Protein analysis by shotgun/bottom-up proteomics

Y Zhang, BR Fonslow, B Shan, MC Baek… - Chemical …, 2013 - ACS Publications
According to Genome Sequencing Project statistics (http://www. ncbi. nlm. nih.
gov/genomes/static/gpstat. html), as of February 16, 2012, complete gene sequences have …

Status of large-scale analysis of post-translational modifications by mass spectrometry

JV Olsen, M Mann - Molecular & cellular proteomics, 2013 - ASBMB
Cellular function can be controlled through the gene expression program, but often protein
post-translational modifications (PTMs) provide a more precise and elegant mechanism. Key …

Universal and confident phosphorylation site localization using phosphoRS

T Taus, T Köcher, P Pichler, C Paschke… - Journal of proteome …, 2011 - ACS Publications
An algorithm for the assignment of phosphorylation sites in peptides is described. The
program uses tandem mass spectrometry data in conjunction with the respective peptide …

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

JV Olsen, M Vermeulen, A Santamaria, C Kumar… - Science …, 2010 - science.org
Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are
tightly regulated at defined stages of the cell division cycle. Progression through this cycle …

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks

JV Olsen, B Blagoev, F Gnad, B Macek, C Kumar… - Cell, 2006 - cell.com
Cell signaling mechanisms often transmit information via posttranslational protein
modifications, most importantly reversible protein phosphorylation. Here we develop and …

Decoding signalling networks by mass spectrometry-based proteomics

C Choudhary, M Mann - Nature reviews Molecular cell biology, 2010 - nature.com
Signalling networks regulate essentially all of the biology of cells and organisms in normal
and disease states. Signalling is often studied using antibody-based techniques such as …

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

J Villén, SP Gygi - Nature protocols, 2008 - nature.com
The success in profiling the phosphoproteome by mass spectrometry-based proteomics has
been intimately related to the availability of methods that selectively enrich for …

A perspective on the Maillard reaction and the analysis of protein glycation by mass spectrometry: probing the pathogenesis of chronic disease

Q Zhang, JM Ames, RD Smith… - Journal of proteome …, 2009 - ACS Publications
The Maillard reaction, starting from the glycation of protein and progressing to the formation
of advanced glycation end-products (AGEs), is implicated in the development of …

Analytical strategies for phosphoproteomics

TE Thingholm, ON Jensen, MR Larsen - Proteomics, 2009 - Wiley Online Library
Protein phosphorylation is a key regulator of cellular signaling pathways. It is involved in
most cellular events in which the complex interplay between protein kinases and protein …

Systematic evaluation of protein reduction and alkylation reveals massive unspecific side effects by iodine-containing reagents

T Müller, D Winter - Molecular & cellular proteomics, 2017 - ASBMB
Reduction and alkylation of cysteine residues is part of virtually any proteomics workflow.
Despite its frequent use, up to date no systematic investigation of the impact of different …