ProteomeXchange provides globally coordinated proteomics data submission and dissemination

…, G Mayer, L Gatto, A Campos, RJ Chalkley… - Nature …, 2014 - nature.com
Individual resources can join ProteomeXchange by implementing the ProteomeXchange
data submission and dissemination guidelines, and metadata requirements. In the current …

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

K Vosseller, JC Trinidad, RJ Chalkley… - Molecular & Cellular …, 2006 - ASBMB
O-GlcNAc is a widespread dynamic carbohydrate modification of cytosolic and nuclear
proteins with features analogous to phosphorylation. O-GlcNAc acts critically in many cellular …

[HTML][HTML] Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography

…, G Schmitt-Ulms, RJ Chalkley, J Hirsch… - Molecular & Cellular …, 2003 - ASBMB
In order to identify and compare the protein content of very low quantity samples of high
complexity, a protocol has been established that combines the differential profiling strength of a …

[PDF][PDF] Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock

K Kaasik, S Kivimäe, JJ Allen, RJ Chalkley, Y Huang… - Cell metabolism, 2013 - cell.com
Posttranslational modifications play central roles in myriad biological pathways including
circadian regulation. We employed a circadian proteomic approach to demonstrate that …

Lessons in de novo peptide sequencing by tandem mass spectrometry

KF Medzihradszky, RJ Chalkley - Mass spectrometry reviews, 2015 - Wiley Online Library
Mass spectrometry has become the method of choice for the qualitative and quantitative
characterization of protein mixtures isolated from all kinds of living organisms. The raw data in …

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

RJ Chalkley, A Thalhammer… - Proceedings of the …, 2009 - National Acad Sciences
Protein O-GlcNAcylation occurs in all animals and plants and is implicated in modulation of
a wide range of cytosolic and nuclear protein functions, including gene silencing, nutrient …

[HTML][HTML] Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis

…, K Alagesan, M Bern, W Cao, RJ Chalkley… - Nature …, 2021 - nature.com
Glycoproteomics is a powerful yet analytically challenging research tool. Software packages
aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but …

[HTML][HTML] Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision …

RJ Chalkley, PR Baker, L Huang, KC Hansen… - Molecular & Cellular …, 2005 - ASBMB
A thorough analysis of the protein interaction partners of the yeast GTPase Gsp1p was
carried out by a multidimensional chromatography strategy of strong cation exchange …

[HTML][HTML] A combinatorial code for the interaction of α-synuclein with membranes

S Kubo, VM Nemani, RJ Chalkley, MD Anthony… - Journal of Biological …, 2005 - ASBMB
Considerable genetic and pathological evidence has implicated the small, soluble protein α-synuclein
in the pathogenesis of familial and sporadic forms of Parkinsons disease (PD). …

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

RJ Chalkley, PR Baker, KF Medzihradszky… - Molecular & Cellular …, 2008 - ASBMB
Mass spectrometric analyses of protein digests produce large numbers of fragmentation
spectra that are not identified by routine database searching strategies. Some of these spectra …