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List of works by Robert J Chalkley

A proteomics study of brassinosteroid response in Arabidopsis

scientific article

A standardized framing for reporting protein identifications in mzIdentML 1.2

scientific article

Bioinformatic methods to exploit mass spectrometric data for proteomic applications

scientific article

Breaking Up the C Complex Spliceosome Shows Stable Association of Proteins with the Lariat Intron Intermediate ⬇️

scientific article published on April 19, 2011

Cell cycle-dependent phosphorylation of human CDC5 regulates RNA processing.

scientific article

Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS

scientific article published on 13 April 2020

Characterizing sialic acid variants at the glycopeptide level.

scientific article

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by s

scientific article

Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors.

scientific article published on 15 April 2013

Double impact of cigarette smoke and mechanical ventilation on the alveolar epithelial type II cell

scientific article

Expanding the use of spectral libraries in proteomics

Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides

scientific article

Glucose Sensor O-GlcNAcylation Coordinates with Phosphorylation to Regulate Circadian Clock ⬇️

scientific article published on February 5, 2013

Glyco-centric lectin magnetic bead array (LeMBA) - proteomics dataset of human serum samples from healthy, Barrett׳s esophagus and esophageal adenocarcinoma individuals.

scientific article published on April 2016

Human antibodies targeting cell surface antigens overexpressed by the hormone refractory metastatic prostate cancer cells: ICAM-1 is a tumor antigen that mediates prostate cancer cell invasion

scientific article

Hyper-O-GlcNAcylation activates nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling through interplay with phosphorylation and acetylation.

scientific article published on 17 April 2017

Identification of O-linked β-D-N-acetylglucosamine-modified proteins from Arabidopsis

scientific article published on January 2012

Identification of novel sites of O-N-acetylglucosamine modification of serum response factor using quadrupole time-of-flight mass spectrometry.

scientific article published in March 2003

Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides

scholarly article

Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities.

scientific article

Improving Peptide identification using empirical scoring systems

scientific article

Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring

scientific article

In-depth analysis of tandem mass spectrometry data from disparate instrument types

scientific article

Instrumentation for LC-MS/MS in Proteomics ⬇️

scientific article published on January 1, 2010

Keratin 20 serine 13 phosphorylation is a stress and intestinal goblet cell marker

scientific article

Lessons in de novo peptide sequencing by tandem mass spectrometry

scientific article

Linking the T Cell Surface Protein CD2 to the Actin-capping Protein CAPZ via CMS and CIN85 ⬇️

scientific article (publication date: 20 June 2003)

MS-viewer: a web-based spectral viewer for proteomics results

scientific article

Matching cross-linked peptide spectra: only as good as the worse identification

scientific article published on 12 December 2013

Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites

scientific article published on 16 September 2020

Modification Site Localization in Peptides

scientific article published in January 2016

Modification site localization scoring integrated into a search engine.

scientific article

Modification site localization scoring: strategies and performance

scientific article

Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters

scientific article published on 28 January 2022

Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis

scientific article published on 31 July 2013

N-Glycopeptide Profiling in Arabidopsis Inflorescence

scientific article published on 11 April 2016

NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling

scientific article published on 20 November 2014

O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry

scientific article published on February 2006

O-linked β-N-acetylglucosamine (O-GlcNAc) site thr-87 regulates synapsin I localization to synapses and size of the reserve pool of synaptic vesicles

scientific article

O-sulfonation of serine and threonine: mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes.

scientific article published on 29 January 2004

On Credibility, Clarity, and Compliance.

scientific article published on 3 June 2015

Peripheral Elevation of a Klotho Fragment Enhances Brain Function and Resilience in Young, Aging, and α-Synuclein Transgenic Mice

scientific article

Processing RNA-seq Data to Create a Sequence Database for Proteomics Shotgun Data Analysis

Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.

scientific article published on 31 October 2013

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)

Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis.

scientific article published on 2 February 2017

Proteomics Standards Initiative Extended FASTA Format

scientific article published on 23 May 2019

Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis

scientific article

Prp8 positioning of U5 snRNA is linked to 5' splice site recognition.

scientific article published on 27 February 2018

Rearrangements within human spliceosomes captured after exon ligation.

scientific article

Receptor tyrosine kinase signaling – a proteomic perspective ⬇️

scientific article published on November 5, 2010

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles

scientific article (publication date: July 2009)

Regulated expression of apolipoprotein E by human retinal pigment epithelial cells ⬇️

scientific article published on November 1, 2003

Revealing nascent proteomics in signaling pathways and cell differentiation.

scientific article published on 21 February 2018

Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry.

scientific article published on 30 June 2006

The DegraBase: a database of proteolysis in healthy and apoptotic human cells

scientific article published on 20 December 2012

The Induction of Serine/Threonine Protein Phosphorylations by a PDGFR/TrkA Chimera in Stably Transfected PC12 Cells ⬇️

scientific article published on October 25, 2011

The PSI-MOD community standard for representation of protein modification data.

scientific article

The RasGAP proteins Ira2 and neurofibromin are negatively regulated by Gpb1 in yeast and ETEA in humans

scientific article

The effect of using an inappropriate protein database for proteomic data analysis

scientific article

The effectiveness of filtering glycopeptide peak list files for Y ions

scientific article published on 17 February 2020

The mzIdentML data standard version 1.2, supporting advances in proteome informatics.

scientific article

Tissue-Specific Glycosylation at the Glycopeptide Level

scientific article published on 20 May 2015

Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in VDR transactivation during keratinocyte differentiation.

scientific article

Use of a glycosylation site database to improve glycopeptide identification from complex mixtures.

scientific article

Use of a mutant OGA for detecting O-GlcNAc modified proteins

scientific article

iPRG 2011: A Study on the Identification of Electron Transfer Dissociation (ETD) Mass Spectra

iPRG 2012 Study: Detecting Modified Peptides in a Complex Mixture

iPRG 2012 Study: Detecting Modified Peptides in a Complex Mixture.

scientific article published in January 2012

iPRG-2013: Proteome Informatics Research Group Study: Using RNA-Seq Data to Refine Proteomic Data Analysis

iPRG-2013: Proteome Informatics Research Group Study: Using RNA-Seq Data to Refine Proteomic Data Analysis.

scientific article

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