AlphaCross-XL: A Seamless Tool for Automated and Proteome-Scale Mapping of Cross-Linked Peptides Onto 3D Protein Structures

Sanjyot Vinayak Shenoy; Deeptarup Biswas; Arthur Zalevsky; Audrey Kishishita; Ayushi Verma; Ishan Upadhay; Yi He; Andrej Sali; Rosa Viner; Kamal Mandal; Sanjeeva Srivastava; Arun P Wiita

doi:10.1016/j.mcpro.2025.101057

AlphaCross-XL: A Seamless Tool for Automated and Proteome-Scale Mapping of Cross-Linked Peptides Onto 3D Protein Structures

Mol Cell Proteomics. 2025 Oct;24(10):101057. doi: 10.1016/j.mcpro.2025.101057. Epub 2025 Aug 19.

Authors

Affiliations

¹ Department of Mathematics, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
² Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
³ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
⁴ Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
⁵ Department of Aerospace Engineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
⁶ Thermo Fisher Scientific, San Jose, California, USA.
⁷ Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA. Electronic address: kamal.mandal@gbu.edu.in.
⁸ Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India. Electronic address: sanjeeva@iitb.ac.in.
⁹ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA; Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA. Electronic address: arun.wiita@ucsf.edu.

Abstract

Crosslinking mass spectrometry (XL-MS) is an exciting proteomics technology to capture native protein conformations in real time within biological systems. Historically, however, implementation of this technology has typically been limited to single purified recombinant proteins or in vitro-assembled protein complexes. These limitations are associated with inherent challenges in XL-MS analysis, including extremely low abundance of crosslinked (XL) peptides and complex deconvolution of XL peptide-derived spectral data. However, impressive recent developments in computation and instrumentation have now made it feasible to address biological questions using proteome-wide XL-MS analysis. Although some XL mapping software tools exist, these require manual input of specific Protein Data Bank structures at the single protein level and do not function at the high-throughput scale required to analyze datasets derived from thousands of proteins. To address this need, we therefore sought to develop a strategy enabling automated mapping of XL peptides onto the 3D structures of proteins, at a proteome-wide scale. Herein, we describe AlphaCross-XL, a first-in-class seamless computational tool for automated mapping of XL peptides onto the protein structures for intraprotein crosslinks and loop links. The AlphaCross-XL software first retrieves protein structures from the AlphaFold Protein Structure Database and maps all the identified crosslinks onto the 3D structure. It also calculates the Euclidian distance between the crosslinked residues and reports the violated and satisfied crosslink distances based on a user-defined distance threshold, which is visually discriminated by color in PyMOL. Last, the tool also supports further validation of user-submitted protein structures, which can include any computer-predicted protein structure and experimentally derived protein structures (i.e., from Protein Data Bank). AlphaCross-XL is available at https://github.com/sanjyotshenoy/alphacross-xl.

Keywords: AlphaFold; XL-MS; crosslinking mass spectrometry; mass spectrometry; proteomics; structural biology.

MeSH terms

Cross-Linking Reagents / chemistry
Humans
Mass Spectrometry / methods
Peptides* / chemistry
Protein Conformation
Proteome* / chemistry
Proteomics* / methods
Software*

Substances

Peptides
Proteome
Cross-Linking Reagents

Grants and funding

R01 CA290875/CA/NCI NIH HHS/United States