A Review on Quantitative Multiplexed Proteomics

Abstract

Over the last few decades, mass spectrometry‐based proteomics has become an increasingly powerful tool that is now able to routinely detect and quantify thousands of proteins. A major advance for global protein quantification was the introduction of isobaric tags, which, in a single experiment, enabled the global quantification of proteins across multiple samples. Herein, these methods are referred to as multiplexed proteomics. The principles, advantages, and drawbacks of various multiplexed proteomics techniques are discussed and compared with alternative approaches. We also discuss how the emerging combination of multiplexing with targeted proteomics might enable the reliable and high‐quality quantification of very low abundance proteins across multiple conditions. Lastly, we suggest that fusing multiplexed proteomics with data‐independent acquisition approaches might enable the comparison of hundreds of different samples without missing values, while maintaining the superb measurement precision and accuracy obtainable with isobaric tag quantification.

Genetics’ Piece of the PI: Inferring the Origin of Complex Traits and Diseases from Proteome‐Wide Protein–Protein Interaction Dynamics

“…Beyond sequencing considerations, pooling and demultiplexing individual backgrounds can also be prohibitive. As an example, multiplexing in targeted MS‐based proteomics is possible through the use of isobaric mass tags; however, the maximum number of samples that can be pooled in a single experiment is currently less than a dozen . Using chromosomal barcoding techniques, it is possible to uniquely tag hundreds or thousands of genetically distinct, whole‐genome sequenced individuals to augment these already valuable resources for both the genomics and proteomics communities.…”

Current trends in isotope‐coded derivatization liquid chromatographic‐mass spectrometric analyses with special emphasis on their biomedical application

“…Other applications such as environmental and food analysis were briefly summarized as some of the used ICD reagents in these fields were further used for analyzing biological specimens or have a strong potential to be used in the biomedical field. Regarding ICD for proteomics, many summarizing reviews for this topic have been published very recently (Bąchor, Waliczek, Stefanowicz, & Szewczuk, 2019;Hoedt, Zhang, & Neubert, 2019;Liu et al, 2019;Pappireddi, Martin, & Wühr, 2019;Patole & Bindschedler, 2019), and so they will not be covered in this article.…”

Mass Spectrometry Advances and Perspectives for the Characterization of Emerging Adoptive Cell Therapies

“…This increasingly utilized acquisition mode responds to the missing data (e.g. unselected parent ions) issue encountered with the stochastic parent ion selection in DDA [4,34].…”

“…Other DIA approaches have been developed such as MS E [31], multiplex (MSX) [32], or variable Sequential Window Acquisition of All Theoretical Fragment Ions (SWATH) [33], and have been reviewed elsewhere [30]. This increasingly utilized acquisition mode responds to the missing data (e.g., unselected parent ions) issue encountered with the stochastic parent ion selection in DDA [4,34].…”

“…In untargeted bottom-up proteomics, hundreds to thousands of proteins are quantified in an experiment across different conditions (e.g., engineered vs. control T-cells). In DDA, relative abundance of each protein can be calculated from label-free quantitative information [53,54] or samples to be compared can be differentially labeled (e.g., isotope labels) for increased throughput, as reviewed recently elsewhere [34,55]. Label free quantification (LFQ) of proteins is based on spectral counting or ion signal abundance [56].…”