100% protein sequence coverage: a modern form of surrealism in proteomics

B Meyer, DG Papasotiriou, M Karas - Amino acids, 2011 - Springer
This review intends not only to discuss the current possibilities to gain 100% sequence
coverage for proteins, but also to point out the critical limits to such an attempt. The aim of …

Mass spectrometry and the cellular surfaceome

J Pauwels, D Fijałkowska, S Eyckerman… - Mass spectrometry …, 2022 - Wiley Online Library
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is
involved in multiple vital cellular processes, such as the communication of cells with their …

[HTML][HTML] Multi-enzyme digestion FASP and the 'Total Protein Approach'-based absolute quantification of the Escherichia coli proteome

JR Wiśniewski, D Rakus - Journal of proteomics, 2014 - Elsevier
We describe a proteomic approach combining the multi-enzyme digestion FASP-sample
processing strategy and the 'Total Protein Approach'applied to absolute quantification of …

A systematic survey of in vivo obligate chaperonin‐dependent substrates

K Fujiwara, Y Ishihama, K Nakahigashi, T Soga… - The EMBO …, 2010 - embopress.org
Chaperonins are absolutely required for the folding of a subset of proteins in the cell. An
earlier proteome‐wide analysis of Escherichia coli chaperonin GroEL/GroES (GroE) …

[HTML][HTML] Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants

T Masuda, N Saito, M Tomita, Y Ishihama - Molecular & Cellular Proteomics, 2009 - Elsevier
We developed a sample preparation protocol for rapid and unbiased analysis of the
membrane proteome using an alimentary canal-mimicking system in which proteases are …

One-Dimensional Capillary Liquid Chromatographic Separation Coupled with Tandem Mass Spectrometry Unveils the Escherichia coli Proteome on a Microarray …

M Iwasaki, S Miwa, T Ikegami, M Tomita… - Analytical …, 2010 - ACS Publications
We successfully identified the proteome expressed in Escherichia coli (E. coli) cells on a
microarray scale using one-dimensional capillary liquid chromatography-tandem mass …

Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol

KK Cheng, BS Lee, T Masuda, T Ito, K Ikeda… - Nature …, 2014 - nature.com
Comparative whole-genome sequencing enables the identification of specific mutations
during adaptation of bacteria to new environments and allelic replacement can establish …

Strategy for SRM-based verification of biomarker candidates discovered by iTRAQ method in limited breast cancer tissue samples

S Muraoka, H Kume, S Watanabe… - Journal of proteome …, 2012 - ACS Publications
Since LC–MS-based quantitative proteomics has become increasingly applied to a wide
range of biological applications over the past decade, numerous studies have performed …

Proteomic analysis of ganglioside‐associated membrane molecules: substantial basis for molecular clustering

N Hashimoto, K Hamamura, N Kotani, K Furukawa… - …, 2012 - Wiley Online Library
Ganglioside GD 3 is specifically expressed in human melanomas, and plays a role in the
enhancement of malignant phenotypes of melanoma cells. To analyze the mechanisms by …

A Protein Cleavage Platform Based on Selective Formylation at Cysteine Residues

N Zenmyo, Y Matsumoto, A Yasuda… - Journal of the …, 2024 - ACS Publications
Site-selective cleavage of the peptide backbone in proteins is an important class of post-
translational modification (PTM) in nature. However, the organic chemistry for such site …