DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics

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Highlights

• •Retention time shift can lead to inversion of elution order of peptides.
• •Global alignment methods are suboptimal for alignment of distant runs.
• •DIAlignR employs hybrid (global + local) RT alignment approach.
• •DIAlignR can align swapped peaks accurately across distant runs.

     

Quantitative Multiplex Substrate Profiling of Peptidases by Mass Spectrometry

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Highlights

• •Quantitative substrate profiling method for characterizing peptidase specificity.
• •Applicable to both purified peptidases and peptidases in complex biological samples.
• •TMT labeling improves throughput, accuracy and reproducibility of the assay.
• •Design of fluorescent probes to monitor peptidase activity based on substrate data.

     

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.

     

Intact Transition Epitope Mapping – Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE),

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Highlights

• •Multiplex epitope mapping/antigenic determinant identification in the gas phase.
• •Intact transition and controlled dissociation of immune complexes by MS.
• •Simultaneous identification and amino acid sequence determination of epitopes.
• •Simplified in-solution sample handling because of ion manipulation and filtering by MS.

     

TMT Labeling for the Masses: A Robust and Cost-efficient,In-solution Labeling Approach

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Highlights

• •TMT labeling protocol with excellent intra- and interlaboratory reproducibility.
• •Complete in-solution labeling of peptides using 1/8 of recommended TMT quantities.
• •Demonstration of utility for deep-scale (phospho)proteome analysis.

     

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.

     

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.

     

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.

     

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

     

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

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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.

     

Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of the Sarcomeric Subproteome

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Highlights

• •A new strategy for simultaneous quantification of protein expression and modification.
• •This top-down LC/MS-based method shows high reproducibility and high throughput.
• •Quantification at the intact protein level with results comparable to Western blot.
• •This top-down proteomics method is applicable to different species and tissues.

     

Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework

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Highlights

• •Deep learning-based hybrid de novo sequencing with database search strategy.
• •Accurate identifications via ability to revise confidence scores and amino acids.
• •Discovery of >10,000 potential new HLA antigens and human phosphopeptides.
• •A dataset of >26 million annotated HCD spectra from Q Exactive instruments.

     

Quantitative Microproteomics Based Characterization of the Central and Peripheral Nervous System of a Mouse Model of Krabbe Disease

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Highlights

• •Quantitative microproteomics to study the CNS and PNS of the Twitcher mouse.
• •10plex TMT experiments on corpus callosum, motor cortex and sciatic nerves extracts.
• •More than 400 proteins groups deregulated between Twitcher and wildtype mice.
• •New insights into the molecular mechanisms of Krabbe disease.

     

Deep Protein Methylation Profiling by Combined Chemical and Immunoaffinity Approaches Reveals Novel PRMT1 Targets

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Highlights

• •Enrichment of methyl peptides using two orthogonal techniques.
• •Knockdown of PRMT1 leads to substantial changes in protein arginine “methylome”.
• •Discrimination of ADMA and SDMA using characteristic neutral losses.
• •Identification of PRMT1 targets and substrate scavenged by other PRMTs in the absence of PRMT1 activity.

     

Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry

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Highlights

• •Targeted mass spectrometry assay to quantify prion protein (PrP) in spinal fluid.
• •Precise measurement of PrP peptide concentration across protein domains.
• •Peptides are uniformly decreased in symptomatic prion disease patients.
• •Assay applicable to humans and preclinical species for drug development.

     

NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions

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Highlights

• •NNAlign_MA enables full deconvolution of single MHC specificities from MS assays.
• •NNAlign_MA expands MHC allelic coverage, improving identification of T-cell epitopes.
• •NNAlign_MA was benchmarked on MHC classes I and II, outperforming current methods.
• •NNAlign_MA offers a universal solution to analyze and exploit MHC peptidomics data.

     

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.

     

Comprehensive Analysis of the Lysine Succinylome and Protein Co-modifications in Developing Rice Seeds

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Highlights

• •Nonenzymatically Ksu proteins shown different pattern from native cell Ksu proteins.
• •Motif preference of Ksu proteins was associated with different biological processes.
• •Up to 67 developing rice seeds proteins contain PTMs of Kac, Ksu, Kcr, Kmal, and Khib.
• •Some lysine residues of the key pathway enzymes are modified by succinylation.

     

Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics

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Highlights

• •The developed Ac-LysargiNase showed higher stability and activity than before.
• •The merged spectra of the mirror peptides achieved nearly complete ion coverage.
• •pNovoM obviously increased the efficiency and accuracy of peptide sequencing.
• •The mirror enzymatic strategy achieved precision de novo sequencing on proteome scales.

     

Evaluation of Serum Glycoprotein Biomarker Candidates for Detection of Esophageal Adenocarcinoma and Surveillance of Barrett's Esophagus

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Highlights

• •C9, GSN, PON1, and PON3 validated as serum biomarker candidates of EAC.
• •Multimarker panel with AUROC of 0.93 to aid current endoscopy surveillance of BE.
• •Induction of tissue C9 in BE, dysplastic BE and EAC.
• •Alteration of complement pathway glycoproteins during BE-EAC pathogenesis.