biology

Proteome Analyst

Proteome Analyst 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 Proteome Analyst rather than just read about it. In short: Proteome Analyst (PA) is a freely available web server and online toolkit for predicting protein subcellular localization, or where a protein resides in a cell. In the field of proteomics, accurately predicting a protein's subcellular localization, or where a specific protein is located inside a cell, is an important step in the large scale study of proteins.

Key takeaways

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

Reference excerpt

Proteome Analyst (PA) is a freely available web server and online toolkit for predicting protein subcellular localization, or where a protein resides in a cell. In the field of proteomics, accurately predicting a protein's subcellular localization, or where a specific protein is located inside a cell, is an important step in the large scale study of proteins. This computational prediction problem is known as Protein subcellular localization prediction. Over the last decade, more than a dozen web servers and computer programs have been developed to attempt to solve this problem. Proteome Analyst is an example of one of the better performing subcellular prediction tools. Proteome Analyst makes predictions for both prokaryotic eukaryotic proteins using a text mining approach. Proteome Analyst was originally developed by the Proteome Analyst Research Group at the University of Alberta, and was initially released in March 2004. It was recently updated in January 2014.

Input/Output and Method Users can submit requests to the Proteome Analyst web server by selecting the organism type and then uploading a text file containing the protein sequence in a FASTA format. Proteome Analyst then uses BLAST to look for similar proteins in the Uniprot database with annotation on subcellular localization information. Proteome Analyst then uses a machine-learned classifier to analyze the annotation text fields of the most similar proteins identified in Uniprot search to make the final subcellular localization predictions. Users can view and download Proteome Analyst's results or ask Proteome Analyst to explain its predictions.

Technology Proteome Analyst consists of >30,000 lines of Java code and can be deployed on computer cluster to accelerate its speed and performance using multiple CPUs. The initial release of Proteome Analyst used Naïve Bayes classifier to perform its predictions. The current version of Proteome Analyst uses Support Vector Machine classifiers. Currently Proteome Analyst supports subcellular predictions for five organism types (Eurkayotes including animal, plant, fungi, and prokaryotes including gram-positive and gram-negative bacteria).

See also Protein Subcellular localization Proteomics Bioinformatics

References

Worked examples

Example 1 — a first encounter with Proteome Analyst

Start with the simplest possible case. Write down what Proteome Analyst 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 Proteome Analyst 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 Proteome Analyst 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 Proteome Analyst

In research: Proteome Analyst 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 Proteome Analyst 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: Proteome Analyst is common in secondary-school and first-year university syllabi. It links to neighbouring topics Protein databases, so understanding it makes those chapters shorter.
In everyday life: Look for Proteome Analyst 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.

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How to study Proteome Analyst in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Proteome Analyst 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 Proteome Analyst out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Proteome Analyst in simple terms?

Why does Proteome Analyst 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 Proteome Analyst?

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 Proteome Analyst.