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TAILS N-terminomics of the human dental pulp stroma and the odontoblast layer

ABSTRACT: We report the targeted analysis of the human dental pulp stroma and the odontoblast layer using the positional proteomics technique TAILS N-terminomics, which allowed us to capture both naturally blocked and unblocked protein N-termini, and to identify differences between e.g. the dental pulp proteomes of older and younger donors. Noteworthy, these differences were most pronounced in the odontoblast region. Note: This study is a follow-up on PXD002264.

INSTRUMENT(S): 6520A Quadrupole Time-of-Flight LC/MS

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Prof. Christopher Mark Overall

PROVIDER: MSV000083951 | MassIVE | Mon Jun 10 14:08:00 BST 2019

SECONDARY ACCESSION(S): PXD006557

REPOSITORIES: MassIVE

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The Human Odontoblast Cell Layer and Dental Pulp Proteomes and N-Terminomes.

Abbey S R SR Eckhard U U Solis N N Marino G G Matthew I I Overall C M CM

Journal of dental research 20171016 3

The proteome and N-terminome of the human odontoblast cell layer were identified for the first time by shotgun proteomic and terminal amine isotopic labeling of substrates (TAILS) N-terminomic analyses, respectively, and compared with that of human dental pulp stroma from 26 third molar teeth. After reverse-phase liquid chromatography-tandem mass spectrometry, >170,000 spectra from the shotgun and TAILS analyses were matched by 4 search engines to 4,888 and 12,063 peptides in the odontoblast cel ...[more]

PMID: 29035686

Similar Datasets

TAILS N-terminomics of the human dental pulp stroma and the odontoblast layer

Project description:We report the targeted analysis of the human dental pulp stroma and the odontoblast layer using the positional proteomics technique TAILS N-terminomics, which allowed us to capture both naturally blocked and unblocked protein N-termini, and to identify differences between e.g. the dental pulp proteomes of older and younger donors. Noteworthy, these differences were most pronounced in the odontoblast region. Note: This study is a follow-up on PXD002264.

2017-10-20 | PXD006557 | Pride

Human Dental Pulp TAILS N-terminomics

Project description:We report the targeted analysis of the human dental pulp proteome and N-terminome using the positional proteomics technique TAILS, which allowed us to capture both naturally blocked and unblocked protein N-termini. Furthermore, by using a proteomically barely studied human tissue in combination with a non-shotgun proteomics approach, we were able to identify many so far missing proteins (PE level 2-4), and established together with our previously published studies on human erythrocytes (Lange et al. 2014) and platelets (Prudova et al. 2014), a general workflow suitable for the in-depth and high-throughput analysis of protein N-termini in human specimen, as envisioned by the Chromosome-centric Human Proteome Project.

2015-08-18 | PXD002264 | Pride

Human Dental Pulp TAILS N-terminomics

2018-06-26 | MSV000082509 | MassIVE

N-terminomics/TAILS profiling of macrophages after chemical inhibition of legumain

Project description:We developed a legumain inhibitor and activtiy based probes. Murine RAW264.7 cells were subjected to N-terminomics and shotgun proteomics analysis.

2019-09-05 | PXD015200 | Pride

TAILS N-terminomics and proteomics reveal complex regulation of proteolytic cleavage by O-glycosylation.

Project description: Not available

| S-EPMC5961060 | biostudies-literature

TAILS N-terminomics of human platelets reveals pervasive metalloproteinase-dependent proteolytic processing in storage.

Project description: Not available

| S-EPMC4271184 | biostudies-literature

N-terminomics/TAILS profiling of proteases and their substrates in ulcerative colitis

Project description:Dysregulated protease activity is often implicated in the initiation of inflammation and immune cell recruitment in gastrointestinal inflammatory diseases. Using N-terminomics/TAILS (terminal amine isotopic labeling of substrates), we compared proteases, along with their substrates and inhibitors, between colonic mucosal biopsies of healthy patients and those with ulcerative colitis (UC). Among the 1,642 N-termini enriched using TAILS, increased endogenous processing of proteins was identified in UC compared to healthy patients. Changes in the reactome pathways for proteins associated with metabolism, adherens junction proteins (E-cadherin, liver-intestinal cadherin, catenin alpha-1 and catenin delta-1) and neutrophil degranulation were identified between the two groups. Increased neutrophil infiltration and distinct proteases observed in ulcerative colitis may result in extensive break down, altered processing or increased remodeling of adherens junctions and other cellular functions. Analysis of the proteolytic preferred cleavage sites indicated that the majority of proteolytic activity and processing comes from host proteases, but that key microbial proteases may also play a role in maintaining homeostasis. Thus, the identification of distinct proteases and processing of their substrates improves the understanding of dysregulated proteolysis in normal intestinal physiology and ulcerative colitis.

2019-09-08 | PXD014479 | Pride

Systematic optimization of C-TAILS approach for deep screening of C-terminomics

Project description:It is well known that protein C-termini play important roles in various biological processes, and thus the precise characterization of C-termini is essential for fully elucidating protein structure and understanding protein functions. Although many efforts have been made in the fields during the latest two decades, the progress is still far behind its counterpart, N-termini, and it necessitates more novel or optimized methods. Herein, we reported an optimized C-termini identification approach based on the C-terminal amine-based isotope labeling of substrates (C-TAILS) method. We optimized the amidation reaction conditions to achieve higher yield of fully amidated product. We evaluated different carboxyl and amine blocking reagents and found the superior performance of Ac-NHS and ethanolamine. Replacement of dimethylation with acetylation for Lys blocking resulted in the identification of 232 C-terminal peptides in E. Coli sample, about 42% higher than the conventional C-TAILS. A systematic data analysis revealed that the optimized method is unbiased to amino acid composition, more reproducible and with higher MASCOT scores. Moreover, the introduction of SCII (Single-Charge Ion Inclusion) method to alleviate the charge deficiency of small peptides allowed an additional 26 % increase in identification number. With the optimized method, we identified 481 C-terminal peptides corresponding to 369 C-termini in E. Coli in a triplicate experiments using 80 μg each. Our optimized method would benefit the deep screening of C-terminomics and possibly help discover some novel C-terminal modifications.

2015-09-15 | PXD002409 | Pride

N-Terminomics TAILS Identifies Host Cell Substrates of Poliovirus and Coxsackievirus B3 3C Proteinases That Modulate Virus Infection.

Project description: Not available

| S-EPMC5874412 | biostudies-literature

mito-TAILS analysis of EPEC infection

Project description:Mito-TAILS N-terminomics analysis of proteolytic events during EPEC infection of human epithelial cells, on whole-cell level and mitochondria.

2020-05-21 | PXD016994 | Pride

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