PT  - JOURNAL ARTICLE
AU  - Zhuo A. Chen
AU  - Lutz Fischer
AU  - Jüergen Cox
AU  - Juri Rappsilber
TI  - Quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers and MaxQuant
AID  - 10.1101/055970
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 055970
4099  - http://biorxiv.org/content/early/2016/05/30/055970.short
4100  - http://biorxiv.org/content/early/2016/05/30/055970.full
AB  - The conceptually simple step from cross-linking/mass spectrometry (CLMS) to quantitative cross-linking/mass spectrometry (QCLMS) is compounded by technical challenges. Currently, quantitative proteomics software is tightly integrated with the protein identification workflow. This prevents automatically quantifying other m/z features in a targeted manner including those associated with cross-linked peptides. Here we present a new release of MaxQuant that permits starting the quantification process from an m/z feature list. Comparing the automated quantification to a carefully manually curated test set of cross-linked peptides obtained by cross-linking C3 and C3b with BS3 and isotope-labeled BS3-d4 revealed a number of observations: 1) Fully automated process using MaxQuant can quantify cross-links in our reference dataset with 68% recall rate and 88% accuracy. 2) Hidden quantification errors can be converted into exposed failures by label-swap replica, which makes label-swap replica an essential part of QCLMS. 3) Cross-links that failed during automated quantification can be recovered by semi-automated re-quantification. The integrated workflow of MaxQuant and semi-automated assessment provides the maximum of quantified cross-links. In contrast, work on larger data sets or by less experienced users will benefit from full automation in MaxQuant.BS3Bis[sulfosuccinimidyl] suberateCLMSCross-linking/mass spectrometryMS1the initial mass-to-charge-ratio (m/z) spectrum collected for all components in a sample.QCLMSQuantitative cross-linking/mass spectrometry