Protein Mass Spectrometry and Proteomics: Search Engines and Database Algorithms

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Description

This lecture covers the principles of protein mass spectrometry and proteomics, focusing on search engines like Mascot and database algorithms. It explains the conversion of mass spectra into peak lists, identification of proteins, and quantification methods. Various search software such as Andromeda, Byonic, and Comet are discussed, along with their features and applications. The lecture also delves into validation techniques, false discovery rate estimation, and relative quantification using isobaric tagging data.

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https://mediaspace.epfl.ch/media/0_vx1tnizi

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Related lectures (61)

Related concepts (170)

Proteomics

Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body. The proteome is the entire set of proteins produced or modified by an organism or system.

Mass spectrometry

Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a mass spectrum, a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio.

False positive rate

In statistics, when performing multiple comparisons, a false positive ratio (also known as fall-out or false alarm ratio) is the probability of falsely rejecting the null hypothesis for a particular test. The false positive rate is calculated as the ratio between the number of negative events wrongly categorized as positive (false positives) and the total number of actual negative events (regardless of classification). The false positive rate (or "false alarm rate") usually refers to the expectancy of the false positive ratio.

Tandem mass spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A common use of tandem MS is the analysis of biomolecules, such as proteins and peptides. The molecules of a given sample are ionized and the first spectrometer (designated MS1) separates these ions by their mass-to-charge ratio (often given as m/z or m/Q).

Search engine

A search engine is a software system that finds web pages that match a web search. They search the World Wide Web in a systematic way for particular information specified in a textual web search query. The search results are generally presented in a line of results, often referred to as search engine results pages (SERPs). The information may be a mix of hyperlinks to web pages, images, videos, infographics, articles, and other types of files. Some search engines also mine data available in databases or open directories.