Biology subjects

Fischer, L.

Publications and source records attributed to Fischer, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Mechanochemical synchronization of force oscillations in connective tissue models

Cells in a tissue coordinate their behavior collectively by mechanical and chemical feedback with their surroundings. To study how such feedback mechanisms interact, we embed multicellular spheroids from mouse and primary human fibroblasts of different origin in 3D collagen matrices. Immediately after embedding, spheroids apply steadily increasing, radially symmetric, inward-directed forces to the surrounding matrix. Typically, within a few hours, collective force oscillations emerge with an average time interval of {approx}30 min. Similar force oscillations also arise in engineered, parallel-aligned microtissues attached to flexible pillars. Force oscillations propagate between neighboring cells as a mechanical wave, accompanied by calcium waves that travel at comparable speeds of several hundred m/min. Blocking gap junctions or mechanosensitive Piezo1 channels impairs these oscillations, indicating that calcium signaling contributes to their propagation. Their amplitude and frequency are regulated by integrin-mediated feedback in actin-rich protrusions and by ERK signaling, which also controls collective invasion into the surrounding matrix. Neighboring spheroids mechanically synchronize their force oscillations in phase and frequency over distances of up to {approx}2 mm without direct contact. Together, our results show that oscillatory mechanochemical feedback enables multicellular systems to coordinate force generation and invasive migration across cellular and millimeter length scales in 3D matrices.

biophysics↗

bioRxiv2026

Durable suppression of viremia by lipid nanoparticle-formulated RNA encoding for a highly potent HIV-1 neutralizing antibody

Recombinant broadly neutralizing antibodies (bNAbs) are promising tools to treat and prevent HIV-1 infection but are associated with manufacturing challenges. To overcome this limitation, we encoded the potent bNAb 1-18-LS on RNA (1-18-LS RibobNAb) for delivery via lipid nanoparticles (LNPs). Indicating high in vivo antibody expression, a 30 ug RNA-LNP intravenous injection resulted in an average peak 1-18-LS RibobNAb serum concentration of 1,061 ug/mL in human neonatal Fc receptor-transgenic mice. Notably, weekly 30 ug RNA-LNP doses maintained higher trough bNAb levels than 500 ug protein injections. Highlighting potent antiviral activity, RNA-LNP-mediated 1-18-LS RibobNAb monotherapy of viremic HIV-1YU2-infected humanized mice resulted in durable HIV-1 suppression without emerging viral escape. Importantly, 1-18-LS RNA-LNP treatment also fully controlled infection after interruption of antiretroviral therapy in humanized mice infected with different patient-derived polyclonal HIV-1 isolates. Our findings provide a proof-of-principle for effective RNA-mediated bNAb immunotherapy of HIV-1 infection.

immunology↗

bioRxiv2026

Deoxyribonucleotide dephosphorylation by VENOSA4 supports organellar genome replication in plants

The replication of the three genomes in plant cells during germination is a complex process, which requires a high degree of coordination between the genome-containing compartments: the nucleus, mitochondria, and chloroplasts. The first committed step for the de novo synthesis of deoxynucleoside triphosphates (dNTPs), the building blocks for DNA replication, occurs exclusively in the cytosol. A major unresolved question is how an adequate supply of dNTPs for the organelles is achieved. Here, we show that VENOSA4 (VEN4), a dNTP triphosphohydrolase, is critical for this process in Arabidopsis thaliana. Using isotope feeding combined with mass spectrometry analysis, we demonstrate that VEN4 converts most de novo-synthesized dNTPs to deoxynucleosides (dNs). Preventing this conversion by VEN4 mutation strongly diminishes both cpDNA and mtDNA amounts, but these can be partially rescued by the application of exogenous dNs. Hence, the dNTP catabolic activity of VEN4 ensures that sufficient DNA precursors in form of dNs reach the chloroplasts and the mitochondria to be salvaged there to dNTPs for DNA synthesis. This seemingly counterintuitive coupling of de novo synthesis, dNTP hydrolysis, and salvage may provide a mechanism to control DNA precursor allocation between cellular compartments through selective transport and metabolic trapping.

plant biology↗

bioRxiv2026

Mesoscale medial temporal lobe connectivity patterns relate to tau pathology and memory in older adults

The medial temporal lobe (MTL) is crucial for episodic memory. Tau pathology is a hallmark of Alzheimer's disease (AD) and accumulates in layer-specific patterns in the MTL during aging. It is, however, unclear whether early AD pathology relates to mesoscale network signatures distinct from non-pathological aging. To address this gap, we acquired 7 Tesla submillimeter-resolution resting-state fMRI, plasma-based AD biomarkers, glial fibrillary acidic protein (GFAP) levels, APOE genotype, regional [18F]PI-2620 tau PET burden, and longitudinal episodic memory data in 75 cognitively unimpaired older adults. Older age was associated with lower perirhinal-hippocampal connectivity and lower network segregation, whereas higher plasma-based AD pathology was associated with higher perirhinal-hippocampal connectivity. Furthermore, temporal-lobe tau burden was related to altered connectivity patterns in tau-vulnerable MTL subfields and layers, dependent on GFAP levels. Retrosplenial tau burden was associated with higher hippocampal-retrosplenial connectivity consistent with tau spread along canonical hippocampal output pathways. Finally, higher connectivity within the hippocampus attenuated the negative association between temporal-lobe tau burden and memory performance but predicted unfavorable memory trajectories. Our findings show differential associations of age and AD pathology with mesoscale MTL-connectivity patterns. Importantly, increased hippocampal connectivity may support memory function in the short term while contributing to subsequent memory decline.

neuroscience↗

bioRxiv2026

KlinkPPI: Single Point of Access to Protein-Protein Interactions Across Databases

Protein-protein interaction (PPI) information is distributed across resources that differ in organism coverage, identifier systems, evidence models, confidence scores and access mechanisms, so assembling and comparing evidence for a protein requires source-specific queries, identifier conversion and extensive post-processing. We present KlinkPPI, a web server that retrieves, compares and exports PPI evidence from STRING, BioGRID, IntAct, CORUM, HuRI and Predictomes from a single query. KlinkPPI accepts UniProtKB accessions, NCBI Gene and Ensembl identifiers and gene names, and performs taxonomy-aware mapping to a common identifier space. Users can query individual proteins across all resources available for an organism, or retrieve organism-wide interaction sets. Results are presented per source so that database-specific evidence, annotations and confidence values are retained, while an integrated view exposes coverage and agreement between resources. KlinkPPI deliberately does not merge heterogeneous confidence scores, nor collapse functional associations, complex co-membership, binary interactions and structural predictions into a single consensus network. Results can be exported in PSI-MI TAB 2.8-compatible or Apache Parquet format with user-selected evidence fields. KlinkPPI is freely available at https://rappsilberlab.org/KlinkPPI/ and the source code at https://github.com/Rappsilber-Laboratory/KlinkPPI. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/742057v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@12dcaceorg.highwire.dtl.DTLVardef@15d9d0aorg.highwire.dtl.DTLVardef@f0fc39org.highwire.dtl.DTLVardef@13f172e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

5' Complementarity-Mediated End Joining (5'CMEJ) DNA repair

How cells choose among competing DNA double-strand break repair pathways, and whether the choice differs across the tree of life, remains poorly understood, limiting prediction of CRISPR editing outcomes, particularly in plants. Through a meta-analysis of 2,098 SpCas9 target sites across plants, animals, and an alga, we show that deletion patterns reflect cell-division status rather than taxonomic origin: dividing cells favour polymerase Theta-Mediated End Joining (TMEJ), whereas non-dividing cells employ a largely overlooked pathway, 5 Complementarity-Mediated End Joining (5CMEJ). Unlike the known resection-dependent pathways, which use 3 overhangs, 5CMEJ exploits the 5 overhangs generated by staggered SpCas9 cleavage.

molecular biology↗

bioRxiv2026

CRISPR-Cas9 Induced Knockout of BEL5 in Tetraploid Potato: Optimized Methodology via Repeated de novo Regeneration and Impact on Tuberization

CRISPR-Cas9 has emerged as a powerful tool for targeted genome editing in plants; however, its application in tetraploid potato (Solanum tuberosum ssp. tuberosum) remains challenging due to its vegetative propagation and complex highly heterozygous genome. Availability of whole-genome sequence data for the specific genotype is crucial to ensure complete knockout of all alleles of target genes while minimizing off-target mutations. In this study, using the tetraploid potato cultivar Desiree, we report, a complete CRISPR-Cas9-mediated knockout of the BEL5 gene, encoding a transcription factor, known as one of the key regulators driving tuber formation. We employed Agrobacterium-mediated transformation and demonstrated that repeated de novo regeneration could improve editing efficiency by promoting emergence of new mutations. BEL5 knockout plants exhibited a delayed onset of tuberization under inductive short-day conditions in hydroponics; however, their overall tuber yields were comparable to wild type plants. Based on our results, we propose a regulatory role of BEL5 in the timing of tuber onset but, unexpectedly, its dispensability for tuber development in modern cultivated potato. Besides providing functional insight into the BEL5 role in potato, this study includes a methodological approach for efficient CRISPR-Cas9 gene editing in this vegetatively propagated polyploid crop, along with strategies for detecting mutations in genes that lack clear phenotypic manifestation.

plant biology↗

bioRxiv2026

RNA-Encoded PGT121-LS Anti-HIV Antibody: Comprehensive Preclinical Characterization and Translational Pharmacokinetics

Human Immunodeficiency Virus (HIV)-1 broadly neutralizing antibodies (bNAbs) have demonstrated clinical efficacy, but face manufacturing challenges associated with recombinant protein production and purification. Here, we present a ribonucleic acid (RNA)-encoded bNAb (RibobNAb) platform that enables in vivo antibody production of the clinically validated bNAb PGT121 via lipid nanoparticle (LNP) delivery, supporting rapid evaluation of Fc variants (LS, del294, LS-del294) in vitro and in vivo. We confirmed expression, sub-nanomolar HIV-1 Env binding, and potent neutralization across all RibobNAb variants in vitro. In mice, single RNA-LNP administrations yielded in vivo expression of all RibobNAb variants, with PGT121-LS exhibiting a prolonged half-life compared with PGT121. In non-human primates (NHPs), a single intravenous administration of PGT121-LS RNA-LNP was well tolerated without anti-drug antibody (ADA) formation over 180 days and resulted in PGT121-LS half-lives comparable to the reference protein. Single intramuscular administration showed RibobNAb expression but resulted in ADA development from Day 14 onwards and lower bioavailability. In vivo-expressed PGT121-LS RibobNAb retained identical antiviral functionality to PGT121-LS reference protein. An NHP pharmacokinetics model integrating RNA transfection and translation dynamics enabled allometric scaling and first-in-human dose prediction. We highlight RibobNAbs as an alternative to conventional purified protein antibodies for rapid development of bNAb-based therapeutic strategies. O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/734219v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@141319forg.highwire.dtl.DTLVardef@120caadorg.highwire.dtl.DTLVardef@1da2782org.highwire.dtl.DTLVardef@158064d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

immunology↗

bioRxiv2026

RapCluster: Bridging the Reproducibility Gap in Clustering Analysis

Clustering is ubiquitous across science, yet a text-mining audit of 736,399 open-access articles identified as using clustering (2000-2025) reveals common practice leaves key parameters undocumented or untuned, contributing to the reproducibility crisis in science. We developed an interactive web platform featuring 11 widely adopted clustering algorithms to enable transparent clustering analysis and reporting, aligning practical use with best practices in computational research. Code availabilityThe browser-based clustering analysis platform RapCluster is available for download at https://github.com/lutfia95/RapCluster under MIT License and accessible at https://rappsilberlab.org/rapcluster/ The web version is capacity-limited to 8 GB of memory (ca. 12,000 candidates with 130 features). All source codes used for the analysis are included with the publication.

bioinformatics↗

bioRxiv2026

Paralogous guanine deaminases likely acquired from bacteria by horizontal gene transfer promote purine homeostasis in Caenorhabditis elegans

Disruptions in purine metabolism contribute to a range of human diseases, from rare genetic disorders such as Lesch-Nyhan syndrome and xanthinuria to common conditions including gout and cancer. To better understand the metabolic networks that regulate purine homeostasis, we developed a Caenorhabditis elegans model of xanthine dehydrogenase (xdh-1) deficiency. Remarkably, xdh-1 mutant animals form rare xanthine stones, recapitulating a hallmark of human xanthinuria. To uncover genetic regulators of purine homeostasis, we performed a forward genetic screen for mutations that exacerbate xanthine stone formation in xdh-1 mutants. This approach identified multiple loss-of-function alleles in a previously uncharacterized gene, which we named gda-1. We show that gda-1 encodes an intestinal guanine deaminase that mediates a key enzymatic step in purine catabolism. The C. elegans genome also encodes a paralog, gda-2, which shares guanine deaminase activity but is expressed in distinct tissues. While gda-2 can compensate for gda-1 loss in guanine metabolism, the two genes exhibit non-redundant roles in regulating xanthine accumulation and stone formation. Interestingly, our evolutionary analyses suggest that gda-2 was acquired by nematodes via horizontal gene transfer from bacteria. These findings reveal a spatially regulated purine catabolism pathway in C. elegans and suggest that acquisition of bacterial genes has shaped a core nematode metabolic network.

genetics↗

bioRxiv2026

The in-vivo microstructural profile of human hippocampal subfield CA1 and its relation to memory performance

The hippocampal CA1 subregion supports learning, memory formation, and spatial navigation. Although its three-layered architecture has been described in ex-vivo investigations, the in-vivo microstructural profile of CA1 and its relation to individual variations in memory performance remain poorly characterized. In this study, we used ultra-high field structural MRI at 7 Tesla to investigate the depth-dependent myelination patterns (measured by quantitative T1) of CA1 in younger adults, their relation to the local arterial architecture, and their association with individual differences in cognitive functions, specifically memory performance. Results show that left and right CA1 present depth-dependent patterns of myelination, with the outer and inner compartments showing higher myelination than the middle compartment. No significant relationship between layer-specific myelination of CA1 and distance to the nearest artery was observed. Right CA1 was found to be more myelinated than left CA1. Pairwise correlations and regression models showed that higher left CA1 myelination is linked to higher accuracy in object localization. Together, our data demonstrates the feasibility of describing the three layered myelin architecture of CA1 in vivo, and provides information on how alterations in the architecture of CA1 may relate to alterations in cognitive performance in younger adults.

neuroscience↗

bioRxiv2026

Transcription elongation factor SPT6L recruits ARGONAUTE to guide mRNA cytosine methylation preventing premature termination in plants

In plants, an essential component of the RNA Polymerase II (Pol II) complex, SPT6L, contains a unique C-terminal ARGONAUTE binding domain - AGO-hook. Although it has been recently shown that SPT6L is also part of the Pol V complex, where its AGO-hook might participate in the RNA-directed DNA methylation pathway, several lines of evidence suggest that the AGO-hook should also have a function in the Pol II complex. Here we demonstrate that in Arabidopsis thaliana, SPT6L recruits AGO4 via the AGO-hook domain, independently of Pol V. Using direct RNA sequencing, we show that this interaction is connected with guided deposition of 5-methylcytosine (m5C) on Pol II transcripts. The role of AGO4 in m5C guidance was further supported by increased methylation of GFP transcripts after their targeting by sRNAs in tobacco BY-2 cells. Removing the SPT6L AGO-hook (spt6l{Delta}Ah) in A. thaliana resulted in the hypomethylation of specific m5C sites, mimicking even stronger RNA hypomethylation observed in the ago4 mutant. Native elongating transcript sequencing revealed that impaired targeting of m5C methylation in the spt6l{Delta}Ah mutant was accompanied by Pol II stalling downstream of hypomethylated cytosines. Furthermore, this stalling appeared to be associated with premature transcription termination, which we also detected in published transcriptomes of mutants lacking AGO4, as well as TRM4B that is the major RNA m5C methyltransferase. Our findings uncover a novel "guide-and-modify" mechanism in which SPT6L integrates sRNA-directed epitranscriptomic marking with transcription elongation, ensuring proper mRNA termination.

plant biology↗

bioRxiv2026

Inosine Monophosphate Dehydrogenases are key players for functional development in Arabidopsis

In plants, nucleotide de novo synthesis is required throughout development to provide building blocks for the synthesis of DNA, RNA and nucleotide-derived cofactors. Inosine Monophosphate Dehydrogenases (IMPDH) are key enzymes in de novo guanylate synthesis. The genome of Arabidopsis thaliana encodes two IMPDHs and we identify IMPDH2 as the major isoform, being enzymatically active in the plant cytosol. Bimolecular fluorescence complementation (BIFC) analysis suggests that IMPDH1 and IMPDH2 interact with themselves and with Cytidine Triphosphate Synthetase (CTPS) isoforms, connecting purine and pyrimidine metabolism. Nucleotide quantification identifies IMPDH2 as bottleneck in guanylate biosynthesis, and plants lacking this isoform suffer from nucleotide imbalance and limitation, causing reductions in ribosomal RNAs by reducing Target of Rapamycin (TOR) activity. Impaired photosynthesis and growth were further consequences thereof. In contrast, strong overexpression of IMPDH1 supported growth and led to altered organ development in 10% of corresponding plants presumably due to altered auxin metabolism during embryo development. Significance statementThis study reveals that Inosine Monophosphate Dehydrogenase 2 (IMPDH2) is required for early Arabidopsis development and growth. Knock-out mutants exhibit reduced amounts of metabolites (e.g. XMP, GMP, GTP) accompanied by reduced expression of genes in the GO-Terms Ribosome and Photosynthesis at seedling stage. This leads to reduced chlorophyll levels, impaired photosynthesis, and reduced growth. Marked overexpression of IMPDH1 provoked abnormal organ development in 10% of cases presumably due to altered auxin metabolism.

plant biology↗

bioRxiv2025

MetaXtract: Extracting Metadata from Raw Files for FAIR Data Practices and Workflow Optimisation

Mass spectrometry (MS) experiments generate rich acquisition metadata that are essential for reproducibility, data sharing, and quality control (QC). Because these metadata are typically stored only in vendor-specific formats, they often remain difficult to access. MetaXtract is a lightweight tool that extracts detailed parameters directly from Thermo Fisher raw files and exposes them in structured, tabular formats. By capturing sample information, LC-MS method settings, and scan-level metrics such as retention time, total ion current, and ion injection time, MetaXtract increases transparency and ensures that essential acquisition details accompany published data and results in easy readable form. This supports FAIR data practices by improving the findability, accessibility, interoperability, and reusability of MS datasets after converting them to other formats, thereby increasing the value of deposition in public repositories. The importance of such metadata accessibility was recently highlighted by the crosslinking mass spectrometry community in efforts to advance FAIR data principles, and it extends to MS-based omics approaches more broadly. Importantly, MetaXtract enables search-free, near real-time performance monitoring by relying on acquisition-side signals, providing actionable indicators immediately after data acquisition rather than after database searching. This also caters for laboratory or depository internal streamlined QC and troubleshooting through integration into automated pipelines. By embedding acquisition parameters into routine data handling, MetaXtract strengthens reproducibility, optimises method development, and supports large-scale applications, including machine learning and secondary data analysis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/687968v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@d835e6org.highwire.dtl.DTLVardef@babfaforg.highwire.dtl.DTLVardef@7e9d69org.highwire.dtl.DTLVardef@907993_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMetadata extraction from Thermo Fisher raw files C_LIO_LIEnhanced findability, accessibility, interoperability, and reusability of deposited data C_LIO_LIIntegration into workflows via GUI and command-line modes C_LIO_LITroubleshooting support by visualizing MS1/MS2 scan details C_LIO_LIIndexed MS1/MS2 peak list export enabling machine learning workflows C_LI AvailabilityMetaXtract is available for free download as open-source software at https://github.com/Rappsilber-Laboratory/MetaXtract, the software is licensed under the Apache-2.0 license.

bioinformatics↗

bioRxiv2025

Longitudinal functional connectivity during rest and task is differentially related to Alzheimer's pathology and episodic memory in older adults

Changes in functional connectivity (FC) strength involving the medial temporal lobe (MTL) and posteromedial cortex (PMC) are related to early Alzheimers pathology and alterations in episodic memory performance in cognitively unimpaired older adults, but their dynamics remain unclear. We examined how longitudinal changes in FC involving MTL and PMC during resting-state, episodic memory encoding, and retrieval relate to subsequent amyloid- and tau- PET burden, longitudinal episodic memory performance, and the APOE4 genotype in 152 cognitively unimpaired older adults from the PREVENT-AD cohort. We found APOE4- and fMRI paradigm-dependent associations of change in FC strength with pathology burden and change in episodic memory performance. Decreasing FC over time, or "hypoconnectivity", within PMC during rest in APOE4 carriers and during retrieval in APOE4 non-carriers was related to more amyloid and tau, respectively. Conversely, increasing FC over time, or "hyperconnectivity", within MTL during encoding in APOE4 carriers and between MTL and PMC during retrieval independent of APOE4 status was related to more tau. Further, increasing FC between MTL and PMC during rest, unlike during encoding, was beneficial for episodic memory. Our study highlights that pathology-related episodic memory network changes manifest differently during rest and task and have differential implications for episodic memory trajectories.

neuroscience↗

bioRxiv2025

Assessment of Reported Error Rates in Crosslinking Mass Spectrometry

We benchmarked eight software tools in crosslinking mass spectrometry (MS) to evaluate their accuracy in detecting protein-protein interactions. Whereas about half performed reliably, others reported up to 31-fold more false interactions than indicated by their reported false discovery rates. During this community-driven effort, we helped correct one of the poorer-performing tools. Our findings demonstrate that, with robust algorithms, crosslinking MS can deliver highly dependable insights into biological systems.

bioinformatics↗

bioRxiv2024

Differential effects of aging, Alzheimer's pathology, and APOE4 on longitudinal functional connectivity and episodic memory in older adults

INTRODUCTIONBoth aging and Alzheimers disease (AD) affect episodic memory networks. How this relates to region-specific early differences in functional connectivity (FC), however, remains unclear. METHODSWe assessed resting-state FC strength in the medial temporal lobe (MTL) - posteromedial cortex (PMC) - prefrontal network and cognition over two years in cognitively normal older adults from the PREVENT-AD cohort. RESULTSFC strength within PMC and between posterior hippocampus and inferomedial precuneus decreased in "normal" aging (amyloid- and tau-negative adults). Lower FC strength within PMC was associated with poorer longitudinal episodic memory performance. Increasing FC between anterior hippocampus and superior precuneus was related to higher baseline AD pathology. Higher FC strength was differentially associated with memory trajectories depending on APOE4 genotype. DISCUSSIONFindings suggest differential effects of aging and AD pathology on longitudinal FC. MTL-PMC hypoconnectivity was related to aging and cognitive decline. Furthermore, MTL-PMC hyperconnectivity was related to early AD pathology and cognitive decline in APOE4 carriers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/627967v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@12c0cc9org.highwire.dtl.DTLVardef@fb7c6borg.highwire.dtl.DTLVardef@a56bdforg.highwire.dtl.DTLVardef@4d1773_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO A) "Normal aging" is characterized by a longitudinal decrease in functional connectivity. B) Cognitively unimpaired older adults with more Alzheimers pathology at baseline (measured via cerebrospinal fluid) exhibit a longitudinal increase in functional connectivity. C_FIG

neuroscience↗

bioRxiv2024

Prosit-XL: enhanced cross-linked peptide identification by accurate fragment intensity prediction to study protein-protein interactions and protein structures

It has been shown that integrating peptide property predictions such as fragment intensity into the scoring process of peptide spectrum match can greatly increase the number of confidently identified peptides compared to using traditional scoring methods. Here, we introduce Prosit-XL, a robust and accurate fragment intensity predictor covering the cleavable (DSSO/DSBU) and non-cleavable cross-linkers (DSS/BS3), achieving high accuracy on various holdout sets with consistent performance on external datasets without fine-tuning. Due to the complex nature of false positives in XL-MS, a novel approach to data-driven rescoring was developed that benefits from Prosit-XLs predictions while limiting the overestimation of the false discovery rate (FDR). We first evaluated this approach using two ground truth datasets that demonstrate the accurate and precise FDR estimation. Second, we applied Prosit-XL on a proteome-scale dataset, demonstrating an up to [~]3.4-fold improvement in PPI discovery compared to classic approaches. Finally, Prosit-XL was used to increase the coverage and depth of a spatially resolved interactome map of intact human cytomegalovirus virions, leading to the discovery of previously unobserved interactions between human and cytomegalovirus proteins.

bioinformatics↗