Topic 198

spectrometry mass modifications ms amino peptides translational glycosylation peptide structural ion biochemistry post proteomics dia cysteine acids will acid glycoforms independent analytical proteins identification analysis glycopeptides modification modified purification glycan protein sites synthetic exoglycosidase limitations method glycoprotein methods glycoproteomes digestion glycoproteins accurate strategies glycans structures ions workflows orthogonal swath utility harness glycoproteomics chemical glycopeptide folding unbiased integration enzymatic unmodified detection knowledge purified determines scores cysteines identifications lc presented collision type monosaccharide capabilities laborious provides based macromolecules translationally therefore annotation implemented theoretical optimized systems present allow soft canonical hindered improving verify sometimes acquisition consecutive acrylonitrile our means reactivity hplc substitutions intrinsic

27 items. Top items listed below.

Glycopeptide variable window SWATH for improved Data Independent Acquisition glycoprotein analysis 198 45 8 4

Discovery of protein modifications using high resolution differential mass spectrometry proteomics 198 45 13 4

DIALib: an automated ion library generator for data independent acquisition mass spectrometry analysis of peptides and glycopeptides 198 45 4

Analysis of site and structure specific core fucosylation in liver disease progression using exoglycosidase-assisted data-independent LC-MS/MS 198 45 8

Improved discrimination of asymmetric and symmetric arginine dimethylation by optimization of the normalized collision energy in LC-MS proteomics 198 45

Analysis of coagulation factor IX in bioreactor cell culture medium predicts yield and quality of the purified product 198 45

Correlating glycoforms of DC-SIGN with stability using a combination of enzymatic digestion and ion mobility MS 198 45 8

Mapping physiological ADP-ribosylation using Activated Ion Electron Transfer Dissociation (AI-ETD) 198 45 8

AA_stat enables extensive characterization of artefact and post-translational modifications in bottom-up proteomics 198 13 4

Towards middle-up analysis of polyclonal antibodies: subclass-specific N-glycosylation profiling of murine immunoglobulin G (IgG) by means of HPLC-MS 198 45

Separation and identification of permethylated glycan isomers by reversed phase nanoLC-NSI-MSn 198 45 4

Chemical modification of proteins by insertion of synthetic peptides using tandem protein trans-splicing 198 129 18 8

Identification of sulfenylated cysteines in Arabidopsis thaliana proteins using a disulfide-linked peptide reporter 198 45 16 8 3

Native Hydrogen/Deuterium Exchange Mass Spectrometry of Structured DNA Oligonucleotides 198 45 8

Global impact of phosphorylation on protein endurance 45 18 4

From Chemoproteomic-Detected Amino Acids to Genomic Coordinates: Insights into Precise Multi-omic Data Integration 198 4

Chemical probe-based Nanopore Sequencing to Selectively Assess the RNA modifications 198 7 4

hu.MAP 2.0: Integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies 198 45 4

A new paradigm for Prelamin A proteolytic processing by ZMPSTE24: the upstream SY^LL cleavage occurs first and there is no CaaX processing by ZMPSTE24 198 129 45 8

Pathogenetic Perspective of Missense Mutations of ORF3a Protein of SARS-CoV2 198 37 1

More benign random peptides in E. coli are enriched for similar amino acids as young animal but not plant genes 198 129 5

Systematic protein complex profiling and differential analysis from co-fractionation mass spectrometry data 45 26 4

Myofibrillar Structural Variability Underlies Contractile Function in Stem Cell-Derived Cardiomyocytes 198 57 18

FLEXIQuant-LF: Robust Regression to Quantify Protein Modification Extent in Label-Free Proteomics Data 13 4

Deep ubiquitination site profiling by single-shot data-independent acquisition mass spectrometry 45 18 4

An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells 198 33

Increasing proteome coverage using cysteine-specific DIA Mass spectrometry - Cys-DIA 45 4

Acoustic Ejection Mass Spectrometry for High-Throughput Analysis 198 45 18 4

Mechanical and signaling mechanisms that guide pre-implantation embryo movement. 198 118

Global Profiling of the Lysine Crotonylome in Different Pluripotent States 45 20 3

Fast and Comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco 45 4

Structure Prediction and Characterization of Uncharacterized ABC Transporter ATP-Binding Protein Rv0986 of Mycobacterium tuberculosis (Strain ATCC 25618 / H37Rv) 198 12

C Terminus of DJ-1 Determines Its Homodimerization, Deglycation Activity and Suppression of Ferroptosis 198 63 3

PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results 45 4

Optimization of data-independent acquisition using predicted libraries for deep and accurate proteome profiling 45 4

Mass spectrometric method for the unambiguous profiling of cellular dynamic glycosylation. 45 18

SugarQuant: a streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics 45 18 4

MetaLab 2.0 enables accurate post-translational modifications profiling in metaproteomics 125 45 4

SARS-CoV-2 Nucleocapsid protein is decorated with multiple N- and O-glycans. 103 1

Spritz: A Proteogenomic Database Engine 45 13 4

MealTime-MS: A Machine Learning-Guided Real-Time Mass SpectrometryAnalysis for Protein Identification and Efficient DynamicExclusion 45 4

Global chemical modifications comparison of human plasma proteomes from two different age groups 45 15 8

Oxidations and amino acid substitutions in urinary proteins are the distinguishing characteristics of aging 45 15

Selective Labeling and Identification of the Tumor Cell Proteome of Pancreatic Cancer In Vivo 45 14 3

Dynamic changes in the urine proteome of tumor-bearing mouse models of B16 melanoma and RM-1 prostate cancer 45 15 14 9

Deducing the N- and O- glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2 1

MSImpute: Imputation of label-free mass spectrometry peptides by low-rank approximation 45 4

Phosphoproteomics after nitrate treatments reveal an important role for PIN2 phosphorylation in control of root system architecture. 16 9 3

Probing SWATH-MS as a tool for proteome level quantification in a non-model fish 45 4

Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology 45 4

Binding of Calcium and Magnesium to Cardiac Troponin C 198 8

DIA-based systems biology approach unveils novel E3-dependent responses to a metabolic shift 45 4

Precursor intensity-based label-free quantification software tools for proteomic and multi-omic analysis within the Galaxy Platform. 45 4

Glycoproteomic measurement of site-specific polysialylation 6

A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research 45 1

Selected reaction monitoring for the quantification of Escherichia coli ribosomal proteins 45 18 4

Visualization of the HIV-1 Env Glycan Shield Across Scales 45 8

A Simple Optimization Workflow to Enable Precise and Accurate Imputation of Missing Values in Proteomic Datasets 4

A validated strategy to infer protein biomarkers from RNA-Seq by combining multiple mRNA splice variants and time-delay 45 9 4

Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry 45 18 8

CBRPP: a new RNA-centric method to study RNA-protein interactions 151 45 33 3

CIRFESS: An interactive resource for querying the set of theoretically detectable peptides for cell surface and extracellular enrichment proteomic studies 45 4

A hybrid spectral library combining DIA-MS data and a targeted virtual library substantially deepens the proteome coverage 45 4

Leveraging immonium ions for identifying and targeting acyl-lysine modifications in proteomic datasets 45 4

Systematic Identification of Protein Phosphorylation-Mediated Interactions 45 8 3

Multi-platforms approach for plasma proteomics: complementarity of Olink PEA technology to mass spectrometry-based protein profiling 45 4

Quantitative data independent acquisition glycoproteomics of sparkling wine 45

Quantitative Method for Assessing the Role of Lysine & Arginine Post-Translational Modifications in Nonalcoholic Steatohepatitis 45

Identification and Characterization of a Residual Host Cell Protein Hexosaminidase B Associated with N-glycan Degradation During the Stability Study of a Therapeutic Recombinant Monoclonal Antibody Product 45

Pinpointing of cysteine oxidation sites in vivo by high-resolution proteomics reveals mechanism of redox-dependent inhibition of STING 45 3

MMS2plot: an R package for visualizing multiple MS/MS spectra for groups of modified and non-modified peptides 45 13 4

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection 45 26 4

Mass-spectrometry-based near complete draft of the Saccharomyces cerevisiae proteome 45 4

Perturbing proteomes at single residue resolution using base editing 139 33 9 4

In-depth characterization of Staurosporine induced proteome thermal stability changes 45 18 4

Expanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS 45 18 4

Glycoinformatics approach for identifying target positions to inhibit initial binding of SARS-CoV-2 S1 protein to the host cell 1

Cell culture NAIL-MS allows insight into human RNA modification dynamics in vivo 45 18

Identification, Mapping and Relative Quantitation of SARS-CoV-2 Spike Glycopeptides by Mass-Retention Time Fingerprinting 45 4

Combinatorial native MS and LC-MS/MS approach reveals high intrinsic phosphorylation of human Tau but minimal levels of other key modifications 45

A simple method to quantify protein abundances from one thousand cells 45 18 4

Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae 45 4

Evolution of structural dynamics in bilobed proteins 63 8 3

Detection of differential RNA modifications from direct RNA sequencing of human cell lines 147 13 4

An atlas of Arabidopsis protein S-Acylation reveals its widespread role in plant cell organisation of and function. 16 8

An improved comprehensive strategy for deep and quantitative N-glycomics based on optimization of sample preparation, isotope-based data quality control and quantification, new N-glycan libraries and new algorithms 45 4

Rapid Development of Improved Data-dependent Acquisition Strategies. 45 4

Enrichment-Free Identification of Native Definitive (EnFIND) O-glycoproteome of antibodies in autoimmune diseases 45 18

Quantifying dynamic protein acetylation using quantitative stoichiometry 45 31 9

The Profiling of Bisecting N-acetylglucosamine (GlcNAc) Modification in Human Amniotic Membrane by Glycomic and Glycoproteomic Analyses 45

Comparative multiplexed interactomics of SARS-CoV-2 and homologous coronavirus non-structural proteins identifies unique and shared host-cell dependencies 1

dagLogo: an R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data 140 62 4

Identification of ubiquitin Ser57 kinases regulating the oxidative stress response in yeast 102 34 3

Uptake of exogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae 69 34 3

Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome 151 8 3

Mass spectrometry analysis of newly emerging coronavirus HCoV-19 spike S protein and human ACE2 reveals camouflaging glycans and unique post-translational modifications 1

Protein Abundance Prediction Through Machine Learning Methods 45 26 4

Assignment of coronavirus spike protein site-specific glycosylation using GlycReSoft 45 4

Measuring site-specific glycosylation similarity between influenza A virus variants with statistical certainty 24

DeepLC can predict retention times for peptides that carry as-yet unseen modifications 62 26 13 4