Xilmass is a novel algorithm to identify cross-linked peptides. Xilmass uses a new way to compose the search database and then scores each experimental spectrum against complete theoretical spectra. Xilmass can handle for both labeled and unlabeled cross-linkers.
Chemical cross-linking coupled with mass spectrometry (XL-MS) plays an important role in unravelling protein interactions and supports the determination of protein structure. This technique enables the study of proteins that are non-crystallizable or have a protein size above 50 kDa. The identification of the resulting MS/MS spectra from XL-MS experimennt is a computationally challenging task. First, the search space is tremendously increased due to considering all peptide-to-peptide combinations. Second, these experimental MS/MS spectra are more complex than a MS/MS spectrum derived from a single peptide; because these spectra contain fragment ions from two peptides. Third, the peptide mixture contains only few cross-linked peptides compared to single peptides in the mixture. In addition, there is a high dynamic range of cross-linked products due to the fact that cross-linking can occur between residues of the same protein (intra-protein cross-linked peptides), between residues of different proteins (inter-protein cross-linked peptides), or even between two cross-linked peptides (higher order cross-liked peptides). Although several computational approaches are available for the identification of spectra from cross-linked peptides, there still remains a room for improvement. Some of the available approaches are based on the linearization of cross-linked peptide-pairs or the usage of peptide labeling to facilitate cross-linked peptide identification. Here, we introduce Xilmass, a novel algorithm to identify cross-linked peptides that uses a new way to construct the search database and scores each experimental spectrum against each of the complete theoretical spectra.
Xilmass provides a user-friendly a graphical user interface (GUI) to run cross-linked peptides identifications. Additionally, it also offers the command line (CLI) version for the automation.
If you have any question or suggestion about Xilmass, please contact us immediately!
We are happy to annouce that Xilmass has been recently accepted!
The original data set that was used for the Xilmass publication is avaliable at PRIDE with the accession number of PXD003880.
If you perform your search to identify cross-linked peptides by Xilmass, please include the reference above.
Download the latest version of Xilmass algorithm here.
You can run Xilmass as CLI or our user-friendly GUI.
See the wiki.