An Introduction to Advanced Targeted Acquisition Methods
| Autor: | van Bentum, Mirjam, Selbach, Matthias |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
RT
retention time SIL stable isotope labeled Proteomics targeted proteomics SRM TOMAHAQ triggered-by-offset multiplexed accurate-mass high-resolution and absolute quantification SILAC stable isotope labeling by amino acids in cell culture PRM DIA data-independent acquisition Review maxIT maximum injection time or fill time Mass Spectrometry PRM parallel reaction monitoring Animals Humans SRM selected reaction monitoring QqTOF quadrupole-TOF MaxQuant.Live LOQ limit of quantification IS-PRM LOD limit of detection iRT TOMAHAQ iRT indexed retention time TMT tandem mass tag Picky DDA data-dependent acquisition QqQ triple quadrupole mass spectrometer MRM QqOrbi quadrupole-Orbitrap Peptides SureQuant MRM multiple reaction monitoring |
| Zdroj: | Molecular & Cellular Proteomics : MCP |
| ISSN: | 1535-9484 1535-9476 |
| Popis: | Targeted proteomics via selected reaction monitoring (SRM) or parallel reaction monitoring (PRM) enables fast and sensitive detection of a preselected set of target peptides. However, the number of peptides that can be monitored in conventional targeting methods is usually rather small. Recently, a series of methods has been described that employ intelligent acquisition strategies to increase the efficiency of mass spectrometers to detect target peptides. These methods are based on one of two strategies. First, retention time adjustment-based methods enable intelligent scheduling of target peptide retention times. These include Picky, iRT, as well as spike-in free real-time adjustment methods such as MaxQuant.Live. Second, in spike-in triggered acquisition methods such as SureQuant, Pseudo-PRM, TOMAHAQ, and Scout-MRM, targeted scans are initiated by abundant labeled synthetic peptides added to samples before the run. Both strategies enable the mass spectrometer to better focus data acquisition time on target peptides. This either enables more sensitive detection or a higher number of targets per run. Here, we provide an overview of available advanced targeting methods and highlight their intrinsic strengths and weaknesses and compatibility with specific experimental setups. Our goal is to provide a basic introduction to advanced targeting methods for people starting to work in this field. Graphical abstract Highlights • Advanced acquisition methods improve focus of mass spectrometers on target peptides. • This review discusses existing methods based on two strategies. • Retention time adjustment-based methods enable intelligent scheduling of peptide RTs. • In spike-in triggered acquisition methods targeted scans are initiated by spike-ins. In Brief The analytical power of targeted proteomics depends on how efficiently the mass spectrometer detects target peptides. A number of “smart” acquisition approaches have been developed that enable more targets per run and improve analytical performance such as sensitivity, specificity, and quantitative accuracy. This review provides an introduction to these methods and highlights their inherent strengths and weaknesses. |
| Databáze: | OpenAIRE |
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