Topic 45

spectrometry mass ms chromatography proteomics biochemistry lc peptides proteins liquid proteome proteomic protein peptide tandem identification analysis method quantitative quantification dia identified samples profiling ion sample based acquisition spectra metabolomics modifications abundance coupled untargeted workflow approach methods metabolites bioinformatics maldi translational biomarkers data ions labeling spectrometer spectral isotope identify proteomes coverage total using developed biological analytical spectrometric high digestion tof metabolism fragmentation glycosylation glycan discovery abundant preparation targeted strategy metabolite orbitrap accurate acid purification independent modification enrichment monitoring swath analyzed metabolic validated glycans glycopeptides library throughput ionization identifications lipid database enables reproducibility tryptic fractionation lysate glycopeptide optimized separation lipids tool

382 items. Top items listed below.

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

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

Global impact of phosphorylation on protein endurance 45 18 4

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

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

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

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

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

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

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

Urine proteome changes in an α-synuclein transgenic mouse model of Parkinson's disease 45 15

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

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

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

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

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

Proteomic changes in bacteria caused by exposure to environmental conditions can be detected by Matrix-Assisted Laser Desorption/Ionization - Time of Flight (MALDI-ToF) Mass Spectrometry 45 12 5

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

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

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

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

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

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

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

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

Urinary proteome profiling for stratifying patients with familial Parkinsons disease 45

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

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

Quantitative sub-cellular acyl-CoA analysis reveals distinct nuclear regulation 45 18

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

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

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

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

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

Using Multilayer Heterogeneous Networks to Infer Functions of Phosphorylated Sites 112 45 4

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

Peak identification and quantification by proteomic mass spectrogram decomposition 45 4

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

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

DreamAI: algorithm for the imputation of proteomics data 45 26 4

A generalizable method for false-discovery rate estimation in mass spectrometry-based lipidomics 45 4

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

High-density, targeted monitoring of tyrosine phosphorylation reveals activated signaling networks in human tumors 45 4

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

Systematic Identification of Protein Phosphorylation-Mediated Interactions 45 8 3

Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer's disease 45 32 15

Biomarker model for cancer: Development of fast LC-MS/MS method for reduced and oxidized glutathione 45 15

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

A comprehensive proteomic SWATH-MS workflow for profiling blood extracellular vesicles: a new avenue for glioma tumour surveillance 45 4

A Metabolomic Study of Cervical Dystonia 45 15 9

PulseDIA: in-depth data independent acquisition mass spectrometry using enhanced gas phase fractionation 45 15

Phenotype Prediction using a Tensor Representation and Deep Learning from Data Independent Acquisition Mass Spectrometry 45 26 4

Serial surface mass spectrometry metabolomics on sample-limited tissue archives reveals signatures for predicting pediatric brain tumor relapse 45 18 4

Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae 45 4

Protein Abundance Prediction Through Machine Learning Methods 45 26 4

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

Urine proteome changes in a chronic unpredictable mild stress (CUMS) mouse model of major depressive disorder 45 15 10

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

Robust Inference of Kinase Activity using Functional Networks 45 4

Proteomics study of colorectal cancer and adenomatous polyps identifies TFR1, SAHH, and HV307 as potential biomarkers for screening 45 10 9

Broad-range RNA modification analysis of complex biological samples using rapid C18-UPLC-MS 45 4

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

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

Dynamic binning peak detection and assessment of various lipidomics liquid chromatography-mass spectrometry pre-processing platforms 45 4

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens 125 101 45 4

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

Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by data independent acquisition proteomics 45 14 9

Tail-Robust Quantile Normalization 45 4

Quantifying dynamic protein acetylation using quantitative stoichiometry 45 31 9

Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell 45 18

Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002 45 8

MS-CleanR: A feature-filtering approach to improve annotation rate in untargeted LC-MS based metabolomics 45 13 4

A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts 45 18 4

DPHL: A pan-human protein mass spectrometry library for robust biomarker discovery using Data-Independent Acquisition and Parallel Reaction Monitoring 45 4

Metabolite profiling of experimental cutaneous leishmaniasis lesions demonstrates significant perturbations in tissue phospholipids 45 10

Quantitative LCMS for ceramides/dihydroceramides: pregnancy baseline biomarkers and potential metabolic messengers 45 18 15

SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs 191 76 24 1

Nonspecific Cleavages Arising from Reconstitution of Trypsin under Mildly Acidic Conditions 45

Integrated metabolome and transcriptome analyses provide insight into colon cancer development by the gut microbiota 101 29 9

Comprehensive cell surface proteomics defines markers of classical, intermediate and non-classical monocytes 45 27 3

Spritz: A Proteogenomic Database Engine 45 13 4

Proximity Labeling-assisted Identification of Endogenous Kinase Substrates 102 45 3

Supervised and Unsupervised Classification of Cocoa Bean Origin and Processing using Liquid Chromatography-Mass Spectrometry 45 4

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

Gene co-expression analysis of human RNASEH2A reveals functional networks associated with DNA replication, DNA damage response, and cell cycle regulation 120 9 3

Harnessing machine learning to unravel protein degradation in Escherichia coli 45 12

Benchmarking non-targeted metabolomics using yeast derived libraries 45 4

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

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

CETSA MS profiling for a comparative assessment of FDA approved antivirals repurposed for COVID-19 therapy identifies Trip13 as a Remdesivir off-target 44 41 1

Development and Comparative Evaluation of Endolysosomal Proximity Labeling-based Proteomic Methods in Human iPSC-derived Neurons 45 18 4

TMT-Based Quantitative Proteomic Analysis of Intestinal Organoids Infected by Listeria monocytogenes with Different Virulence 45 12

A Consensus Proteomic Analysis of Alzheimer's Disease Brain and Cerebrospinal Fluid Reveals Early Changes in Energy Metabolism Associated with Microglia and Astrocyte Activation 32 9

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

An interaction network of RNA-binding proteins involved in Drosophila oogenesis 49 45 34 9 8 3

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

Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection 103 1

Mapping metabolic oscillations during cell cycle progression 45

Optimizing accuracy and depth of protein quantification in experiments using isobaric carriers 45 18 4