Mitochondrial Oxidative Phosphorylation Complex Regulates NLRP3 Inflammasome Activation and Predicts Patient Survival in Nasopharyngeal Carcinoma

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Highlights

• •Flow cytometry analysis is used to isolate ASC speck⁽⁺⁾ NPC cells.
• •Proteome analysis of ASC speck⁽⁺⁾ NPC cells reveals enriched mitochondrial OxPhos proteins.
• •OxPhos proteins mediate NLRP3 inflammasome activation through mtROS.
• •OxPhos proteins, NDUFB8 and ATP5B are correlated with NPC local recurrence.

     

HIGD2A is Required for Assembly of the COX3 Module of Human Mitochondrial Complex IV

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Highlights

• •Quantitative proteomics reveals HIGD2A is required for assembly of the COX3 module.
• •Pulse-SILAC demonstrates that HIGD2A is involved in COX3 biogenesis.
• •Supercomplexes in HIGD2A knockout cells are depleted of COX3.
• •HIGD2A is the first assembly factor identified for the COX3 module of Complex IV.

     

Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network

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Highlights

• •Sin3 paralog identity influences Sin3 complex composition.
• •Chemical cross-linking mass spectrometry identifies domains in SIN3A and SIN3B that mediate complex formation.
• •Complex subunit homology to yeast Sin3 complex components may assist in defining distinct forms of the Sin3 complex in humans.
• •A nuclear import signal within SIN3B is identified via chemical cross-linking mass spectrometry.

     

The Secretome Profiling of a Pediatric Airway Epithelium Infected with hRSV Identified Aberrant Apical/Basolateral Trafficking and Novel Immune Modulating (CXCL6, CXCL16, CSF3) and Antiviral (CEACAM1) Proteins

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Highlights

• •Proteome of airway secretions derived from mock- and hRSV-infected WD-PBEC cultures.
• •A polarised secretome in uninfected WD-PBECs, skewed in hRSV-infected cultures.
• •CXCL6, CXCL16, CECACAM1 and CSF3 induced only upon hRSV-infection.
• •Detection of CXCL6, CXCL16 and CSF3 in NPAs from hRSV-positive children.

     

Citrus Vascular Proteomics Highlights the Role of Peroxidases and Serine Proteases during Huanglongbing Disease Progression

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Highlights

• •HLB is the most devastating citrus disease associated with the pathogen CLas.
• •Proteases and peroxidases accumulated in plant vascular tissue after CLas infection.
• •Dynamic changes in serine protease activity occur across genotypes and environments.

     

Reproducibility,Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition

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Highlights

• •Provision of data generated on the basis of a gold standard spike-in sample set.
• •Choice of spectral library has great impact on identification and quantification.
• •DIA is superior to DDA in quantification reproducibility, specificity and accuracy.
• •DIA outperforms DDA in the quantification of low protein amounts.
• •Quantification on peptide level is generally preferable.

     

Proteome-wide Analysis Reveals Substrates of E3 Ligase RNF146 Targeted for Degradation

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Highlights

• •Proteome analyses reveal RNF146 and TNKS1/2 substrates targeted for degradation.
• •RNF146 KO and TNKS1/2 DKO cells display significantly different proteomes.
• •RNF146 has both TNKS-dependent and -independent substrates.

     

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

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Highlights

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

     

An in-depth Comparison of the Pediatric and Adult Urinary N-glycomes

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Highlights

• •N-glycan patterns are distinct in pediatric and adult urine.
• •Sex differences of N-glycans are much larger in adults.
• •Pediatric urine has almost no sex differences in N-glycan levels.
• •In adults, the majority of N-glycans were more abundant in males.

     

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

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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.

     

Accurate MS-based Rab10 Phosphorylation Stoichiometry Determination as Readout for LRRK2 Activity in Parkinson's Disease

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Highlights

• •MS-based clinical assay that accurately determines phospho Rab10 occupancy.
• •Stable isotope labeled phosphopeptide injected as a standard with endogenous tryptic phospho Rab peptide for accurate ratio determination.
• •Determination of pRab levels in neutrophils of Parkinson disease patients.
• •Relevance of pRab levels as marker of PD.

     

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

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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.

     

Phosphoproteomic Approaches to Discover Novel Substrates of Mycobacterial Ser/Thr Protein Kinases

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Highlights

• •Mapping kinase-substrate relationships is vital in discovering new tuberculosis drug targets.
• •LC-MS/MS-based phosphoproteomics expand mycobacterial STPK substrate catalogues.
• •We review and integrate MS-generated datasets on novel candidate substrates.
• •Validation studies are necessary to confirm true physiological substrates of STPKs.

     

Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes

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Highlights

• •Guidelines for studying protein complexes via co-fractionation mass spectrometry.
• •A novel procedure for profiling gold standard protein complexes in CF-MS data.
• •Recommendations for efficient CF-MS fractionation collection.
• •Scoring metric recommendations for precise and sensitive CF-MS data analysis.

     

Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands

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Highlights

• •Curation of 2066 phosphorylated HLA class I peptides from immunopeptidomics data.
• •Determination of 22 HLA class I binding motifs for phosphorylated peptides.
• •Observation of a higher frequency of phosphorylated ligands binding HLA-C molecules.
• •Development of a predictor of phosphorylated peptide interactions with HLA class I.

     

Characterizing Patients with Recurrent Urinary Tract Infections in Vesicoureteral Reflux: A Pilot Study of the Urinary Proteome

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Highlights

• •Urinary proteomes of patients with recurrent UTI, renal scarring, and VUR.
• •80 proteins differentially expressed, compared to healthy controls.
• •62 proteins may be indicative of susceptibility for UTI.
• •Altered acute phase response, extracellular matrix and carbohydrate metabolism.

     

Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing

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Highlights

• •Quantitative proteome of neonatal, young, and aged OPCs.
• •50% of the proteome is differentially expressed between neonatal and adult OPCs.
• •Myelin proteins are increased, and cholesterol synthesis proteins decreased with age.
• •Proteins associated with other neurodegenerative diseases are increased in aged OPCs.

     

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

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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.

     

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal,Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction

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Highlights

• •Universal and detergent-free proteomic sample preparation.
• •Based on three simple mandatory steps (acidification, neutralization, digestion).
• •Enhances proteome coverage especially for challenging samples.
• •Improves quantitative reproducibility compared with ISD-Urea, FASP and SP3.

     

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

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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.