Cargando…

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

SIMPLE SUMMARY: We reanalyzed a publicly available breast cancer proteomics dataset consisting of 122 human tumor samples using a scalable cloud computing workflow. By doing so, we were able to search these files against millions of known human sequence variants and hundreds of common post-translati...

Descripción completa

Detalles Bibliográficos
Autores principales:	Prakash, Amol, Taylor, Lorne, Varkey, Manu, Hoxie, Nate, Mohammed, Yassene, Goo, Young Ah, Peterman, Scott, Moghekar, Abhay, Yuan, Yuting, Glaros, Trevor, Steele, Joel R., Faridi, Pouya, Parihari, Shashwati, Srivastava, Sanjeeva, Otto, Joseph J., Nyalwidhe, Julius O., Semmes, O. John, Moran, Michael F., Madugundu, Anil, Mun, Dong Gi, Pandey, Akhilesh, Mahoney, Keira E., Shabanowitz, Jeffrey, Saxena, Satya, Orsburn, Benjamin C.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2021
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8534219/ https://www.ncbi.nlm.nih.gov/pubmed/34680183 http://dx.doi.org/10.3390/cancers13205034

Ejemplares similares

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts
por: Tabb, David L., et al.
Publicado: (2015)

Cloud Computing Based Immunopeptidomics Utilizing Community Curated Variant Libraries Simplifies and Improves Neo-Antigen Discovery in Metastatic Melanoma
por: Prakash, Amol, et al.
Publicado: (2021)

Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer
por: Tong, Mengsha, et al.
Publicado: (2018)

MHC Phosphopeptides: Promising Targets for Immunotherapy of Cancer and Other Chronic Diseases
por: Mahoney, Keira E., et al.
Publicado: (2021)

QC Metrics from CPTAC Raw LC-MS/MS Data Interpreted through Multivariate Statistics
por: Wang, Xia, et al.
Publicado: (2014)

Right data for right patient—a precisionFDA NCI–CPTAC Multi-omics Mislabeling Challenge
por: Boja, Emily, et al.
Publicado: (2018)

Phosphotyrosine profiling of human cerebrospinal fluid
por: Sathe, Gajanan, et al.
Publicado: (2018)

Targeted Identification of Metastasis-associated Cell-surface Sialoglycoproteins in Prostate Cancer
por: Yang, Lifang, et al.
Publicado: (2011)

The Viral Oncoprotein Tax Sequesters DNA Damage Response Factors by Tethering MDC1 to Chromatin
por: Belgnaoui, S. Mehdi, et al.
Publicado: (2010)

A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors
por: Halder, Ankit, et al.
Publicado: (2023)

Overlooked Binary Compounds Uncovered in the Reinspection of the La–Au System: Synthesis, Crystal Structures, and Electronic Properties of La(7)Au(3), La(3)Au(2), and La(3)Au(4)
por: Ovchinnikov, Alexander, et al.
Publicado: (2021)

Interdependent Phosphorylation within the Kinase Domain T-loop Regulates CHK2 Activity
por: Guo, Xin, et al.
Publicado: (2010)

Dysregulated expression of cell surface glycoprotein CDCP1 in prostate cancer
por: Yang, Lifang, et al.
Publicado: (2015)

promor: a comprehensive R package for label-free proteomics data analysis and predictive modeling
por: Ranathunge, Chathurani, et al.
Publicado: (2023)

T-Cell Infiltration and Clonality May Identify Distinct Survival Groups in Colorectal Cancer: Development and Validation of a Prognostic Model Based on The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC)
por: Campana, Luca G., et al.
Publicado: (2022)

Murine xenograft bioreactors for human immunopeptidome discovery
por: Heather, James M., et al.
Publicado: (2019)

Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in‐depth proteomic analysis
por: Correll, Vanessa L., et al.
Publicado: (2022)

Site-Specific Intact N-Linked Glycopeptide Characterization of Prostate-Specific Membrane Antigen from Metastatic Prostate Cancer Cells
por: Mackay, Stephen, et al.
Publicado: (2022)

Direct N-Glycosylation Profiling of Urine and Prostatic Fluid Glycoproteins and Extracellular Vesicles
por: Blaschke, Calvin R. K., et al.
Publicado: (2021)

A first dataset toward a standardized community-driven global mapping of the human immunopeptidome
por: Faridi, Pouya, et al.
Publicado: (2016)

Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer
por: Kim, Yunee, et al.
Publicado: (2016)

Soluble HLA peptidome: A new resource for cancer biomarkers
por: Tanuwidjaya, Erwin, et al.
Publicado: (2022)

Con: Alzheimer's disease and circadian dysfunction: chicken or egg?
por: Moghekar, Abhay, et al.
Publicado: (2012)

Comparison of antiplatelet activity of garlic tablets with cardio-protective dose of aspirin in healthy volunteers: a randomized clinical trial
por: Shafiekhani, Mojtaba, et al.
Publicado: (2016)

Variable Metastatic Potentials Correlate with Differential Plectin and Vimentin Expression in Syngeneic Androgen Independent Prostate Cancer Cells
por: Burch, Tanya C., et al.
Publicado: (2013)

Mitochondria Biogenesis and Bioenergetics Gene Profiles in Isogenic Prostate Cells with Different Malignant Phenotypes
por: Burch, Tanya C., et al.
Publicado: (2016)

Sphygmology of Ibn Sina, a Message for Future
por: Zarshenas, Mohammad M., et al.
Publicado: (2013)

Spares management handbook
por: Orsburn, Douglas K
Publicado: (1991)

Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics
por: Orsburn, Benjamin C.
Publicado: (2021)

Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric
por: Orsburn, Benjamin C.
Publicado: (2021)

Metabolomic, proteomic and single cell proteomic analysis of cancer cells treated with the KRAS(G12D) inhibitor MRTX1133
por: Orsburn, Benjamin C.
Publicado: (2023)

Time-of-Flight Fragmentation Spectra Generated by the Proteomic Analysis of Single Human Cells Do Not Exhibit Atypical Fragmentation Patterns
por: Orsburn, Benjamin C.
Publicado: (2023)

Acetic acid is a superior acidifier for sub-nanogram and single cell proteomic studies
por: Orsburn, Benjamin C.
Publicado: (2023)

An integrated method for single cell proteomics with simultaneous measurements of intracellular drug concentration implicates new mechanisms for adaptation to KRAS(G12D) inhibitors
por: Orsburn, Benjamin C.
Publicado: (2023)

Metabolomic, Proteomic, and Single-Cell Proteomic Analysis of Cancer Cells Treated with the KRAS(G12D) Inhibitor MRTX1133
por: Orsburn, Benjamin C.
Publicado: (2023)

The Cannabis Proteome Draft Map Project
por: Jenkins, Conor, et al.
Publicado: (2020)

Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid
por: Na, Chan Hyun, et al.
Publicado: (2020)

Mapping the micro-proteome of the nuclear lamina and lamina-associated domains
por: Wong, Xianrong, et al.
Publicado: (2021)

Proteomic Signatures of Diffuse and Intestinal Subtypes of Gastric Cancer
por: Singh, Smrita, et al.
Publicado: (2021)

Proteomics in Health and Disease
por: Wright Jr, George L., et al.
Publicado: (2003)

Cannot write session to /tmp/vufind_sessions/sess_sshjmn6rhoavh4fvep5f3tqj3a