Lecture

Protein Mass Spectrometry and Proteomics: Search Engines and Database Algorithms

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In course

CH-419: Protein mass spectrometry and proteomics

In systems biology, proteomics represents an essential pillar. The understanding of protein function and regulation provides key information to decipher the complexity of living systems. Proteomic technology now enables deep quantitative proteome mapping v ...

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.

Instructor

Loïc Dayon

Teaching & PhD Courses Protein mass spectrometry and proteomics CH-419 In systems biology, proteomics represents an essential pillar. The understanding of protein function and regulation provides key information to decipher the complexity of living systems. Proteomic technology now enables deep quantitative proteome mapping via mass spectrometry.

Official source

Related concepts (32)

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).

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.

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.

Ion-mobility spectrometry–mass spectrometry

Ion mobility spectrometry–mass spectrometry (IMS-MS) is an analytical chemistry method that separates gas phase ions based on their interaction with a collision gas and their masses. In the first step, the ions are separated according to their mobility through a buffer gas on a millisecond timescale using an ion mobility spectrometer. The separated ions are then introduced into a mass analyzer in a second step where their mass-to-charge ratios can be determined on a microsecond timescale.

False discovery rate

In statistics, the false discovery rate (FDR) is a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons. FDR-controlling procedures are designed to control the FDR, which is the expected proportion of "discoveries" (rejected null hypotheses) that are false (incorrect rejections of the null). Equivalently, the FDR is the expected ratio of the number of false positive classifications (false discoveries) to the total number of positive classifications (rejections of the null).

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