Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant.
Zhuo A ChenLutz FischerJürgen CoxJuri RappsilberPublished in: Molecular & cellular proteomics : MCP (2016)
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 BS(3) and isotope-labeled BS(3)-d4 revealed a number of observations: (1) Fully automated process using MaxQuant can quantify cross-links in our reference data set 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.
Keyphrases
- mass spectrometry
- deep learning
- machine learning
- high resolution
- high throughput
- gas chromatography
- liquid chromatography
- electronic health record
- high performance liquid chromatography
- big data
- molecular dynamics simulations
- capillary electrophoresis
- amino acid
- artificial intelligence
- emergency department
- magnetic resonance
- computed tomography
- small molecule
- magnetic resonance imaging
- tandem mass spectrometry
- binding protein
- pet ct
- drug induced
- protein protein