Common Metabolic Pathways Implicated in Resistance to Chemotherapy Point to a Key Mitochondrial Role in Breast Cancer,

1. Download : Download high-res image (130KB)
2. Download : Download full-size image

Highlights

• •OMICS distinguish cancer cells from resistant or cancer stem cells.
• •Bactericidal antibiotics and mitochondria.
• •Linezolid and anticancer therapy.

     

Integration and Analysis of CPTAC Proteomics Data in the Context of Cancer Genomics in the cBioPortal

1. Download : Download high-res image (137KB)
2. Download : Download full-size image

Highlights

• •Support for mass spectrometry-based proteomics in cBioPortal.
• •User-friendly web interface, a web API, and an R client to query proteogenomic data.
• •Integration of Clinical Proteomics Tumor Analysis Consortium data with cBioPortal.

     

Metabolic,Anti-apoptotic and Immune Evasion Strategies of Primary Human Myeloma Cells Indicate Adaptations to Hypoxia*

1. Download : Download high-res image (116KB)
2. Download : Download full-size image

Highlights

• •In-depth proteome profiling of primary human myeloma cells
• •Characteristics of myeloma cells are related to hypoxic bone marrow conditions
• •Myeloma cells show specific immune evasion strategies
• •Metabolic adaptations involve tumor and stroma cells

     

Surface Loops in a Single SH2 Domain Are Capable of Encoding the Spectrum of Specificity of the SH2 Family,

1. Download : Download high-res image (119KB)
2. Download : Download full-size image

Highlights

• •Surface loops play an essential role in SH2 domain specificity.
• •Diverse specificities may be obtained from a single SH2 domain by combinatorial mutations in the EF and BG loops.
• •The specificity of a loop mutant correlates with the sequence characteristics of the bait peptide used in its isolation.

     

Functional Proteomics and Deep Network Interrogation Reveal a Complex Mechanism of Action of Midostaurin in Lung Cancer Cells

1. Download : Download high-res image (94KB)
2. Download : Download full-size image

Highlights

• •Anticancer activity of midostaurin but not other PKC inhibitors in NSCLC cells.
• •Mechanism of action by network-based integration of chemo- and phosphoproteomics.
• •Midostaurin polypharmacology by simultaneous inhibition of TBK1, PDPK1 and AURKA.
• •Design of synergistic drug combination with PLK1 inhibitor by pathway validation.

     

Identification of Tumor Antigens Among the HLA Peptidomes of Glioblastoma Tumors and Plasma

1. Download : Download high-res image (95KB)
2. Download : Download full-size image

Highlights

• •The plasma-soluble HLA peptidome of Glioblastoma contains many tumor antigens.
• •This sHLA peptidome may serve as a rich source for disease biomarkers.
• •The sHLA peptidomes are highly correlated with the tumor's membranal HLA peptidomes.
• •The HLA peptidomes differ significantly from the proteomes of the tumors.

     

Identification of Salivary Biomarkers for Oral Cancer Detection with Untargeted and Targeted Quantitative Proteomics Approaches

1. Download : Download high-res image (173KB)
2. Download : Download full-size image

Highlights

• •iTRAQ-based analysis of saliva samples from oral cancer patients.
• •Proteome profiling of saliva samples from patients with oral premalignant lesions.
• •Verification of salivary biomarker candidates with MRM-MS and immunoassays.
• •Identification of salivary proteins as potential biomarkers of oral cancer.

     

Quantitative Mass Spectrometry to Interrogate Proteomic Heterogeneity in Metastatic Lung Adenocarcinoma and Validate a Novel Somatic Mutation CDK12-G879V

1. Download : Download high-res image (203KB)
2. Download : Download full-size image

Highlights

• •Serial biopsies and autopsy from a metastatic lung cancer patient over 7 years.
• •Tumor heterogeneity characterized by quantifying the proteome and phosphoproteome.
• •Patient-specific database built using whole genome sequencing data from tumors.
• •MRM assay and functional validation of a novel lung-specific CDK12-G879V mutant.

     

psims - A Declarative Writer for mzML and mzIdentML for Python

1. Download : Download high-res image (48KB)
2. Download : Download full-size image

Highlights

• •Incrementally build mzML 1.1, and mzIdentML 1.2 files in Python over a file stream.
• •Traverse controlled vocabularies using common mapping patterns.
• •Generate byte offset index as the document streams.
• •Manage referential integrity on-the-fly.

     

DECA,A Comprehensive,Automatic Post-processing Program for HDX-MS Data*

1. Download : Download high-res image (128KB)
2. Download : Download full-size image

Highlights

• •Open source software for comprehensive HDX-MS data analysis.
• •Automatic back-exchange correction options.
• •Rigorous statistical analysis of the significance of uptake differences.
• •High quality visualization tools.

     

Evaluation of Serum Glycoprotein Biomarker Candidates for Detection of Esophageal Adenocarcinoma and Surveillance of Barrett's Esophagus

1. Download : Download high-res image (137KB)
2. Download : Download full-size image

Highlights

• •C9, GSN, PON1, and PON3 validated as serum biomarker candidates of EAC.
• •Multimarker panel with AUROC of 0.93 to aid current endoscopy surveillance of BE.
• •Induction of tissue C9 in BE, dysplastic BE and EAC.
• •Alteration of complement pathway glycoproteins during BE-EAC pathogenesis.

     

Identification of Candidate Plasma Protein Biomarkers for Cervical Cancer Using the Multiplex Proximity Extension Assay

1. Download : Download high-res image (94KB)
2. Download : Download full-size image

Highlights

• •HPV is being introduced as the primary test in cervical cancer screening programs.
• •New biomarkers are needed for co-testing of women HPV positive in screening.
• •Analysis of plasma from women with invasive cervical cancer identified a 11-marker panel.
• •This signature shows high sensitivity and specificity to identify women with cancer.

     

Microvesicle Proteomic Profiling of Uterine Liquid Biopsy for Ovarian Cancer Early Detection

1. Download : Download high-res image (62KB)
2. Download : Download full-size image

Highlights

• •Microvesicle proteomics of 187 utero-tubal lavage samples for early diagnosis of HGOC.
• •Machine learning-based classification of a 9-protein signature with high predictive power.
• •Signature has 70‥ sensitivity and 76.2‥ specificity, predicting stage I lesions.

     

Spatial Distribution of Endogenous Tissue Protease Activity in Gastric Carcinoma Mapped by MALDI Mass Spectrometry Imaging

1. Download : Download high-res image (100KB)
2. Download : Download full-size image

Highlights

• •New MALDI MS imaging sample preparation workflow reveals tissue protease activity.
• •Differential time- and inhibitor concentration-dependence confirm active proteases.
• •Mouse gastric tumor displays high protease activity compared to surrounding tissue.
• •Proteomic data and biochemical protease activity assay support MALDI MSI results.

     

Identification of a Specific Translational Machinery via TCTP–EF1A2 Interaction Regulating NF1-associated Tumor Growth by Affinity Purification and Data-independent Mass Spectrometry Acquisition (AP-DIA),

1. Download : Download high-res image (193KB)
2. Download : Download full-size image

Highlights

• •AP-DIA/SWATH analysis to identify TCTP-interacting proteins in NF1 tumor cells.
• •A highly specific TCTP–EF1A2 interaction but rather than TCTP–EF1A1 interaction.
• •TCTP–EF1A2 interaction mediating formation of EF1A2-elogation factor complex.
• •TCTP–EF1A2 dependent translation machinery regulating NF1 tumor cell growth.

     

Proteomic Profiling of Human Prostate Cancer-associated Fibroblasts (CAF) Reveals LOXL2-dependent Regulation of the Tumor Microenvironment

1. Download : Download high-res image (105KB)
2. Download : Download full-size image

Highlights

• •Quantitative (phoshpo)proteome of primary cell cultures of patient-matched prostate CAF and NPF.
• •Key CAF-associated proteins validated using orthogonal methodologies.
• •LOXL2 inhibitors D-penicillamine and PXS-S2A impaired CAF migration and ECM alignment.
• •Pre-treatment with LOXL2 inhibitors impaired migratory capacity of RWPE-2 cells in co-culture.

     

gpGrouper: A Peptide Grouping Algorithm for Gene-Centric Inference and Quantitation of Bottom-Up Proteomics Data

1. Download : Download high-res image (162KB)
2. Download : Download full-size image

Highlights

• •Gene-centric inference algorithm with classification for distinguishable groups.
• •Shared peptides are split proportionally to corresponding unique peptide ratios.
• •iBAQ values are calculated for label-free, isotopic or isobaric labeling methods.
• •Universally handles single or mixed species PDX data with accurate deconvolution.

     

Macrophage Phosphoproteome Analysis Reveals MINCLE-dependent and -independent Mycobacterial Cord Factor Signaling

1. Download : Download high-res image (102KB)
2. Download : Download full-size image

Highlights

• •quantitative phosphoproteome analysis of TDM-activated macrophages.
• •distinct Mincle-dependent and independent phosphorylation and gene regulations.
• •Mincle-dependent activation of PI3K/AKT signaling by TDM.
• •Mincle-independent macrophage response is linked to cell cycle regulation.

     

A Targeted Mass Spectrometry Strategy for Developing Proteomic Biomarkers: A Case Study of Epithelial Ovarian Cancer

1. Download : Download high-res image (120KB)
2. Download : Download full-size image

Highlights

• •Rigorous experimental design and data analysis for large-scale SRM studies.
• •Plasma-based biomarker signature combined with CA125 for ovarian cancer detection.
• •Broadly applicable strategy for the development of diagnostic biomarker assays.

     

Why Glycosylation Matters in Building a Better Flu Vaccine

1. Download : Download high-res image (59KB)
2. Download : Download full-size image

Highlights

• •Glycosylation is not currently considered in flu vaccine design.
• •Glycosylation influences on immunodominance are not well understood.
• •Identification of site-specific glycosylation using mass spectrometry has matured.
• •New methods are needed to quantify site-specific glycosylation for vaccine design.