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.

     

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.

     

Serum Protein Profiling Reveals a Landscape of Inflammation and Immune Signaling in Early-stage COVID-19 Infection

1. Download : Download high-res image (353KB)
2. Download : Download full-size image

Highlights

• •In-depth profiling of the serum proteome in early-stage COVID-19 patients.
• •A landscape of inflammation and immune signaling related to the SARS-CoV-2 infection.
• •CCL2 and CXCL10 medicated cytokine signaling pathways may correlate with neutrophil and lymphocyte respectively.

     

Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry

1. Download : Download high-res image (129KB)
2. Download : Download full-size image

Highlights

• •Cross-linked peptides are physically separated from mono-linked peptides in the gas-phase by TIMS ion mobility.
• •Development of a novel data acquisition routine that a-priori distinguishes cross-linked from mono-linked peptides called caps-PASEF.
• •First application of PhoX-driven cross-linking mass spectrometry on the timsTOF Pro.
• •Application of cross-linking mass spectrometry to medium to high complexity samples.

     

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.

     

Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9

1. Download : Download high-res image (245KB)
2. Download : Download full-size image

Highlights

• •Acute inhibition of growth-regulatory AGC-kinases Sch9, PKA and Ypk1.
• •Phospho-proteomic profiling of 6373 phsopho-sites.
• •Ypk1 regulates phospho-sites in RRxS/T-context and functionally overlaps with PKA.
• •Ypk1 and PKA activate trehalase activity of Nth1.

     

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.

     

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable,Isotopically Coded,and Mass Spectrometry-cleavable Chemical Crosslinker

1. Download : Download high-res image (248KB)
2. Download : Download full-size image

Highlights

• •Used affinity-enrichable, isotopically coded, and MS-cleavable crosslinker.
• •Targeted acquisition strategy based on isotopic-coding described and evaluated.
• •Novel data analysis pipeline developed provides improved crosslink identification.
• •Large dataset reveals hundreds of mitochondrial protein-protein interactions.

     

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.

     

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.

     

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.

     

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.

     

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.

     

Modulation of Natural HLA-B*27:05 Ligandome by Ankylosing Spondylitis-associated Endoplasmic Reticulum Aminopeptidase 2 (ERAP2)

1. Download : Download high-res image (213KB)
2. Download : Download full-size image

Highlights

• •HLA-B*27:05 and ERAP2 are risk factors for ankylosing spondylitis.
• •The effects of ERAP2 on the B*27:05 ligandome are defined.
• •P1, P2, P3, P7, and PΩ peptide positions are influenced by ERAP2.
• •These effects provide a basis for the association of ERAP2 with the autoimmune disease.

     

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries

1. Download : Download high-res image (144KB)
2. Download : Download full-size image

Highlights

• •Rapid DIA-only library building with gas-phase fractionation.
• •Recommended DIA acquisition strategies with staggered windows and forbidden zones.
• •Optimized DIA instrument settings for several Thermo Orbitrap instruments.
• •Data analysis tutorial using open source DIA software.

     

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.

     

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.

     

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.