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,

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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.

     

Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks (Gasterosteus aculeatus)

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Highlights

• •Construction of threespine stickleback gill assay library using DDA proteomics
• •Population-specific gill proteome signatures of four ecotypes identified by DIA
• •HSP47 and extracellular matrix proteins highly elevated in warm-adapted sticklebacks
• •Inflammasome and proteolytic proteins highly elevated in freshwater sticklebacks

     

Proteome-wide Tyrosine Phosphorylation Analysis Reveals Dysregulated Signaling Pathways in Ovarian Tumors

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Highlights

• •Multiplexed PTM assays on HuProt array were developed using ovarian tumor lysates.
• •Proteome-wide Tyr phosphorylation with 102 ovarian tumors were performed and analyzed.
• •19 kinases were predicted to have elevated activities in ovarian tumor.
• •Elevated activities of PTK2 and PTK2B were confirmed in ovarian cancer cell lines.

     

Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability,

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Highlights

• •Our search identifies 2,134 kinase-substrate phosphosite pairs in breast cancer.
• •CDKs and MAPKs are dominant regulators of trans substrate-phosphorylation.
• •Druggability, outcomes, and immune signatures related to kinase-substrates.
• •Experimentally validated activated phosphosites of ERBB2, EIF4EBP1, and EGFR.

     

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.

     

Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry

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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.

     

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

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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.

     

Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance,

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Highlights

• •Bayesian Beta-Binomial model integrates ion statistics with peptide ratio agreement.
• •Model appropriately interprets information from low signal peptides.
• •Confidence can be assigned even without replicates.
• •Model adds sensitivity to detection of small changes.

     

High-throughput Identification of FLT3 Wild-type and Mutant Kinase Substrate Preferences and Application to Design of Sensitive In Vitro Kinase Assay Substrates

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Highlights

• •Developed a data processing pipeline to format phosphopeptide identifications.
• •Identified the preferred substrate motif for FLT3 and mutant kinases.
• •Designed and validated a panel of pan-FTL3 artificial substrates.
• •Monitored FLT3 and mutant kinase activity through FAStide phosphorylation.

     

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.

     

Global Interactomics Uncovers Extensive Organellar Targeting by Zika Virus

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Highlights

• •BioID and IP-MS were conducted to generate a global ZIKV-host protein interactome
• •Interactome consists of >3000 high confidence ZIKV-host protein interactions
• •Data mining indicates that ZIKV proteins interact with multiple host cell organelles
• •An important role for peroxisomes in ZIKV infection is uncovered

     

Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers,

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Highlights

• •Shotgun identification of neopeptides released from osteoarthritic cartilage.
• •Specific endogenous peptides from the cartilage ECM are measured by MRM.
• •Identification of neopeptides differentially generated from diseased tissue.
• •The peptide DSNKIETIPN shows the best metrics as biomarker of OA cartilage.

     

Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics

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Highlights

• •Unified identification and quantification error rates for protein quantification.
• •Error propagation using graphical models and Bayesian statistics.
• •Account for uncertainty of missing values instead of overconfident point estimates.
• •Control of differential expression false discovery rate at increased sensitivity.

     

Quantitative Proteomics of the Mitotic Chromosome Scaffold Reveals the Association of BAZ1B with Chromosomal Axes,

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Highlights

• •Quantitative proteomics of mitotic chromosome scaffold isolated from chicken DT40 cells.
• •BAZ1B identified in the isolated mitotic chromosome scaffold localizes to mitotic chromosome axes.
• •BAZ1B knockout caused prophase delay because of altered chromosome condensation timing and impaired mitosis progression.
• •BAZ1B knockout did not affect prometaphase chromosome structure.

     

HLA-DO Modulates the Diversity of the MHC-II Self-peptidome

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Highlights

• •MHC-II-bound peptide repertoires from DO-sufficient and DO-deficient cells.
• •Fewer unique peptides and core epitopes were presented in the absence of DO.
• •Immunopeptidome differences appeared to result from reduced DM editing.
• •DO-dependent self-epitopes elicited CD4 T cell responses in mice.

     

High-density Peptide Arrays Help to Identify Linear Immunogenic B-cell Epitopes in Individuals Naturally Exposed to Malaria Infection

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Highlights

• •Profiling antibody responses of patients with naturally acquired malaria immunity.
• •High-density peptide arrays featuring linear epitopes.
• •Epitope mapping of known and potential novel vaccine candidates.
• •Novel immunogenic epitopes discovered, and known antibody target motifs confirmed.

     

Isomeric Separation and Recognition of Anionic and Zwitterionic N-glycans from Royal Jelly Glycoproteins

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Highlights

• •The N-glycome of honeybee royal jelly is more diverse than previously thought
• •Antennal phosphoethanolamine and glucuronic acid are among the special features
• •Anionic/zwitterionic glycans are recognized by a pentraxin and anti-HNK-1 antibody

     

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

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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.

     

Discovery of a Human Testis-specific Protein Complex TEX101-DPEP3 and Selection of Its Disrupting Antibodies

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Highlights

• •Quantitative co-IP-MS approach to discover the human TEX101 interactome.
• •Validation of the human testis-specific protein complex TEX101-DPEP3.
• •Development of a hybrid immunoassay to screen for disruptors of TEX101-DPEP3 complex.

     

Anticancer Effect of Deuterium Depleted Water - Redox Disbalance Leads to Oxidative Stress

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Highlights

• •The antiproliferation effect of deuterium depleted water (DDW) was confirmed in a cell model.
• •DDW inhibits cell proliferation through causing a ROS disbalance in mitochondria.
• •DDW has a potential as an adjuvant in antitumor therapy.