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.

     

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

1. Download : Download high-res image (158KB)
2. Download : Download full-size image

Highlights

• •Increased proteome coverage with Orbitrap Exploris 480 MS and FAIMS using single compensation voltages and short LC gradients.
• •Towards single-cell proteomics with high-sensitivity analysis of 5 ng HeLa with more than 1,000 proteins identified in 5 minutes using FAIMS and DIA.
• •Deep proteome profiling across twelve rat organs tissues by label-free quantitation using DIA compared to TMT-multiplexing and turboTMT acquisition using phi-SDM.
• •Rapid and sensitive phosphoproteomics with automated enrichment using Ti-IMAC magnetic beads and direct DIA analysis.

     

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.

     

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

1. Download : Download high-res image (140KB)
2. Download : Download full-size image

Highlights

• •Highly parallelizable 4D feature detection in ion mobility enhanced shotgun proteomics.
• •Multidimensional non-linear mass, retention time and ion mobility recalibration.
• •Collision cross section aware matching between runs.
• •Label-free quantification of ion mobility MS data.

     

Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation

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

Highlights

• •Repeatable quantification of 200 proteins in dried blood spots.
• •Determined lower limit of quantification, repeatability, parallelism and stability.
• •Protein stability in DBS stored at ambient temperatures for up to 2 months.
• •Concentration ranges for 200 proteins in 20 healthy individuals.

     

Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition

1. Download : Download high-res image (233KB)
2. Download : Download full-size image

Highlights

• •Modern DIA methods contain high quality MS1 and MS2.
• •We developed a statistical procedure incorporating MS1 and MS2.
• •Benchmarking, the combined method outperformed the individual use of MS1 or MS2.

     

The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis

1. Download : Download high-res image (211KB)
2. Download : Download full-size image

Highlights

• •Mitochondrial heart N terminome shows aminopeptidase processing after MTS cleavage.
• •CLPP-deficiency alters protein processing patterns in mouse heart mitochondria.
• •Candidate substrates identified by N termini accumulation and interaction with inactive ClpXP.
• •UQCRC1, HSPA9 and OAT validated biochemically as high confidence ClpXP substrates.

     

Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks

1. Download : Download high-res image (64KB)
2. Download : Download full-size image

Highlights

• •Co-elution stands out as a global interactome mapping method.
• •Benefits include all-to-all protein analysis and measurement of interactome perturbations.
• •Different separation, quantification and bioinformatic strategies are available.
• •Design considerations depend largely on system under study.

     

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.

     

Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments

1. Download : Download high-res image (187KB)
2. Download : Download full-size image

Highlights

• •Automated statistical approach for detecting uninformative features and outliers.
• •Improved performance on relative protein quantification.
• •An option in the open-source R-based software MSstats.

     

Proteomic Analysis Reveals a Role for RSK in p120-catenin Phosphorylation and Melanoma Cell-Cell Adhesion

1. Download : Download high-res image (164KB)
2. Download : Download full-size image

Highlights

• •BioID reveals the proximity partners of RSK family members.
• •All RSK isoforms associate with and phosphorylate p120ctn on Ser320.
• •RSK negatively regulates adherens junctions and reduces cell-cell adhesion.
• •p120ctn phosphorylation plays a role in the reorganization of proximity partners.

     

Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics

1. Download : Download high-res image (199KB)
2. Download : Download full-size image

Highlights

• •Analysis of product ions produced by 213 nm UVPD is used to refine database search.
• •A product ion at the N-terminus of Pro, y-2, is observed in 213 nm UVPD spectra.
• •213 nm UVPD provides more complete proteoform characterization than HCD.
• •HCD and 213 nm UVPD are complementary fragmentation methods for proteoforms <30 kDa.

     

A Quantitative Tri-fluorescent Yeast Two-hybrid System: From Flow Cytometry to In cellula Affinities

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

Highlights

• •Simultaneous quantification of Bait, Prey and Reporter at the single cell level.
• •Two hours of reaction are enough instead of 24–48 h for conventional assays.
• •Potential expression problems of the Bait and Prey can be easily detected.
• •True positive PPIs feature a distinct pattern of Reporter level versus Bait/Prey level.
• •PPIs with unknown affinities can be ranked using an affinity ladder.

     

The DNA Sensor cGAS is Decorated by Acetylation and Phosphorylation Modifications in the Context of Immune Signaling

1. Download : Download high-res image (285KB)
2. Download : Download full-size image

Highlights

• •cGAS acetylations and phosphorylations under basal and immune-stimulated states.
• •K384 and K414 acetylations and S305 phosphorylation inhibit cGAS-mediated apoptosis.
• •Acetylation at K198 stimulates cGAS-dependent interferon signaling.
• •K198 acetylation is decreased upon herpesvirus infection.

     

Novel Proteome Extraction Method Illustrates a Conserved Immunological Signature of MSI-H Colorectal Tumors

1. Download : Download high-res image (249KB)
2. Download : Download full-size image

Highlights

• •TOP: robust, bio-friendly FFPE proteome extraction method with less fixation bias.
• •Proteome of MSI-H colorectal cancer identifies immunobiology key elements.
• •MSI-H tumor displays an “INFg-STAT1 centric signature”.
• •Long-term IFNg induction In-vitro mimicks MSI-H signature.

     

ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping

1. Download : Download high-res image (209KB)
2. Download : Download full-size image

Highlights

• •ProAlanase is a powerful protease for efficient low pH disulfide bond mapping.
• •High suitability for analysis of histone family members and their PTMs.
• •Accurate phosphorylation profiling in proline-rich proteins.
• •Sequence coverage increase and full de novo sequencing in combination with trypsin.

     

Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular Dystrophy

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

Highlights

• •Proteomics analysis was performed in two murine models of Duchenne muscular dystrophy (mdx and mdx52) at three ages (8, 16 and 80 weeks) and compared with wild-type controls.
• •High-resolution isoelectric focusing liquid chromatography-tandem mass spectrometry enabled the quantification of 4974 proteins in all samples.
• •This study has revealed protein signatures of dystrophin deficiency and the progression of dystrophic pathology.
• •In contrast, the proteomes of the mdx and mdx52 mice were highly similar.
• •Pathway analysis revealed crosstalk between inflammatory, metabolic and muscle growth processes in dystrophic muscle.

     

Combined EGFR and ROCK Inhibition in Triple-negative Breast Cancer Leads to Cell Death Via Impaired Autophagic Flux

1. Download : Download high-res image (244KB)
2. Download : Download full-size image

Highlights

• •We used phosphoproteomics to reveal the underlying mechanisms of drug synergy on EGFR and ROCK co-inhibition in TNBC cells.
• •EGFR inhibition alone induces autophagy activation in TNBC cells as a cytoprotective mechanism.
• •Combinatorial treatment leads to impaired autophagic flux resulting in a strong accumulation of autophagic vacuoles.
• •We hypothesize that ROCKi-induced cytoskeletal changes impair autophagosome clearance ultimately leading to cell death.

     

Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular Classification

1. Download : Download high-res image (209KB)
2. Download : Download full-size image

Highlights

• •Two molecular groups in anal squamous carcinoma according proteomic profile.
• •Differences in possible targeted processes such as metabolism or immune response.
• •Different percentage of tumor lymphocyte infiltration.
• •Difference in the frequency of ATM variants, related to PPAR inhibitors.