Unknown

Dataset Information

0

MS Annika: A New Cross-Linking Search Engine.


ABSTRACT: Cross-linking mass spectrometry (XL-MS) has become a powerful technique that enables insights into protein structures and protein interactions. The development of cleavable cross-linkers has further promoted XL-MS through search space reduction, thereby allowing for proteome-wide studies. These new analysis possibilities foster the development of new cross-linkers, which not every search engine can deal with out of the box. In addition, some search engines for XL-MS data also struggle with the validation of identified cross-linked peptides, that is, false discovery rate (FDR) estimation, as FDR calculation is hampered by the fact that not only one but two peptides in a single spectrum have to be correct. We here present our new search engine, MS Annika, which can identify cross-linked peptides in MS2 spectra from a wide variety of cleavable cross-linkers. We show that MS Annika provides realistic estimates of FDRs without the need of arbitrary score cutoffs, being able to provide on average 44% more identifications at a similar or better true FDR than comparable tools. In addition, MS Annika can be used on proteome-wide studies due to fast, parallelized processing and provides a way to visualize the identified cross-links in protein 3D structures.

SUBMITTER: Pirklbauer GJ 

PROVIDER: S-EPMC8155564 | biostudies-literature |

REPOSITORIES: biostudies-literature

Similar Datasets

2021-05-27 | PXD022772 | Pride
| S-EPMC11165154 | biostudies-literature
| S-EPMC6030971 | biostudies-literature
| S-EPMC6042696 | biostudies-literature
| PRJEB4647 | ENA
| S-EPMC8187950 | biostudies-literature
| S-EPMC2749473 | biostudies-literature
| S-EPMC4301746 | biostudies-literature
2019-07-23 | PXD014705 |
| S-EPMC2401330 | biostudies-literature