An Introduction to Advanced Targeted Acquisition Methods

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Highlights

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  Advanced acquisition methods improve focus of mass spectrometers on target peptides.

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  This review discusses existing methods based on two strategies.

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  Retention time adjustment-based methods enable intelligent scheduling of peptide RTs.

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  In spike-in triggered acquisition methods targeted scans are initiated by spike-ins.

Abstract

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.

Keywords

targeted proteomics

PRM

SRM

MRM

Picky

iRT

MaxQuant.Live

IS-PRM

SureQuant

TOMAHAQ

Abbreviations

DDA

data-dependent acquisition

DIA

data-independent acquisition

iRT

indexed retention time

LOD

limit of detection

LOQ

limit of quantification

maxIT

maximum injection time or fill time

MRM

multiple reaction monitoring

PRM

parallel reaction monitoring

QqOrbi

quadrupole-Orbitrap

QqQ

triple quadrupole mass spectrometer

QqTOF

quadrupole-TOF

RT

retention time

SIL

stable isotope labeled

SILAC

stable isotope labeling by amino acids in cell culture

SRM

selected reaction monitoring

TMT

tandem mass tag

TOMAHAQ

triggered-by-offset, multiplexed, accurate-mass, high-resolution, and absolute quantification

© 2021 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.