Reagents for Isobaric Labeling Peptides in Quantitative Proteomics

Ren, Yan; He, Yuexin; Lin, Zhilong; Zi, Jian; Yang, Huanming; Zhang, Shenyan; Lou, Xiaomin; Wang, Quanhui; Li, Shuwei; Liu, Siqi

doi:10.1021/acs.analchem.8b00321

Cited by 31 publications

(37 citation statements)

References 30 publications

(55 reference statements)

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“…However, the commercially available reagents for isobaric peptides labeling (TMT and iTRAQ) have some drawbacks, such as high cost in experiments, especially in quantitation for the modified peptides, and inconvenient handling for variable sizes of samples. Recently, Ren and co-workers [36] developed a set of 10-plex isobaric tags (IBT) with high stability and low cost, which is an improved version of 6-plex DiART. IBT 10-plex reagents were applied for dynamic monitoring of the quantitative responses of stimulated phosphoproteome.…”

Section: Tmtmentioning

confidence: 99%

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

et al. 2019

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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.

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Section: Tmtmentioning

confidence: 99%

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

et al. 2019

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“…Here, we investigated growth, physiology and proteomics of an oceanic Synechococcus sp. strain WH8102 (hereafter WH8102), grown in two N sources (nitrate and urea) under three temperature conditions (22, 25, and 28°C) using a newly developed isobaric tag (IBT)-based quantitative proteomic approach (Ren et al, 2018). The purpose of this study was to provide insights into the acclimation mechanisms of Synechococcus grown in different N sources to future ocean warming.…”

Section: Introductionmentioning

confidence: 99%

Proteomic Response to Rising Temperature in the Marine Cyanobacterium Synechococcus Grown in Different Nitrogen Sources

Chen

Xue

et al. 2019

Front. Microbiol.

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Synechococcus is one of the most important contributors to global primary productivity, and ocean warming is predicted to increase abundance and distribution of Synechococcus in the ocean. Here, we investigated molecular response of an oceanic Synechococcus strain WH8102 grown in two nitrogen sources (nitrate and urea) under present (25°C) and predicted future (28°C) temperature conditions using an isobaric tag (IBT)-based quantitative proteomic approach. Rising temperature decreased growth rate, contents of chlorophyll a, protein and sugar in the nitrate-grown cells, but only decreased protein content and significantly increased zeaxanthin content of the urea-grown cells. Expressions of CsoS2 protein involved in carboxysome formation and ribosomal subunits in both nitrate- and urea-grown cells were significantly decreased in rising temperature, whereas carbohydrate selective porin and sucrose-phosphate synthase (SPS) were remarkably up-regulated, and carbohydrate degradation associated proteins, i.e., glycogen phosphorylase kinase, fructokinase and glucose-6-phosphate dehydrogenase, were down-regulated in the urea-grown cells. Rising temperature also increased expressions of three redox-sensitive enzymes (peroxiredoxin, thioredoxin, and CP12) in both nitrate- and urea-grown cells. Our results indicated that rising temperature did not enhance cell growth of Synechococcus ; on the contrary, it impaired cell functions, and this might influence cell abundance and distribution of Synechococcus in a future ocean.

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“…The presence of isobaric peptides (Motorykin et al 2014), can frequently form when nearby PTM's co-localise on the same peptide (Ren et al 2018). This is an inherent issue in MS/MS spectra database search for spectra matches due to the mass shift caused by an unknown modification (Motorykin et al 2014).…”

Section: Characterisation Of Wash and Elute Fractions (Dda)mentioning

confidence: 99%

“…This is an inherent issue in MS/MS spectra database search for spectra matches due to the mass shift caused by an unknown modification (Motorykin et al 2014). Discrimination of such peptides by DDA is insufficient as the precursor masses can be the same (Ren et al 2018). The same precursor mass can be hundreds of isobaric forms and these modifications can hide fundamental information about biological systems and PTM crosstalk (Ren et al 2018).…”

Section: Characterisation Of Wash and Elute Fractions (Dda)mentioning

confidence: 99%

“…Discrimination of such peptides by DDA is insufficient as the precursor masses can be the same (Ren et al 2018). The same precursor mass can be hundreds of isobaric forms and these modifications can hide fundamental information about biological systems and PTM crosstalk (Ren et al 2018). Independently of quantitation method, the profile of the fragment ions is required to discriminate isobaric forms (Ren et al 2018).…”

Section: Characterisation Of Wash and Elute Fractions (Dda)mentioning

confidence: 99%

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Vitamin K and equine osteocalcin: an enigma explored

Skinner¹

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Vitamin K has received considerably less attention over the past 50 years compared to other fat soluble vitamins. Intakes of vitamin K beyond that required for normal blood coagulation were believed to confer no additional benefits, and therefore rarely investigated. The requirements and physiological role of vitamin K appeared to be secure. This view of vitamin K has changed recently following the delineation of its cofactor role in protein carboxylation, and the growing awareness of its interactions with other essential metabolic functions, beyond that of blood coagulation; there is much to be discovered. At present, seventeen vitamin Kdependent proteins (VKDPs) have been characterised, but the functionality of some still remains to be elucidated. Vitamin K has recently been implicated in osteoarthritis and accumulating evidence from human studies supports a protective role for vitamin K. To date however, little research into the role vitamin K may play in equine bone development exists. Developmental orthopaedic disease (DOD) is a term that encompasses a number of bone related conditions in the horse. It is a significant cause of lameness and wastage in a number of breeds, in particular Thoroughbreds and Warmbloods. It has clinical features in common with that of osteoporosis and osteoarthritis in the elderly. The VKDP osteocalcin is one of the few that has been extensively studied in humans and rodents. Located within bone, this protein plays a vital role in bone metabolism, facilitating the binding of bone minerals with protein. Decreased functionality of this protein has been found to be associated with increased fracture risk and osteoporosis in humans. The studies in this program were initiated to establish the relationship between vitamin K status and the development of DOD in foals. As bone development begins in utero, the first step was to examine placental transfer of the vitamin and then determine availability to the foal through milk. It was found in the initial experiments (Chapter 3), that foals at birth, had negligible concentrations of vitamin K1 (<0.01ng/mL) in both umbilical cord and foal plasma. The results clearly demonstrated that there is limited trans-placental transfer of vitamin K in the horse. It was also shown that milk can be enriched with vitamin K by supplementation of the mare with the vitamin. These studies confirmed that plasma concentrations were not a reliable measure of overall vitamin K status. Circulating osteocalcin and, its carboxylation status, has been proposed as one of the indicators of vitamin K status and a 'biomarker' of bone metabolism. Current assays available to measure Publications included in this thesis "No publications included". v

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Reagents for Isobaric Labeling Peptides in Quantitative Proteomics

Cited by 31 publications

References 30 publications

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

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

Proteomic Response to Rising Temperature in the Marine Cyanobacterium Synechococcus Grown in Different Nitrogen Sources

Vitamin K and equine osteocalcin: an enigma explored

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