Immediate Adaptation Analysis Implicates BCL6 as an EGFR-TKI Combination Therapy Target in NSCLC

1. Download : Download high-res image (422KB)
2. Download : Download full-size image

Highlights

• •EGFR-TKI molecular response profiling covering 10138 proteins and 13486 mRNAs.
• •EGFR-TKI combination therapy screen using a library of 528 compounds.
• •Several new candidate EGFR-TKI escape mechanisms and combination therapy targets.
• •Combined targeting of the oncogene BCL6 and EGFR results in synergy in NSCLC cells.

     

Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS

1. Download : Download high-res image (91KB)
2. Download : Download full-size image

Highlights

• •Brain membrane protein extraction.
• •Protein prenylation.
• •Prenyl peptide capture and characterization by LC-MS/MS.
• •HCD and EThcD peptide fragmentation.

     

An Interaction Network of RNA-Binding Proteins Involved in Drosophila Oogenesis

1. Download : Download high-res image (92KB)
2. Download : Download full-size image

Highlights

• •Label-free and dimethyl labeling MS analysis of 6 RBPs from Drosophila ovaries.
• •Functionally related RBPs show overlapping proteomes.
• •Selective co-purification of splicing factors and translational regulators.
• •Validation of 26 novel interactions by co-immunoprecipitation.

     

Integrative Metabolic Pathway Analysis Reveals Novel Therapeutic Targets in Osteoarthritis

1. Download : Download high-res image (221KB)
2. Download : Download full-size image

Highlights

• •SILAC-based protein quantification of OA hBMSCs undergoing chondrogenesis.
• •Spatially-resolved metabolomics by MSI of hBMSCs in chondrogenic differentiation.
• •Differential metabolic pathways involved in OA compared to control hBMSCs.
• •UDP-glucuronic acid/UDP-GlcNAc synthesis is decreased in chondrogenic OA hBMSCs.

     

Robust Summarization and Inference in Proteome-wide Label-free Quantification

1. Download : Download high-res image (204KB)
2. Download : Download full-size image

Highlights

• •In depth performance assessment of leading tools for differential protein abundance.
• •Novel fast modular framework MSqRobSum for robust protein summarization and inference.
• •MsqRobSum outperforms leading protein summarization-based tools.
• •MSqRobSum is on par with top-performing peptide based tool MSqRob.

     

Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant

1. Download : Download high-res image (118KB)
2. Download : Download full-size image

Highlights

• •MSFragger now supports raw timsTOF PASEF data.
• •IonQuant performs fast and accurate feature detection and quantification.
• •MSFragger and IonQuant provide excellent performance for timsTOF PASEF data.
• •Flexibility allows for complex analyses, such as semi-enzymatic and open search.

     

The Challenge of Classifying Metastatic Cell Properties by Molecular Profiling Exemplified with Cutaneous Melanoma Cells and Their Cerebral Metastasis from Patient Derived Mouse Xenografts

1. Download : Download high-res image (212KB)
2. Download : Download full-size image

Highlights

• •Comprehensive molecular profiling of cutaneous and cerebellar metastasis variants.
• •Identification of differentially regulated metastasis-associated molecules.
• •Evidence for individually distinct patterns of metastasis-associated molecules.
• •Highlighting the evident need for establishing meta-analyses strategies.

     

An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics

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

Highlights

• •Higher AGC significantly improves quantitation quality in single-cell analysis.
• •The boosting-to-sample ratio should be carefully evaluated and optimized.
• •iBASIL allows for precise quantitation of 1,500 proteins from 104 AML single cells.
• •iBASIL recapitulates major biological differences in different AML single cells.

     

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease

1. Download : Download high-res image (90KB)
2. Download : Download full-size image

Highlights

• •Laser microdissection of highly vulnerable hippocampal region.
• •Proteomic analysis of postmortem human brain tissue of AD and control cases.
• •Decreased levels of presynaptic proteins, but not postsynaptic proteins, in AD.
• •Immunohistochemistry verifies decreased levels of selected presynaptic proteins.

     

Phosphotyrosine-based Phosphoproteomics for Target Identification and Drug Response Prediction in AML Cell Lines

1. Download : Download high-res image (172KB)
2. Download : Download full-size image

Highlights

• •pY phosphoproteomes and dedicated ranking analyses for 16 AML cell lines.
• •RTK drivers, 6 mutant cell lines confirmed, identification for 4 more cell lines.
• •MAPK1/3 phosphorylation for cell lines without TK driver, indicating RAS mutation.
• •Drug target space phosphorylation correlates with drug IC50s in specific cell lines.

     

Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome

1. Download : Download high-res image (212KB)
2. Download : Download full-size image

Highlights

• •Detection of low-abundance phosphotyrosine-containing peptides is challenging.
• •Multiplexed TMT allows inclusion of modification(pTyr)-saturated boost channels.
• •Boost channels facilitate selection of pTyr precursor ions for fragmentation.
• •Quantitation depth is increased while maintaining accuracy and precision.

     

Integration of IgA and IgG Autoantigens Improves Performance of Biomarker Panels for Early Diagnosis of Lung Cancer

1. Download : Download high-res image (252KB)
2. Download : Download full-size image

Highlights

• •HuProt array-based identification of autoantigens in serum of early lung cancer.
• •Independent validation of early lung cancer biomarker candidates with ELISA.
• •Bioinformatics-aided identification of a biomarker panel.
• •Independent verification of the panel with ELISA and immunohistochemistry.

     

Molecular Dynamics Simulation-assisted Ionic Liquid Screening for Deep Coverage Proteome Analysis

1. Download : Download high-res image (123KB)
2. Download : Download full-size image

Highlights

• •Mechanistic insights into ionic liquids and proteins at molecular level.
• •Extractants prescreen for proteome analysis with MD simulation system.
• •A loss-less sample preparation method developed for in-depth proteome profiling.
• •Over 3,300 proteins were confidently identified from 1,000 HeLa cells in a 1 h run.
• •Label-free quantitative proteome analysis of human liver cancer tissues.

     

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis

1. Download : Download high-res image (302KB)
2. Download : Download full-size image

Highlights

• •DEqMS is a method for statistical analysis of quantitative MS-data.
• •Variance estimates based on the actual MS-data structure.
• •Improved statistical power and accuracy in protein differential analysis.
• •DEqMS is available as a user-friendly R package in Bioconductor.

     

Identification of Tumor Antigens in the HLA Peptidome of Patient-derived Xenograft Tumors in Mouse

1. Download : Download high-res image (147KB)
2. Download : Download full-size image

Highlights

• •Sufficient tumor tissues are often unavailable large HLA peptidome discovery.
• •Using patient derived xenograft (PDX) tumors can overcome this limitation.
• •The large PDX HLA peptidomes expand significantly those of the original biopsies.
• •The HLA peptidomes of the PDX tumors included many tumor antigens.

     

Data,Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing

1. Download : Download high-res image (114KB)
2. Download : Download full-size image

Highlights

• •In-depth proteomes of 4 SARS-CoV-2 cell line models (Vero E6, Calu-3, Caco-2, A549).
• •Proteomic evidence for thousands of Chlorocebus sabaeus proteins.
• •Proteomic response of Vero E6 cells to SARS-CoV-2 infection.
• •Synthetic peptides, spectral libraries, and targeted assays for SARS-CoV-2 proteins.

     

AMPK Interactome Reveals New Function in Non-homologous End Joining DNA Repair

1. Download : Download high-res image (195KB)
2. Download : Download full-size image

Highlights

• •Each component of the AMPK trimeric complex was profiled by interaction proteomics.
• •The subunit composition of the AMPK complex directs interactions to distinct proteins.
• •AMPK interacts with Artemis and plays a role in Non-Homologous End Joining.