Trends in the Design of New Isobaric Labeling Reagents for Quantitative Proteomics

Abstract

Modern mass spectrometry is one of the most frequently used methods of quantitative proteomics, enabling determination of the amount of peptides in a sample. Although mass spectrometry is not inherently a quantitative method due to differences in the ionization efficiency of various analytes, the application of isotope-coded labeling allows relative quantification of proteins and proteins. Over the past decade, a new method for derivatization of tryptic peptides using isobaric labels has been proposed. The labels consist of reporter and balanced groups. They have the same molecular weights and chemical properties, but differ in the distribution of stable heavy isotopes. These tags are designed in such a way that during high energy collision induced dissociation (CID) by tandem mass spectrometry, the isobaric tag is fragmented in the specific linker region, yielding reporter ions with different masses. The mass shifts among the reporter groups are compensated by the balancing groups so that the overall mass is the same for all forms of the reagent. Samples of peptides are labeled with the isobaric mass tags in parallel and combined for analysis. Quantification of individual peptides is achieved by comparing the intensity of reporter ions in the tandem mass (MS/MS) spectra. Isobaric markers have found a wide range of potential applications in proteomics. However, the currently available isobaric labeling reagents have some drawbacks, such as high cost of production, insufficient selectivity of the derivatization, and relatively limited enhancement of sensitivity of the analysis. Therefore, efforts have been devoted to the development of new isobaric markers with increased usability. The search for new isobaric markers is focused on developing a more selective method of introducing a tag into a peptide molecule, increasing the multiplexicity of markers, lowering the cost of synthesis, and increasing the sensitivity of measurement by using ionization tags containing quaternary ammonium salts. Here, the trends in the design of new isobaric labeling reagents for quantitative proteomics isobaric derivatization strategies in proteomics are reviewed, with a particular emphasis on isobaric ionization tags. The presented review focused on different types of isobaric reagents used in quantitative proteomics, their chemistry, and advantages offer by their application.

Proteomics of Brucella

“…The important features of employed methods and their individual merits have been reviewed extensively in 2012 [22]. Concomitant with analysis techniques, MS data analysis software has matured in the last years [23], now offering robust, label-free quantification and multiplexing of up to 10 samples [24] in one MS run. Since 2012, some of these technological advances have been implemented, yet traditional methods have remained popular in Brucella proteomics.…”

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

“…A very interesting example for NHS esters is the isobaric tag for relative and absolute quantification (iTRAQ) reagents. These reagents are used mainly in the field of proteomics and a very recent review has reported about the current trends in their design and development (Bąchor et al, ). However, these reagents are also used for the labeling of amino acids.…”

“…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.…”

“…very interesting example for NHS esters is the isobaric tag for relative and absolute quantification (iTRAQ) reagents. These reagents are used mainly in the field of proteomics and a very recent review has reported about the current trends in their design and development(Bąchor et al, 2019). However, these reagents are also used for the labeling of amino acids.Takach, O'shea, and Liu, Huang, Cai, Yuan, and Feng (2014) utilized iTRAQ reagents coupled with UPLC-MS/MS for the quantification of amino acids in rodent biofluids and tissues.…”

Enrichment of Cysteine-Containing Peptide by On-Resin Capturing and Fixed Charge Tag Derivatization for Sensitive ESI-MS Detection

“…The 2,4,6-triphenylpyridinium-modified peptides generate an abundant protonated 2,4,6-triphenylpyridinium ion in MS/MS experiments. This fragment was found to be a promising reporter ion for the multiple reactions monitoring (MRM) analysis [16].…”