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List of works by Ruedi Aebersold

7(th) HUPO World Congress of Proteomics: launching the second phase of the HUPOPlasma Proteome Project (PPP-2) 16-20 August 2008, Amsterdam, The Netherlands.

scientific article

A Bovine PeptideAtlas of milk and mammary gland proteomes ⬇️

scientific article published on September 1, 2012

A Candida albicans PeptideAtlas

scientific article published on 26 June 2013

A Case for a Human Immuno-Peptidome Project Consortium

scientific article

A Class of Environmental and Endogenous Toxins Induces BRCA2 Haploinsufficiency and Genome Instability.

scientific article

A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery

scientific article published on 05 June 2015

A Conserved Mito-Cytosolic Translational Balance Links Two Longevity Pathways

scientific article published on 20 February 2020

A DNA-damage selective role for BRCA1 E3 ligase in claspin ubiquitylation, CHK1 activation, and DNA repair.

scientific article

A G protein gamma subunit shares homology with ras proteins.

scientific article published in May 1989

A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS

scientific article published on 05 February 2020

A High-Density Map for Navigating the Human Polycomb Complexome

scientific journal article

A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein

scientific article

A Proteomic Connectivity Map.

scientific article published in April 2018

A Simplified Gradient Solvent Delivery System for Capillary Liquid Chromatography–Electrospray Ionization Mass Spectrometry

scientific article published on 01 December 1998

A Targeted Mass Spectrometry Strategy for Developing Proteomic Biomarkers: A Case Study of Epithelial Ovarian Cancer

scientific article published on 09 July 2019

A Web Resource for Improved Analysis of AP-MS Protein Interaction Data

scientific article published in May 2013

A cellular gene encodes scrapie PrP 27-30 protein

scientific article

A common open representation of mass spectrometry data and its application to proteomics research

scientific article

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

scientific article

A comprehensive characterization of the T-cell antigen receptor complex composition by microcapillary liquid chromatography-tandem mass spectrometry

scientific article published on June 2000

A computational tool to detect and avoid redundancy in selected reaction monitoring

scientific article

A curated collection of tissue microarray images and clinical outcome data of prostate cancer patients

scientific article

A database of mass spectrometric assays for the yeast proteome

scientific article

A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry

scientific article published on 21 July 2004

A first dataset toward a standardized community-driven global mapping of the human immunopeptidome

scientific article

A guided tour of the Trans-Proteomic Pipeline

scientific article

A high density map for navigating the human Polycomb complexome

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas

scientific article

A high-quality catalog of the Drosophila melanogaster proteome

scientific article

A high-stringency blueprint of the human proteome

scientific article published on 16 October 2020

A human proteome detection and quantitation project

scientific article published on 07 January 2009

A mass spectrometric journey into protein and proteome research

scientific article published on July 2003

A mass spectrometric-derived cell surface protein atlas

scientific article

A mass spectrometry-based approach for probing enzyme active sites: identification of Glu 127 in Cellulomonas fimi exoglycanase as the residue modified by N-bromoacetyl cellobiosylamine

scientific article

A mass spectrometry-based hybrid method for structural modeling of protein complexes

scientific article published on 09 February 2014

A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine op

scientific article

A mouse plasma peptide atlas as a resource for disease proteomics

scientific article published on 3 June 2008

A multicenter study benchmarks software tools for label-free proteome quantification

scientific article published on 03 October 2016

A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model

scientific article published on 06 May 2019

A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A

scientific article

A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity

scientific article

A proteome catalog of Drosophila melanogaster: an essential resource for targeted quantitative proteomics

scientific article published on 4 May 2007

A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans

scientific article

A repository of assays to quantify 10,000 human proteins by SWATH-MS.

scientific article

A serum protein profile predictive of the resistance to neoadjuvant chemotherapy in advanced breast cancers

scientific article

A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry

scientific article

A statistical method for chromatographic alignment of LC-MS data

scientific article

A statistical model for identifying proteins by tandem mass spectrometry

scientific article (publication date: September 2003)

A stress test for mass spectrometry-based proteomics

scientific article published in June 2009

A systematic approach to modeling, capturing, and disseminating proteomics experimental data

scientific article

A systematic approach to the analysis of protein phosphorylation

scientific article published in April 2001

A tissue-based draft map of the murine MHC class I immunopeptidome

article by Heiko Schuster et al published 7 August 2018 in Scientific Data

A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry

scientific article

A uniform proteomics MS/MS analysis platform utilizing open XML file formats

scientific article

A web site for the rat serum protein study group

scientific article published on 01 December 1999

AP-SWATH reveals direct involvement of VCP/p97 in integrated stress response signaling through facilitating CReP/PPP1R15B degradation

scientific article published on 29 March 2018

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry ⬇️

scientific article published on March 18, 2011

ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage ⬇️

scientific article published on December 7, 2010

Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis

scientific article published on 18 June 2015

Absolute quantification of microbial proteomes at different states by directed mass spectrometry

scientific article

Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags

scientific article published on January 2007

Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags

scientific article published in July 2004

Absolute quantitation of 2-D protein spots

scientific article

Abundance ratio-dependent proteomic analysis by mass spectrometry

scientific article

Accelerated Protein Biomarker Discovery from FFPE Tissue Samples Using Single-Shot, Short Gradient Microflow SWATH MS

scientific article published on 13 February 2020

Activation and serine phosphorylation of the p56lck protein tyrosine kinase in response to antigen receptor cross-linking in B lymphocytes

scientific article

Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus.

scientific article

Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides

scientific article

Advances in protein complex analysis using mass spectrometry

scientific article

Advances in proteome analysis by mass spectrometry

scientific article

Advances in proteomic workflows for systems biology

scientific article

Advances in quantitative proteomics using stable isotope tags

scientific article

Advances in quantitative proteomics via stable isotope tagging and mass spectrometry

scientific article

Advancing cell biology through proteomics in space and time (PROSPECTS).

scientific article published on 6 February 2012

Advancing translational research and precision medicine with targeted proteomics

scientific article published on 22 February 2018

An Integrated Microfluidics-Tandem Mass Spectrometry System for Automated Protein Analysis ⬇️

scientific article published on September 15, 1998

An SMC-domain protein in fission yeast links telomeres to the meiotic centrosome

scientific article

An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data

scientific article

An automated pipeline for high-throughput label-free quantitative proteomics

scientific article

An ent-kaurene that inhibits mitotic chromosome movement and binds the kinetochore protein ran-binding protein 2.

scientific article published on August 2006

An essential 45 kDa yeast transmembrane protein reacts with anti-nuclear pore antibodies: purification of the protein, immunolocalization and cloning of the gene

scientific article published on October 1, 1991

An essential switch in subunit composition of a chromatin remodeling complex during neural development

scientific journal article

An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells

scientific article published on 19 February 2007

An integrated mass spectrometric and computational framework for the analysis of protein interaction networks

scientific article published on 25 February 2007

An integrated workflow for charting the human interaction proteome: insights into the PP2A system

scientific article

An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures

scientific article published on 29 May 2008

An open-source computational and data resource to analyze digital maps of immunopeptidomes

scientific article

Analysis and validation of proteomic data generated by tandem mass spectrometry

scientific article

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry

scientific article

Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry

scientific article

Analysis of membrane proteins by two-dimensional electrophoresis: comparison of the proteins extracted from normal or Plasmodium falciparum-infected erythrocyte ghosts

scientific article published in December 1999

Analysis of protein complexes using mass spectrometry

scientific article

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

scientific article published on January 2006

Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.

scientific article published on February 2004

Analytical and micropreparative peptide mapping by high performance liquid chromatography/electrospray mass spectrometry of proteins purified by gel electrophoresis

scientific article published on August 1993

Androgen receptor represses the neuroendocrine transdifferentiation process in prostate cancer cells

scientific article published on 29 May 2003

Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies

scientific article

Application of SWATH Proteomics to Mouse Biology

scientific article published on 19 June 2017

Applications and Developments in Targeted Proteomics: From SRM to DIA/SWATH

scientific article published on 01 August 2016

Applications of targeted proteomics in systems biology and translational medicine

scientific article

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

scientific article published on September 2009

Approaches to labeling and identification of active site residues in glycosidases

scientific article

Approaching complete peroxisome characterization by gas-phase fractionation

scientific article published in September 2002

Arabidopsis proteome and the mass spectral assay library

scientific article published on 22 November 2019

Architecture and conformational switch mechanism of the ryanodine receptor

scientific article

Architecture of the large subunit of the mammalian mitochondrial ribosome

scientific article

Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics

scientific article

Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics

scientific article (publication date: October 2007)

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation

scientific article published on 29 June 2015

Atbf1 is required for the Pit1 gene early activation

scholarly article

Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase

scientific article

Author Correction: Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals

scientific article published on 01 August 2019

Author Correction: Proteomic and interactomic insights into the molecular basis of cell functional diversity

scientific article published on 17 April 2020

Author Correction: Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex

scientific article published on 14 March 2018

Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

scientific article

Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

Automated chemical synthesis of a protein growth factor for hemopoietic cells, interleukin-3.

scientific article published on January 1986

Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software

scientific article published in July 2006

Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies

scientific article

Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry

scientific article

Automated workflow for large-scale selected reaction monitoring experiments

scientific article published on 10 February 2012

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4–6, 2005

article

B cell antigen receptor cross-linking induces phosphorylation of the p21ras oncoprotein activators SHC and mSOS1 as well as assembly of complexes containing SHC, GRB-2, mSOS1, and a 145-kDa tyrosine-phosphorylated protein

scientific journal article

Bace2 is a β cell-enriched protease that regulates pancreatic β cell function and mass

scientific article published on September 2011

Bacterial effector binds host cell adenylyl cyclase to potentiate Gαs-dependent cAMP production

scientific article

Beyond ATM: The protein kinase landscape of the DNA damage response ⬇️

scientific article published on 08 May 2011

Biomarker Validation in Blood Specimens by Selected Reaction Monitoring Mass Spectrometry of N-Glycosites ⬇️

scientific article published on January 1, 2011

BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers

scientific article published on July 2009

Biosynthesis of dermatan sulfate: chondroitin-glucuronate C5-epimerase is identical to SART2

scientific article

Both phosphatidylinositol 3-kinase and phosphatidylinositol 4-kinase products are increased by antigen receptor signaling in B cells

scientific article published on January 1994

Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry

scientific article published on 01 July 2019

Building ProteomeTools based on a complete synthetic human proteome

scientific article

Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics

scientific article

Building consensus spectral libraries for peptide identification in proteomics

scientific article

Building high-quality assay libraries for targeted analysis of SWATH MS data

scientific article

CD28 stimulation regulates its association withN-ethylmaleimide-sensitive fusion protein and other proteins involved in vesicle sorting ⬇️

scientific article published on January 1, 2001

CTCF physically links cohesin to chromatin

scientific article

Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer

scientific article

Cell polarity protein Spa2P associates with proteins involved in actin function in Saccharomyces cerevisiae

scientific article

Ceramide profiling of complex lipid mixtures by electrospray ionization mass spectrometry

scientific article published on 01 January 1997

Challenges and opportunities in proteomics data analysis

scientific article

Characterization and kinetic analysis of the intracellular domain of human protein tyrosine phosphatase beta (HPTP beta) using synthetic phosphopeptides

scientific article published on March 1994

Characterization of a DNA exit gate in the human cohesin ring.

scientific article published on November 2014

Characterization of a major protein in GLUT4 vesicles. Concentration in the vesicles and insulin-stimulated translocation to the plasma membrane

scientific journal article

Characterization of an activated ribosomal S6 kinase variant from maturing sea star oocytes: association with phosphatase 2A and substrate specificity

scientific article published in November 1999

Characterization of human serum amyloid A protein isoforms separated by two-dimensional electrophoresis by liquid chromatography/electrospray ionization tandem mass spectrometry

scientific article

Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis

scientific article

Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry

scientific article

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

scientific article

Chemical Cross-Linking/Mass Spectrometry Maps the Amyloid β Peptide Binding Region on Both Apolipoprotein E Domains

scientific article published on 21 January 2015

Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9

scientific article published on 26 February 2020

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

scientific article published on 17 June 2014

Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes

scientific article published on February 2004

ChromID identifies the protein interactome at chromatin marks

scientific article published on 02 March 2020

Colloidal silver staining of electroblotted proteins for high sensitivity peptide mapping by liquid chromatography-electrospray ionization tandem mass spectrometry

scientific article published on 01 May 1997

Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

scientific article published on 20 March 2018

Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.

scientific article published on 7 June 2019

Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases

scientific article published on 28 July 2009

Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics

scientific article published on 17 December 2007

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

scientific article

Comparative ’omics analyses differentiateMycobacterium tuberculosisandMycobacterium bovisand reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

article

Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification

scientific article published on February 2009

Comparison of pancreas juice proteins from cancer versus pancreatitis using quantitative proteomic analysis

scientific article published on January 2007

Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology

scientific article published on 13 October 2003

Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae

scientific article published in April 2002

Complex-centric proteome profiling by SEC-SWATH-MS

Complex-centric proteome profiling by SEC-SWATH-MS

Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes

scientific article published on 20 July 2020

Comprehensive Description of the N-Glycoproteome of Mouse Pancreatic β-Cells and Human Islets ⬇️

scientific article published on January 27, 2012

Comprehensive analyses of prostate gene expression: convergence of expressed sequence tag databases, transcript profiling and proteomics

scientific article published on 01 May 2000

Comprehensive proteome analysis of human skeletal muscle in cachexia and sarcopenia: a pilot study

scientific article published on 15 March 2017

Comprehensive proteomics

scientific article published on October 2010

Comprehensive quantitative analysis of central carbon and amino‐acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics ⬇️

scientific article published on February 1, 2011

Computational prediction of proteotypic peptides for quantitative proteomics

scientific article published on 31 December 2006

Confident site localization using a simulated phosphopeptide spectral library

scientific article published on 27 March 2015

Conformational control and DNA-binding mechanism of the metazoan origin recognition complex

article published in the Proceedings of the National Academy of Sciences of the United States of America

Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics

scientific article published on 12 March 2014

Constellations in a cellular universe

scientific article published in Nature

Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF-α Signaling

scientific article

Convergent network effects along the axis of gene expression during prostate cancer progression

scientific article published on 14 December 2020

Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans

scientific article

Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach

scientific article

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

scientific article

Covalent attachment of peptides for high sensitivity solid-phase sequence analysis

scientific article published in May 1990

Cross-link guided molecular modeling with ROSETTA

scientific article

Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

scientific article

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

scientific article

Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage ⬇️

scientific article published on March 6, 2012

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation

scientific article

Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER

scientific article

CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation

scientific article published on 02 September 2019

DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments.

scientific article published on 30 December 2014

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

scientific article published on 11 August 2020

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

scientific article

Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial

scholarly article by Christina Ludwig et al published 13 August 2018 in Molecular Systems Biology

Deciphering MET-dependent modulation of global cellular responses to DNA damage by quantitative phosphoproteomics

scientific article published on 26 April 2020

Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins

scientific article

Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival

scientific article published on 15 August 2017

Design and synthesis of visible isotope-coded affinity tags for the absolute quantification of specific proteins in complex mixtures

scientific article published in March 2004

Development and validation of a spectral library searching method for peptide identification from MS/MS.

scientific article

Development of a Multiplexed Microcapillary Liquid Chromatography System for High-Throughput Proteome Analysis

article

Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial

scientific article published in 2021

Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform

scientific article

Differential glucose repression in common yeast strains in response to HXK2 deletion

scientific article published on 22 January 2010

Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation.

scientific article published in January 2001

Direct analytical sample quality assessment for biomarker investigation: qualifying cerebrospinal fluid samples

scientific article

Direct identification of a G protein ubiquitination site by mass spectrometry

scientific article

Direct identification of ligand-receptor interactions on living cells and tissues

scientific article

Directed mass spectrometry: towards hypothesis-driven proteomics

scientific article published on 21 September 2009

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

scientific article published on 25 April 2019

Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling

scientific journal article

Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics

scientific article published on 29 December 2003

Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis

scientific article

Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides

scientific article published on 12 December 2005

Early Steps in Autophagy Depend on Direct Phosphorylation of Atg9 by the Atg1 Kinase.

scientific article published in February 2014

Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase.

scientific article published on 16 January 2014

Editorial: from data to results

scientific article published on 3 October 2011

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

scientific article published on 18 March 2015

Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome

scientific article

Electrophoresis combined with novel mass spectrometry techniques: powerful tools for the analysis of proteins and proteomes.

scientific article published on July 1998

Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data

scientific article published on 01 August 2019

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

scientific article (publication date: 15 October 2002)

Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations

scientific article

Enzymatic generation of peptides flanked by basic amino acids to obtain MS/MS spectra with 2× sequence coverage

scientific article published on December 2014

Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals

scientific article

Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers

scientific article

Equipping scientists for the new biology

scientific article published on 01 April 2000

Erratum: A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans

scholarly article published in Nature Methods

Erratum: Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex.

erratum

Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry ⬇️

scientific article published on November 20, 2011

Evaluation of two-dimensional phosphopeptide maps by electrospray ionization mass spectrometry of recovered peptides

scientific article published on 01 November 1994

Evolution of organelle-associated protein profiling

scientific article published on 07 December 2008

Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography

scientific article published on 27 January 2012

Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance

scientific article published on 06 July 2021

Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas

scientific article

F2(Pmp)2-TAM zeta 3, a novel competitive inhibitor of the binding of ZAP-70 to the T cell antigen receptor, blocks early T cell signaling

scientific article published on January 1995

FRI-297-Trans-signaling blockade induces mature-onset obesity and insulin resistance in mice via suppression of PPARalpha

scholarly article

False discovery rate estimation for cross-linked peptides identified by mass spectrometry

scientific article published on 8 July 2012

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

scientific article

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study

scientific article published on 22 May 2019

From genome to proteome--aim of human proteomics.

scientific article published in October 2004

Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics

scientific article

Functionalized membrane supports for covalent protein microsequence analysis

scientific article published in April 1991

GIT1 Mediates Src-dependent Activation of Phospholipase Cγ by Angiotensin II and Epidermal Growth Factor ⬇️

scientific article (publication date: 12 December 2003)

Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone

scientific article published on 6 February 2004

Generating and navigating proteome maps using mass spectrometry.

scientific article published on 14 October 2010

Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins

scientific article published on 12 February 2019

Generic comparison of protein inference engines

scientific article published on 4 November 2011

Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis

scholarly article by Teresa Cortes et al published January 2014 in Cell Reports

Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis

scientific article

Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results

Genotype–phenotype relationships in light of a modular protein interaction landscape ⬇️

scientific article published on March 26, 2013

Germ-free and microbiota-associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes

scientific article published on 18 February 2020

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

scientific article

Global Metabonomic and Proteomic Analysis of Human Conjunctival Epithelial Cells (IOBA-NHC) in Response to Hyperosmotic Stress

scientific article published on 11 August 2015

Glu280 is the nucleophile in the active site of Clostridium thermocellum CelC, a family A endo-beta-1,4-glucanase

scientific article published on 01 July 1993

Glucagon-Induced Acetylation of Foxa2 Regulates Hepatic Lipid Metabolism ⬇️

scientific article published on February 14, 2013

Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness.

scientific article

Guidelines for reporting the use of mass spectrometry in proteomics.

scientific article

HUPO Plasma Proteome Project 2007 Workshop Report

Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry

scientific article published on May 2009

High sensitivity analysis of proteins and peptides by capillary electrophoresis-tandem mass spectrometry: recent developments in technology and applications.

scientific article published in May 1998

High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites

scientific article published on 20 July 2007

High sensitivity identification of proteins by electrospray ionization tandem mass spectrometry: initial comparison between an ion trap mass spectrometer and a triple quadrupole mass spectrometer

scientific article published on 01 March 1997

High throughput protein characterization by automated reverse‐phase chromatography/electrospray tandem mass spectrometry ⬇️

scientific article published on March 1, 1998

High throughput proteome screening for biomarker detection

scientific article published on 5 January 2005

High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry

scientific article published on 17 December 2004

High-accuracy proteome maps of human body fluids

scientific article published on January 2006

High-sensitivity determination of tyrosine-phosphorylated peptides by on-line enzyme reactor and electrospray ionization mass spectrometry

scientific article published on January 1995

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

scientific article

High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification

scientific article published on 18 September 2019

Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan

scientific article published in May 2014

Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.

scientific article published on 30 August 2016

How many human proteoforms are there?

scientific article published in February 2018

Human Plasma PeptideAtlas

scientific article published on August 2005

Human Proteome Organisation Proteomics Standards Initiative Pre-Congress Initiative

article

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

scientific article

Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition

scientific article published on 10 February 2013

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

scientific article

Huntingtin's spherical solenoid structure enables polyglutamine tract-dependent modulation of its structure and function

scientific article published on 22 March 2016

ICAT-MS-MS time course analysis of atrophying mouse skeletal muscle cytosolic subproteome

scientific article published on 25 July 2005

IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics

scientific article published on 21 June 2011

Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex

scientific article

Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster

scientific article

Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry ⬇️

scientific article (publication date: June 2003)

Identification of CDK2 substrates in human cell lysates

scientific article published on 13 October 2008

Identification of Cdk targets that control cytokinesis

scientific article

Identification of Glu340 as the active-site nucleophile in human glucocerebrosidase by use of electrospray tandem mass spectrometry

scientific article published on 01 April 1994

Identification of Protein Abundance Changes in Hepatocellular Carcinoma Tissues using PCT-SWATH

scientific article published on 19 November 2018

Identification of Proteins in Single-Cell Capillary Electrophoresis Fingerprints Based on Comigration with Standard Proteins ⬇️

scientific article published on July 15, 2003

Identification of TFB5, a new component of general transcription and DNA repair factor IIH.

scientific article

Identification of a Novel Phosphorylation Site, Ser-170, as a Regulator of Bad Pro-apoptotic Activity ⬇️

scientific article published on November 20, 2001

Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry

scientific article

Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring

scientific article

Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells

scientific article

Identification of cross-linked peptides from large sequence databases

scientific article published on 09 March 2008

Identification of gel-separated proteins by liquid chromatography-electrospray tandem mass spectrometry: comparison of methods and their limitations.

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Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, according to the HUPO Human Proteome Project

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SWATH-MS Analysis of FFPE Tissues Identifies Stathmin as a Potential Marker of Endometrial Cancer in Patients Exposed to Tamoxifen

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Strategies to enable large-scale proteomics for reproducible research

scientific article published on 30 July 2020

Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry-based proteomics

scientific article published on 23 November 2011

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

scientific article

Structural analysis of vascular endothelial growth factor receptor-2/ligand complexes by small-angle X-ray solution scattering.

scientific article

Structural and biochemical characterization of the Cop9 signalosome CSN5/CSN6 heterodimer

scientific article

Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle

scientific article published on 31 March 2016

Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex.

scientific article

Structural features of Argonaute-GW182 protein interactions

scientific article

Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex

scientific article published on 23 December 2017

Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex.

scientific article

Structure of a human cap-dependent 48S translation pre-initiation complex

scientific article published in February 2018

Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution ⬇️

scientific article published on November 22, 2010

Structures of human PRC2 with its cofactors AEBP2 and JARID2.

scientific article

SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling

scientific article published on October 2007

Surfaceome of classical Hodgkin and non-Hodgkin lymphoma

scientific article published on August 2015

Synthesis and evaluation of superparamagnetic silica particles for extraction of glycopeptides in the microtiter plate format

scientific article

Synthesis of the protein-sequencing reagent 4-(3-pyridinylmethylaminocarboxypropyl) phenyl isothiocyanate and characterization of 4-(3-pyridinylmethylaminocarboxypropyl) phenylthiohydantoins

scientific article published on 01 January 1995

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

scientific article published on 12 December 2016

System-based proteomic analysis of the interferon response in human liver cells

scientific article

Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics.

scientific article

Systematic LC-MS analysis of labile post-translational modifications in complex mixtures

scientific article published in May 2009

Systematic Proteomic Analysis Identifies β-Site Amyloid Precursor Protein Cleaving Enzyme 2 and 1 (BACE2 and BACE1) Substrates in Pancreatic β-Cells ⬇️

scientific article published on February 19, 2013

Systematic characterization of pan-cancer mutation clusters.

scientific article published on 23 March 2018

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

scientific article published on 6 February 2013

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells.

scientific article published on 31 October 2017

Systematic quantification of peptides/proteins in urine using selected reaction monitoring ⬇️

scientific article published on February 16, 2011

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines

scientific article published on 24 November 2017

Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer.

scientific article

Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis

scientific article published on 12 October 2017

Systems proteomics of liver mitochondria function

scientific article

Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization

scientific article published on 25 July 2016

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

scientific article published on August 2016

TRIM24 Is an Oncogenic Transcriptional Activator in Prostate Cancer

scientific article published on 24 May 2016

Tandem mass spectrometry protein identification on a PC grid

scientific article published on January 2007

Target of Rapamycin Complex 2 Regulates Actin Polarization and Endocytosis via Multiple Pathways

scientific article published on 16 April 2015

Targeted Proteomics

scientific article published on 01 April 2012

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

scientific article

Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach

scientific article published on 17 January 2014

Targeted protein quantification using sparse reference labeling

scientific article published on 19 January 2014

Targeted proteome investigation via selected reaction monitoring mass spectrometry

scientific article published on 08 May 2012

Targeted proteomic strategy for clinical biomarker discovery

scientific article published on 11 December 2008

Targeted proteomics of the eicosanoid biosynthetic pathway completes an integrated genomics-proteomics-metabolomics picture of cellular metabolism

scientific article

Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet

scientific article published on 16 July 2013

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring

scientific article published on 13 April 2008

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast

scientific article published on January 2013

The 2023 Report on the Proteome from the HUPO Human Proteome Project

scholarly article published on 17 January 2024

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data

scientific article

The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis

scientific article published on 04 April 2019

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome.

scientific article

The Drosophila FoxA Ortholog Fork Head Regulates Growth and Gene Expression Downstream of Target of Rapamycin ⬇️

scientific article published on December 31, 2010

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

scientific article

The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

scientific article published on 7 April 2016

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article

The GTPase Nog1 co-ordinates the assembly, maturation and quality control of distant ribosomal functional centers

scientific article published on 07 January 2020

The HUPO initiative on Model Organism Proteomes, iMOP.

scientific article published in February 2012

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays

scientific article

The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions

scientific article published on 01 September 2019

The Mtb proteome library: A resource of assays to quantify the complete proteome of mycobacterium tuberculosis

scientific article

The PeptideAtlas project

scientific article

The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain

scientific article published on 08 July 2020

The Protein Information and Property Explorer 2: Gaggle‐like exploration of biological proteomic data within one webpage ⬇️

scientific article published on December 6, 2010

The SysteMHC Atlas project

scientific article published on 29 July 2017

The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses

scientific article published on 01 January 2020

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT

scientific article published on 25 June 2003

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the applicatio

scientific article

The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community

scientific article published on 21 December 2012

The calcineurin signaling network evolves via conserved kinase-phosphatase modules that transcend substrate identity

scientific article

The complete structure of the large subunit of the mammalian mitochondrial ribosome

scientific article

The direct recruitment of BLNK to immunoglobulin alpha couples the B-cell antigen receptor to distal signaling pathways

scientific article

The human proteome project: Current state and future direction

scientific article published on 29 April 2011

The impact of genomic variation on protein phosphorylation states and regulatory networks

scientific article published on 01 May 2022

The implications of proteolytic background for shotgun proteomics

scientific article published on 28 May 2007

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification

scientific article published on 12 August 2019

The interdependence of transcript and protein abundance: new data--new complexities

scientific article

The laying hen expresses two different low density lipoprotein receptor-related proteins

scientific article published in October 1991

The minimum information about a proteomics experiment (MIAPE)

scientific article (publication date: August 2007)

The mitochondrial antioxidant defence system and its response to oxidative stress

scientific article

The molecular architecture of the eukaryotic chaperonin TRiC/CCT

scientific article

The mouse metallomic landscape of aging and metabolism

scientific article published on 01 February 2022

The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data

scientific article published on 9 April 2004

The need for national centers for proteomics

scientific article published on 01 July 2002

The pros and cons of peptide-centric proteomics

scientific article published on 01 July 2010

The protein interaction landscape of the human CMGC kinase group

scientific article

The quantitative and condition-dependent Escherichia coli proteome

scientific article published on 07 December 2015

The quantitative proteome of a human cell line.

scientific article

The receptor for yolk lipoprotein deposition in the chicken oocyte

scientific article published in October 1991

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools

scientific article

The structural basis of substrate recognition by the eukaryotic chaperonin TRiC/CCT

scientific journal article

The structure and symmetry of radial spoke protein complex in Chlamydomonas flagella

scientific article published on 21 July 2020

The study of macromolecular complexes by quantitative proteomics

scientific article published on 18 February 2003

The synaptojanin-like protein Inp53/Sjl3 functions with clathrin in a yeast TGN-to-endosome pathway distinct from the GGA protein-dependent pathway

scientific article

The toposome, essential for sea urchin cell adhesion and development, is a modified iron-less calcium-binding transferrin

scientific article published on 24 July 2007

The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes

scientific article

The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).

scientific article published on January 2006

Timescales and bottlenecks in miRNA-dependent gene regulation

scientific article published on 03 December 2013

Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry

scientific article published in December 2001

TraML--a standard format for exchange of selected reaction monitoring transition lists

scientific article published on 12 December 2011

Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets

scientific article

Two-dimensional Blue native/SDS gel electrophoresis of multi-protein complexes from whole cellular lysates: a proteomics approach

scientific article

Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA.

scientific article

Ultra-sensitive proteome profiling of FACS-isolated cell populations by data-independent acquisition-MS: Application to human hematopoietic stem and progenitor cells

scientific article

UniPep--a database for human N-linked glycosites: a resource for biomarker discovery

scientific article published on 10 August 2006

Unique structural features and differential phosphorylation of the 280-kDa component (isozyme) of rat liver acetyl-CoA carboxylase

scientific article published on 01 May 1994

Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97.

scientific article published on 06 April 2017

Updated reference genome sequence and annotation ofMycobacterium bovisAF2122/97

Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications

scientific article published on 23 February 2015

Using spectral libraries for peptide identification from tandem mass spectrometry (MS/MS) data

scientific article

Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition

scientific article published on January 2007

Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis

scientific article published in 2014

Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins ⬇️

scientific article published on January 1, 2011

Visual proteomics of the human pathogen Leptospira interrogans

scientific article

Western Blots versus Selected Reaction Monitoring Assays: Time to Turn the Tables? ⬇️

scientific article published on June 10, 2013

Xwalk: computing and visualizing distances in cross-linking experiments

scientific article

Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A

scientific journal article

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data

scientific article

diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition

scientific article published on 30 November 2020

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates

scientific article

mProphet: automated data processing and statistical validation for large-scale SRM experiments

scientific article

mzDB: a file format using multiple indexing strategies for the efficient analysis of large LC-MS/MS and SWATH-MS data sets

scientific article

openBIS: a flexible framework for managing and analyzing complex data in biology research

scientific article

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library

scientific article published on January 2014

qcML: an exchange format for quality control metrics from mass spectrometry experiments

scientific article published on 23 April 2014

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry

scientific article

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