[HTML][HTML] A composite filter for low FDR of protein-protein interactions detected by in vivo cross-linking

L de Jong, W Roseboom, G Kramer - Journal of proteomics, 2021 - Elsevier
In vivo chemical cross-linking combined with LCMSMS of digested extracts (in vivo CX-MS)
can reveal stable and dynamic protein-protein interactions at proteome-wide scale and at …

In-culture cross-linking of bacterial cells reveals large-scale dynamic protein–protein interactions at the peptide level

L De Jong, EA De Koning, W Roseboom… - Journal of proteome …, 2017 - ACS Publications
Identification of dynamic protein–protein interactions at the peptide level on a proteomic
scale is a challenging approach that is still in its infancy. We have developed a system to …

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

MJ Trnka, PR Baker, PJJ Robinson… - Molecular & Cellular …, 2014 - ASBMB
Chemical cross-linking mass spectrometry identifies interacting surfaces within a protein
assembly through labeling with bifunctional reagents and identifying the covalently modified …

[HTML][HTML] Towards low false discovery rate estimation for protein-protein interactions detected by chemical cross-linking

L de Jong, W Roseboom, G Kramer - Biochimica et Biophysica Acta (BBA) …, 2021 - Elsevier
Chemical cross-linking (CX) of proteins in vivo or in cell free extracts followed by mass
spectrometric (MS) identification of linked peptide pairs (CXMS) can reveal protein-protein …

Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline

A Leitner, T Walzthoeni, R Aebersold - Nature protocols, 2014 - nature.com
Chemical cross-linking in combination with LC-MS/MS (XL-MS) is an emerging technology
to obtain low-resolution structural (distance) restraints of proteins and protein complexes …

Improved strategies for rapid identification of chemically cross-linked peptides using protein interaction reporter technology

MR Hoopmann, CR Weisbrod… - Journal of proteome …, 2010 - ACS Publications
Protein interaction reporter (PIR) technology can enable identification of in vivo protein
interactions with the use of specialized chemical cross-linkers, liquid chromatography, and …

An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function

J Luo, J Fishburn, S Hahn, J Ranish - Molecular & Cellular Proteomics, 2012 - ASBMB
Knowledge of protein structures and protein-protein interactions is essential for
understanding biological processes. Chemical cross-linking combined with mass …

xComb: A cross-linked peptide database approach to protein− protein interaction analysis

A Panchaud, P Singh, SA Shaffer… - Journal of proteome …, 2010 - ACS Publications
We developed an informatic method to identify tandem mass spectra composed of
chemically cross-linked peptides from those of linear peptides and to assign sequence to …

Large-scale and targeted quantitative cross-linking MS using isotope-labeled protein interaction reporter (PIR) cross-linkers

X Zhong, AT Navare, JD Chavez, JK Eng… - Journal of proteome …, 2017 - ACS Publications
Quantitative measurement of chemically cross-linked proteins is crucial to reveal dynamic
information about protein structures and protein–protein interactions and how these are …

CrossWork: software-assisted identification of cross-linked peptides

MI Rasmussen, JC Refsgaard, L Peng, G Houen… - Journal of …, 2011 - Elsevier
The increased interest in chemical cross-linking for probing protein structure and interaction
has led to a large increase in literature describing new cross-linkers and search programs …