Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRM quantification of circulating CFP-10 in TB patients

ABSTRACT: Liquid chromatography coupled mass spectrometry (LC-MS) operating in targeted mass spectrometry (MS) including multiple reaction monitoring (MRM) mode is an accurate analytical method. Integrating with nanoelectrospray-tandem MS (NanoES-MS/MS) and immunoprecipitation (IP), it becomes a promising method in detecting pathogen derived antigens which are at extremely low concentrations, such as mycobacterium tuberculosis (Mtb) secreted 10 kDa culture filtrate antigen (CFP-10). We employed an optimum denaturing condition for trypsin digestion and imunoprecipitation of targeted peptides and applied this method in clinical samples.

ORGANISM(S): Mycobacterium Tuberculosis

SUBMITTER: Qingbo Shu

PROVIDER: PXD021150 | panorama | Thu Apr 14 00:00:00 BST 2022

REPOSITORIES: PanoramaPublic

ACCESS DATA

Json Xml

Publications

Assay design for unambiguous identification and quantification of circulating pathogen-derived peptide biomarkers.

Shu Qingbo Q Liu Shan S Alonzi Tonino T LaCourse Sylvia M SM Singh Dhiraj Kumar DK Bao Duran D Wamalwa Dalton D Jiang Li L Lyon Christopher J CJ John-Stewart Grace G Kaushal Deepak D Goletti Delia D Hu Tony T

Theranostics 20220321 6

Rationale: Circulating pathogen-derived proteins can serve as useful biomarkers for infections but may be detected with poor sensitivity and specificity by standard immunoassays due to masking effects and cross-reactivity. Mass spectrometry (MS)-read immunoassays for biomarker-derived peptides can resolve these issues, but lack standard workflows to select species-specific peptides with strong MS signal that are suitable for antibody generation. Methods:Using a Mycobacterium tub ...[more]

PMID: 35401822

Similar Datasets

MS quantification of circulating CFP-10, p24 and VP40

Project description:Liquid chromatography coupled mass spectrometry (LC-MS) operating in targeted mass spectrometry (MS) including multiple reaction monitoring (MRM) mode is an accurate analytical method. Integrating with nanoelectrospray-tandem MS (NanoES-MS/MS) and immunoprecipitation (IP), it becomes a promising method in detecting serum biomarkers which are at extremely low concentrations, such as mycobacterium tuberculosis (Mtb) secreted 10 kDa culture filtrate antigen (CFP-10). We employed an optimum denaturing condition for trypsin digestion and IP of targeted peptides. The condition shows several advantages over commonly used one, 1) it prevents further dilution of sample, thus enables as-needed sample volume, 2) It ensures liberation of trace amount of antigen peptide under a cost-effective enzyme to substrate mass ratio, 3) It avoids time-consuming and unnecessary reduction of disulfide bonds, as some pathogen antigens don't contain disulfide bond. More importantly, optimum MRM transitions of the targeted peptide and standardized data processing and interpretation algorithm provide confirmative information of it in serum samples. By changing the denaturing buffer, addition of a clean-up step, selection of optimum MRM transitions and better interpreting MS signal, this workflow showed an improved accuracy in clinical samples.

2021-11-09 | PXD021149 | panorama

Targeted LC-MS/MS analysis of oSCRIB protein in HeLa cells.

Project description:LC-MS/MS analysis of small HeLa proteins (approximately 10–15 kDa) for detecting oSCRIB protein with Parallel Reaction Monitoring (PRM) mode.

2022-02-17 | PXD027841 | Pride

Association of immune evasion in myeloid sarcomas with disease manifestation and patients’ survival

Project description:Myeloid sarcomas (MS) comprise rare extramedullary manifestations of myeloid neoplasms (MN) with poor patients’ outcome. While the clinical relevance of the tumor microenvironment (TME) is well established in many malignancies, there exists limited information in MS. Therefore, the expression of the human leukocyte antigen class I (HLA-I) antigens, HLA-I antigen processing and presenting machinery (APM) components and the composition of the tumor microenvironment (TME) were analyzed. RNAseq analysis of a subset of 10 MS patients with preserved and reduced HLA-I HC expression revealed 150 differentially expressed genes in significant reduced expression of inflammatory response genes was found in HLA-I HC high samples.

2024-08-03 | GSE273877 | GEO

Brain antigens stimulate proliferation of T lymphocytes with a pathogenic phenotype in multiple sclerosis patients

Project description:A method to stimulate T lymphocytes with a broad range of brain antigens would facilitate identification of the autoantigens for multiple sclerosis and enable definition of the pathogenic mechanisms important for multiple sclerosis. In previous work we found the obvious approach of culturing leukocytes with homogenized brain tissue does not work because the brain homogenate suppresses antigen-specific lymphocyte proliferation. We now report a method that substantially reduces the suppressive activity. We used this non-suppressive brain homogenate to stimulate leukocytes from multiple sclerosis patients and controls. We also stimulated with common viruses for comparison. We measured proliferation, selected the responding CD3+ cells with flow cytometry, and sequenced their transcriptomes for mRNA and T cell receptor sequences. The mRNA expression suggested the brain-responding cells from MS patients are potentially pathogenic. The T cell receptor repertoire of the brain-responding cells was clonal with minimal overlap with virus antigens.

2022-01-13 | GSE193260 | GEO

Optimizing High-Throughput Shotgun Immunoproteomics for Antigen Identification

Project description:Identification of individual proteins (i.e., antigens) which initiate and/or perpetuate adaptive immune responses has potential to greatly impact pre-clinical and clinical work across numerous fields. To date, however, the methodologies available to identify antigens responsible for driving adaptive immune responses have been plagued by numerous issues which have drastically limited their widespread adoption. Therefore, in this study, we sought to optimize a shotgun immunoproteomics approach to alleviate these persistent issues and create a high-throughput, quantitative methodology for antigen identification. Three individual components of a previously published approach, namely the protein extraction, antigen elution, and LC-MS/MS analysis steps, were optimized in a systematic manner. These studies determined that preparation of protein extracts using a one-step tissue disruption method in immunoprecipitation (IP) buffer, eluting antigens from affinity chromatography columns with 1% trifluoroacetic acid (TFA), and TMT-labeling & multiplexing equal volumes of eluted samples for LC-MS/MS analysis, resulted in quantitative longitudinal antigen identification, with reduced variability between replicates and increased total number of antigens identified. This optimized pipeline provides a multiplexed, highly reproducible, and fully quantitative approach to antigen identification which is broadly applicable to determine the role of antigenic proteins in inciting (i.e. primary antigens) and perpetuating (i.e., secondary antigens) a wide range of diseases.

2023-04-18 | PXD038761 | Pride

Analysis of LDL-associated proteins using the method of digitized native protein mapping

Project description:The method of digitized native protein mapping, combining nondenaturing micro 2DE, grid gel-cutting and quantitative LC-MS/MS (in data-independent acquisition mode, or MSE), was improved by using a new MS/MS mode, ion mobility separation enhanced-MSE (HDMSE) and applied to analyze the area of human plasma low-density lipoproteins (LDL). An 18 mm * 4.8 mm rectangular area which included LDL on a nondenaturing micro 2D gel of human plasma was grid-cut into 72 square gel pieces and subjected to quantitative LC-MS/MS. Compared with MSE, HDMSE showed significantly higher performance, by assigning 50% more proteins and detecting each protein in more squares. Totally 253 proteins were assigned with LC-HDMSE and the quantity distribution of each was reconstructed as a native protein map. The maps showed Apo B-100 was the most abundant protein in the grid-cut area, concentrated at pI 5.4-6.1 and apparent mass ca. 1000 kDa, which corresponded to four gel pieces, squares 39-42. An Excel macro was prepared to search protein maps which show protein quantity peaks localized within the concentrated region of Apo B-100 (squares 39-42). Twenty-two proteins out of the 252 matched this criteria, in which nineteen proteins have been reported to be associated with LDL. This method require only several microliters of a plasma sample and the principle of the protein separation is totally different from ultracentrifugation. The results obtained by this method would provide new insights on the structure and function of LDL.

2016-05-17 | PXD003720 | Pride

Functional Inflammatory Profiles Distinguish Myelin-Reactive T Cells from Patients with Multiple Sclerosis

Project description:Myelin-reactive T cells have been identified in patients with multiple sclerosis (MS) and healthy subjects with comparable frequencies, but the contribution of these autoreactive T cells to disease pathology remains unknown. A total of 13,324 T cell libraries generated from blood of 23 patients and 22 healthy controls were interrogated for reactivity to myelin antigens. Libraries derived from CCR6+ myelin-reactive T cells from patients with MS exhibited significantly enhanced production of IFN-γ, IL-17, and GM-CSF compared to healthy controls. Single-cell clones isolated by MHC/peptide tetramers from CCR6+ T cell libraries also secreted more pro-inflammatory cytokines while clones isolated from controls secreted more IL-10. The transcriptomes of myelin-specific CCR6+ T cells from patients with MS were distinct from those derived from healthy controls, and of note, were enriched in Th17-induced experimental autoimmune encephalitis (EAE) gene signatures and gene signatures derived from Th17 cells isolated other human autoimmune diseases. These data, although not casual, imply that functional differences between antigen specific T cells from MS and healthy controls is fundamental to disease development and support the notion that IL-10 production from myelin-reactive T cells may act to limit disease progression, or even pathogenesis.

2015-05-18 | GSE66763 | GEO

HDACi promotes inflammatory remodeling of the tumor microenvironment to enhance epitope spreading and antitumor immunity

Project description:Adoptive cell therapy (ACT) with tumor-specific memory T cells has shown increasing efficacy in regressing solid tumors. However, tumor antigen heterogeneity represents a longitudinal challenge for durable clinical responses due to the therapeutic selective pressure for immune escape variants. Here, we demonstrate that delivery of class I histone deacetylase inhibitor, MS-275, promotes sustained tumor regression by synergizing with ACT in a coordinated manner to enhance cellular apoptosis. We find that MS-275 alters the tumor inflammatory landscape to support antitumor immunoactivation through the recruitment and maturation of cross-presenting CD103+ and CD8+ dendritic cells and depletion of regulatory T cells. Activated endogenous CD8+ T cell responses against non-target tumor antigens was critically required for the prevention of tumor recurrence. Importantly, MS-275 alters the immunodominance hierarchy by directing epitope spreading towards endogenous retroviral tumor-associated antigen, p15E. Our data suggest that MS-275 multi-mechanistically improves epitope spreading to promote long-term clearance of solid tumors.

2021-07-03 | GSE179337 | GEO

Dendritic Cell Vaccination in Patients With Advanced Colorectal Cancer

Project description:Dendritic cells loaded with tumor antigens induce cytotoxic T-cells which have been proved capable of killing both melanoma and breast cancer cells. Melanoma and colorectal cancer cells express some common antigens. Hence it is possible to use melanoma lysate to load the dendritic cells with tumor antigens similar to the antigens expressed by the patients’ colorectal cancer cells. The patient receives 10 vaccinations with 14 days between each. The parameters for effect are changes in tumor/metastasis size measured with computed tomography (CT), decrease in serum concentration of carcinoembryonic antigen (CEA), performance status measured by the World Health Organization (WHO) criteria, and Quality of Life.

| 2027823 | ecrin-mdr-crc

HDACi Delivery Reprograms Tumor-infiltrating Myeloid Cells to Eliminate Antigen-loss Variants

Project description:Immune recognition of tumor-expressed antigens by cytotoxic CD8+ T lymphocytes is the foundation of adoptive T-cell therapy. However, therapy-induced selective pressure can sculpt the antigenicity of tumors resulting in the outgrowth of variants that have lost the target antigen. Interestingly, tumor relapse resulting from adoptive memory T cell transfer and boosting oncolytic viral vaccination can be prevented using Class I histone deacetylase inhibitor, MS-275. We demonstrate that concomitant drug delivery subverts the phenotype and suppressive function of tumor-infiltrating myeloid cells and reprograms them with the cytotoxic capacity to directly eliminate antigen-negative tumor cells. By enhancing the production of IFNγ within the tumor microenvironment, our data suggest that MS-275 modifies the local cytokine landscape in favor of antitumor myeloid cell polarization.

2017-07-28 | GSE101985 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data