PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome,

1. Download : Download high-res image (110KB)
2. Download : Download full-size image

Highlights

• •PTMiner software for intelligent post-processing of open-search results.
• •Unrestrictive modification site localization based on a Bayesian model.
• •Extended transfer FDR estimation for accurate grouped FDR estimation.
• •Comprehensive PTM characterization in a draft map of human proteome.

     

Nonparametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-binding Proteins*

1. Download : Download high-res image (51KB)
2. Download : Download full-size image

Highlights

• •Method for the analysis of response curves from thermal proteome profiling (TPP).
• •NPARC uses nonparametric statistics and provides false discovery-rate (FDR) control.
• •Increased proteome coverage and sensitivity to identify drug-binding proteins.

     

MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins

1. Download : Download high-res image (138KB)
2. Download : Download full-size image

Highlights

• •New software to determine differentially expressed proteins in quantitative MS experiments.
• •Applicable to any modern quantitative MS setup and study type, including clinical setups.
• •Ultra-sensitive at strict FDR control, up to 1000 additional proteins in a single comparison.
• •Easy to use, fast processing and readily available package, including user friendly manual.

     

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.

     

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

     

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.

     

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.

     

MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides

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

Highlights

• •MaxQuant.Live controls Orbitrap mass analyzers in real-time.
• •Freely available apps enable advanced data acquisition strategies.
• •On-the-fly mass, retention time and intensity recalibration.
• •Global targeting unifies shotgun and targeted proteomics.

     

BioID Performed on Golgi Enriched Fractions Identify C10orf76 as a GBF1 Binding Protein Essential for Golgi Maintenance and Secretion

1. Download : Download high-res image (61KB)
2. Download : Download full-size image

Highlights

• •BioID with Golgi fractions identified C10orf76 as proximal to GBF1.
• •Tagged C10orf76 overlaps with Golgi markers.
• •C10orf76 binds GBF1 and exchanges rapidly between free and bound forms.
• •C10orf76 is essential for maintenance of the Golgi and for secretion.

     

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.

     

microRNA-222 Attenuates Mitochondrial Dysfunction During Transmissible Gastroenteritis Virus Infection

1. Download : Download high-res image (93KB)
2. Download : Download full-size image

Highlights

• •microRNA-222 attenuates TGEV-induced mitochondrial dysfunction.
• •microRNA-222 downregulates THBS1 and CD47.
• •THBS1 is the target of microRNA-222 during TGEV infection.
• •THBS1 and CD47 increase mitochondrial Ca²⁺ level and reduced mitochondrial membrane potential (MMP).

     

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.

     

Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains

1. Download : Download high-res image (74KB)
2. Download : Download full-size image

Highlights

• •Quantitative changes in global proteome and ubiquitinome in Huntington's disease.
• •Differential ubiquitination of wild-type and mutant Htt in mice brain.
• •Enriched pathways include vesicle transport and mRNA processing.
• •Correlation between protein and diGly site fold changes.

     

Integration of Two In-depth Quantitative Proteomics Approaches Determines the Kallikrein-related Peptidase 7 (KLK7) Degradome in Ovarian Cancer Cell Secretome

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

Highlights

• •Kallikrein-related peptidase 7 is over expressed in ovarian cancer.
• •Quantitative PROTOMAP and TAILS approaches identified putative substrates of KLK7.
• •Pro-MMP10 is activated by KLK7.
• •KLK7 cleaves thrombospondin 1 and IGFBP6 in vitro.

     

A New Tool to Reveal Bacterial Signaling Mechanisms in Antibiotic Treatment and Resistance

1. Download : Download high-res image (86KB)
2. Download : Download full-size image

Highlights

• •Quantitative (phospho)proteome analysis of antibiotic treatment in E. coli.
• •Largest bacterial phosphorylation catalogue.
• •Specific phosphorylation motifs changes during resistance development.
• •Phosphorylation mediated signaling could be a potential target for drug design.

     

A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level

1. Download : Download high-res image (83KB)
2. Download : Download full-size image

Highlights

• •Rapamycin and zinc induce moderate but significant mitochondrial proteome changes.
• •The mitochondrial proteins processing system is robust under subtoxic conditions.
• •Rapamycin and zinc perturb the mitochondrial proteins processing system.
• •Rapamycin and zinc perturb the mitochondrial proteins homeostasis.

     

Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry

1. Download : Download high-res image (126KB)
2. Download : Download full-size image

Highlights

• •Quantitative cross-linking mass spectrometry (QCLMS) was automated by Spectronaut.
• •Data-independent acquisition (DIA) was adapted to QCLMS.
• •Accuracy and precision of quantitation improves with DIA over DDA.
• •QCLMS is now ready for use in complex samples.

     

Substantial Influence of ERAP2 on the HLA-B*40:02 Peptidome: Implications for HLA-B*27-Negative Ankylosing Spondylitis

1. Download : Download high-res image (115KB)
2. Download : Download full-size image

Highlights

• •HLA-B*40:02 and ERAP2 are risk factors for ankylosing spondylitis.
• •The effects of ERAP2 on the B*40:02 peptidome are defined.
• •ERAP2 has a major influence mainly due to alterations of N-terminal residues.
• •These effects provide a basis for the association of ERAP2 with disease.

     

FlashPack: Fast and Simple Preparation of Ultrahigh-performance Capillary Columns for LC-MS*

1. Download : Download high-res image (99KB)
2. Download : Download full-size image

Highlights

• •Fast and simple capillary column packing protocol.
• •Low-pressure packing at <100 bars from ultrahigh sorbent suspension concentration.
• •Sorbent particle aggregation leading to blocking of the column entrance is avoided.
• •Effective for long capillary UHPLC column packing with a wide range of sorbents.

     

Chromobodies to Quantify Changes of Endogenous Protein Concentration in Living Cells

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

Highlights

• •Chromobodies are stabilized by antigen binding in live cells.
• •Monitoring changes of endogenous protein levels in living cells with chromobodies.
• •Broadly applicable system to generate turnover-accelerated chromobodies.
• •Quantification of time- and dose-dependent compound effects.