Redundancy and Complementarity between ERAP1 and ERAP2 Revealed by their Effects on the Behcet's Disease-associated HLA-B*51 Peptidome,

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Highlights

• •HLA-B*51 and ERAP1, but not ERAP2, are risk factors for Behçet's disease.
• •The HLA-B*51 peptidome and the effects of ERAP1 and ERAP2 on it are analyzed.
• •ERAP1 and ERAP2 alter multiple features of the HLA-B*51 peptidome in distinct ways.
• •Both enzymes act independently with complementary and partially redundant functions.

     

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

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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.

     

DECA,A Comprehensive,Automatic Post-processing Program for HDX-MS Data*

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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*

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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

     

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

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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.

     

Identification of an Unconventional Subpeptidome Bound to the Behçet's Disease-associated HLA-B*51:01 that is Regulated by Endoplasmic Reticulum Aminopeptidase 1 (ERAP1)

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Highlights

• •A novel HLA-ABC-triple knockout cell model to study the HLA-B*51 peptidome.
• •Enrichment of the unconventional non-Pro/Ala2 HLA-B*51 peptides following ERAP1 silencing.
• •Knockdown of ERAP1 increases the length of non-Pro/Ala2 and Ala2 peptides, not that of Pro2.
• •ERAP1 regulation of HLA-B*51 cell surface expression is cell type dependent.

     

Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation*

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Highlights

• •Characterization of the phagosomal proteome comparing resting and LPS-treated BMDCs.
• •Label-free quantification determined 2843 phagosomal proteins.
• •Reduced recruitment of hydrolases and V-ATPase to phagosomes of LPS-treated cells.
• •Increased recruitment of antigen cross-presentation molecules to these phagosomes.

     

Sample Preparation Scale-Up for Deep N-glycomic Analysis of Human Serum by Capillary Electrophoresis and CE-ESI-MS*

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Highlights

• •Efficient sample preparation workflow for deep N-glycomics analysis from serum.
• •Temperature gradient denaturing protocol to prevent protein precipitation.
• •Decrease of free sugar content in serum enhanced PNGase F digestion efficiency.
• •Modified evaporative labeling method increased fluorophore labeling yield.

     

An Advanced Strategy for Comprehensive Profiling of ADP-ribosylation Sites Using Mass Spectrometry-based Proteomics*

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Highlights

• •Comparing proteolytic digestions and precursor fragmentation methods for MS of ADPr
• •Identification of 11,265 unique ADPr-modified peptides
• •Mapping of hundreds of peptides co-modified by phosphorylation and ADPr
• •ADPr modification of specific residue types displays spatial preferences

     

Conodipine-P1-3, the First Phospholipases A2 Characterized from Injected Cone Snail Venom*

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Highlights

• •Three novel Conodipines P1-3 in the injected venom of Conus purpurascens.
• •Conodipines P1-3 have consensus catalytic characteristics of sPLA₂.
• •We determined multiple modification sites in Conodipines P1-3.
• •Evaluated the activity of Conohyal-P1 by a MS-based method.

     

Metabolic Cross-talk Between Human Bronchial Epithelial Cells and Internalized Staphylococcus aureus as a Driver for Infection*

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Highlights

• •Interplay of epithelial cells and internalized S. aureus was dissected over 96 h.
• •Surviving host cells contain nonreplicating bacteria that persists in the cytoplasm.
• •Competition over resources triggers temporal metabolic changes.
• •Metabolic adaptation of host and bacteria determines the outcome of infection.

     

Salmonella Effectors SseK1 and SseK3 Target Death Domain Proteins in the TNF and TRAIL Signaling Pathways*

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Highlights

• •MS-based method to detect native arginine-GlcNAcylation during Salmonella infection.
• •Demonstration that SseK1 targets TRADD, whereas SseK3 targets the death receptors, TNFR1 and TRAILR.
• •Evidence that effector overexpression results in misleading identification of host targets.
• •Crystal structure of SseK3.

     

Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation*

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Highlights

• •Insoluble protein aggregates preferentially precipitate on microparticles.
• •The protein aggregation capture (PAC) occurs irrespective of microparticle surface chemistry.
• •This process can be exploited for multi-purpose proteomics sample preparation.
• •Facilitates potential for low cost, efficient and high-sensitivity proteomics workflows.

     

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

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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.

     

Fast and Accurate Bacterial Species Identification in Urine Specimens Using LC-MS/MS Mass Spectrometry and Machine Learning*

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Highlights

• •Fast and culture-free method for the identification of the 15 bacterial species causing UTIs.
• •Combination of DIA analysis and machine learning algorithms to define a peptide signature.
• •High accuracy, good linearity and reproducibility, sensitivity below standard threshold.
• •Transferability to other laboratories and other mass spectrometers.

     

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome*

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Highlights

• •Reported proteasomal spliced HLA peptides do not fit the consensus binding motifs.
• •Their MS/MS spectrum matches suggest that many of them are ambiguous.
• •Our workflow is based on de novo sequencing, alignment, and multiple search tools.
• •The upper bound proportion of cis-spliced peptides is 2–6% and likely much smaller.

     

PACAP and Other Neuropeptide Targets Link Chronic Migraine and Opioid-induced Hyperalgesia in Mouse Models*

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Highlights

• •Characterized the peptides involved in migraine and opioid-induced hyperalgesia (OIH).
• •Identified more than 1500 peptides in seven nervous system regions.
• •Discovered seven peptides significantly changed with migraine and nine with OIH.
• •Validated PACAP involvement in both conditions via pharmacological studies.

     

Insulin Induces Microtubule Stabilization and Regulates the Microtubule Plus-end Tracking Protein Network in Adipocytes

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Highlights

• •Insulin Affects the Phosphorylation of G2L1, MARK2, CLIP2, EB1, AGAP3, and CKAP5.
• •Insulin Increases CLASP2 +TIP Density and Decreases CLASP2 +TIP Velocity.
• •Insulin Stimulates CLASP2 and G2L1 Trailing Along Microtubules.
• •Insulin Stimulates α-Tubulin Acetylation at Lysine 40 and Microtubule Stabilization.