Targeted proteomics coming of age – SRM, PRM and DIA performance evaluated from a core facility perspective

Abstract

Quantitative mass spectrometry is a rapidly evolving methodology applied in a large number of omics-type research projects. During the past years, new designs of mass spectrometers have been developed and launched as commercial systems while in parallel new data acquisition schemes and data analysis paradigms have been introduced. Core facilities provide access to such technologies, but also actively support the researchers in finding and applying the best-suited analytical approach. In order to implement a solid fundament for this decision making process, core facilities need to constantly compare and benchmark the various approaches. In this article we compare the quantitative accuracy and precision of current state of the art targeted proteomics approaches single reaction monitoring (SRM), parallel reaction monitoring (PRM) and data independent acquisition (DIA) across multiple liquid chromatography mass spectrometry (LC-MS) platforms, using a readily available commercial standard sample. All workflows are able to reproducibly generate accurate quantitative data. However, SRM and PRM workflows show higher accuracy and precision compared to DIA approaches, especially when analyzing low concentrated analytes.

Comparison of data acquisition modes with Orbitrap high‐resolution mass spectrometry for targeted and non‐targeted residue screening in aquacultured eel

“…Collecting product ion (MS2) data is important in residue analyses to characterize and confirm the identity of possible contaminants . Others have evaluated the different types of MS2 data acquisition modes available on an Orbitrap, especially for proteomic analyses . The application of HRMS screening to chemical contaminants in foods presents unique challenges.…”

“…5 Others have evaluated the different types of MS2 data acquisition modes available on an Orbitrap, especially for proteomic analyses. 6,7 The application of HRMS screening to chemical contaminants in foods presents unique challenges. Specifically, methods need to detect and identify both targeted analytes at the low concentrations as mandated by regulatory agencies and unexpected or non-targeted compounds present in these samples that may currently be missed.…”

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

“…Chimeric MS/MS spectra produced from uDIA are often processed for peptide identification and quantification by comparisons to reference spectra or spectral libraries as originally described by Gillet et al [19]; however, other strategies are also discussed in Section 2. Kockmann et al [31] have made an effort to directly compare SRM, PRM, and uDIA across platforms within their own lab; however, the technological advances of uDIA methods improve rapidly, and newer high-resolution instrument platforms capable of uDIA have since emerged.…”

Advances in proteomic technologies and their scope of application in understanding plant–pathogen interactions

“…Sequential window acquisition of all theoretical spectra (SWATH), a high throughput targeted label-free relative quantification method relies on data-independent acquisition (DIA) mode, wherein the targeted data can be extracted from the globally acquired data. However, this high-throughput and flexibility in targeting from post data acquisition reduces its quantification accuracy as compared to SRM/MRM (Kockmann et al 2016).…”