spectrometry. Recently, PRIDE has been adapted to work with the modern mzML and mzIdentML standards of the Proteomics Standards Initiative. An additional format, dubbed mzTab, can be used as a simplified way to submit quantitative proteomics data. As there are many types of different mass spectrometry instruments and software formats are currently on the market, wet-lab scientists without a strong bioinformatics background or informatics support were having problems converting their data to PRIDE XML. The development of PRIDE Converter helped to tackle this situation. PRIDE Converter is a tool, written in the Java programming language, that converts 15 different input mass spectrometry data formats into PRIDE XML via a wizard-like graphical user interface. It is freely available and is open source under the permissive Apache License. A new version of PRIDE Converter was released in 2012 as PRIDE Converter 2. This new version constituted a complete rewrite, focused on easy adaptability to different (and evolving) data sources.

Browsing, searching and data mining PRIDE Currently, data can be queried from PRIDE via the PRIDE web interface, through the stand-alone Java client PRIDE Inspector, or coupled directly to several search engines through PeptideShaker. Moreover, a new RESTful API allows convenient programmatic access to the PRIDE archive. The extensive use of controlled vocabularies (CVs) and ontologies for flexible yet context-sensitive annotation of data, along with the ability to perform intelligent queries by these annotations, are key features of PRIDE.

Involvement in ProteomeXchange The ProteomeXchange consortium has been set up to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, and to encourage optimal data dissemination. The consortium contains several member databases, including PRIDE and PeptideAtlas. The earliest conception of ProteomeXchange stems from a meeting at the HUPO 2005 conference in Munich, where the main proteomics data repositories at the time agreed in principle to exchange their data, and thus provide a means for the user to find public proteomics data at any of the participating databases. Due to the rapid development of the field, and the need to first develop suitable standards for data exchange, it took almost ten years from that meeting to actually implement this system, an effort that was funded by the 'ProteomeXchange' Coordination Action grant of the European Commission's Seventh Framework Programme.

Data recovery after the discontinuation of Peptidome The NCBI Peptidome database was discontinued in 2011, yet a joint effort by the PRIDE and Peptidome teams resulted in the transfer of all Peptidome data to PRIDE.

References

External links PRIDE homepage

Worked examples

Example 1 — a first encounter with Proteomics Identifications Database

Start with the simplest possible case. Write down what Proteomics Identifications Database claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Proteomics Identifications Database before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Proteomics Identifications Database ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Proteomics Identifications Database

In research: Proteomics Identifications Database appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Proteomics Identifications Database in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Proteomics Identifications Database is common in secondary-school and first-year university syllabi. It links to neighbouring topics Protein databases, Proteomics, Science and technology in Cambridgeshire, so understanding it makes those chapters shorter.
In everyday life: Look for Proteomics Identifications Database outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

Ask Teacher Smith questions about this articleOpens your AI tutor with a question about “Proteomics Identifications Database” →

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study Proteomics Identifications Database in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Proteomics Identifications Database means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Proteomics Identifications Database out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Proteomics Identifications Database in simple terms?

Why does Proteomics Identifications Database matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Proteomics Identifications Database?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Proteomics Identifications Database.