FragPipe in Chemoproteomics — Annotated Literature
ABPP / Covalent Profiling and Ligandability Mapping
Profiling the proteome-wide selectivity of diverse electrophiles
Zanon, P.R.A.; Yu, F.; Musacchio, P.Z.; Lewald, L.; Zollo, M.; Krauskopf, K.; Mrdović, D.; Raunft, P.; Maher, T.E.; Cigler, M.; Chang, C.J.; Lang, K.; Toste, F.D.; Nesvizhskii, A.I.; Hacker, S.M.; Nature Chemistry. 2025.
https://doi.org/10.1038/s41557-025-01902-z
Flagship FragPipe chemoproteomics study that established key concepts and workflows for modification-centric covalent proteomics analysis and served as a primary driver for FragPipe development in this domain. FragPipe was used for open searches to identify dominant modification masses, followed by mass-offset and closed searches to localize probe-derived adducts across residues. IonQuant-based quantification enabled residue-level assessment of covalent engagement and chemotype selectivity across diverse electrophiles.
Proteome-wide ligandability maps of drugs with diverse cysteine-reactive chemotypes
Tian, C.; Sun, L.; Liu, K.; et al., Nature Communications. 2025.
https://doi.org/10.1038/s41467-025-60068-x
Large-scale cysteine-reactive ligandability mapping across diverse drug-like electrophiles. FragPipe was used for mass-offset-based identification and localization of covalent adducts on cysteine residues, with IonQuant providing quantitative readouts of engagement. FragPipe enabled systematic comparison of chemotype selectivity and proteome-wide cysteine ligandability profiles.
A highly reactive cysteine-targeted acrylophenone chemical probe that enables peptide/protein bioconjugation and chemoproteomics analysis
Nuber, C.M.; et al., JACS Au. 2025.
https://doi.org/10.1021/jacsau.5c00692
Cysteine-directed activity-based chemoproteomics study introducing a highly reactive acrylophenone probe. FragPipe was used for modification-centric identification and localization of probe-derived adducts via mass-offset and closed searches, followed by IonQuant-based quantification to assess site-specific labeling efficiency and selectivity across the proteome.
Identification of covalent inhibitors of Staphylococcus aureus serine hydrolases important for virulence and biofilm formation
Upadhyay, T.; et al., Nature Communications. 2025;16:5046.
https://doi.org/10.1038/s41467-025-60367-3
Activity-based chemoproteomics study identifying covalent inhibitors of bacterial serine hydrolases relevant to virulence and biofilm formation. FragPipe served as the primary analysis platform for identification and quantification of probe-modified peptides, supporting multiple proteases, probe-derived variable mass modifications, and FDR-controlled validation with IonQuant-based quantification.
Proteome-wide covalent targeting of acidic residues with tunable N-aryl aziridines
Qiu, N.; et al., ChemRxiv. 2025.
https://doi.org/10.26434/chemrxiv-2025-clgct
Proteome-wide covalent ligand discovery targeting aspartate and glutamate residues. FragPipe was used for open and mass-offset searches to identify dominant adduct masses and localize acidic-residue modifications across the proteome, enabling systematic assessment of chemotype selectivity and residue targeting.
Redox and Cysteine Reactivity Profiling
Increased antioxidative defense and reduced advanced glycation end-product formation by metabolic adaptation in non-small-cell lung cancer patients
Tomin, T.; Honeder, S.E.; Liesinger, L.; Gremel, D.; Retzl, B.; Lindenmann, J.; Brcic, L.; Schittmayer, M.; Birner-Gruenberger, R.; Nature Communications. 2025;16:60326.
https://doi.org/10.1038/s41467-025-60326-y
Redox proteomics study comparing tumor and adjacent healthy lung tissue with a focus on cysteine redox state and advanced glycation-related modifications in human clinical samples. FragPipe was used for modification-aware peptide identification and quantitative analysis of chemically modified cysteine peptides, with IonQuant providing MS1-level quantification to support site-resolved redox comparisons across patient samples.
DIA-based label-free redox proteomics identifies prominent cysteine oxidations
Kobayashi, D.; et al., Journal of Proteome Research. 2025.
https://doi.org/10.1021/acs.jproteome.5c00339
Redox chemoproteomics workflow evaluated under DIA acquisition. FragPipe with MSFragger-DIA was used for modification-aware identification of oxidized cysteine peptides, enabling integration of redox-specific peptide identification with DIA-style quantitative analysis.
Photoproximity and Proximity Labeling
Energy-transfer photoproximity labelling in live cells using an organic cofactor
Crocker, L.B.; et al., Nature Chemistry. 2025.
https://doi.org/10.1038/s41557-025-01931-8
Photoproximity labeling strategy for proteome-wide interactome mapping in live cells. FragPipe was used for peptide identification and label-free quantification of proximity-labeled samples, supporting robust interactome comparisons across conditions.
Silicon-rhodamine-enabled identification for near-infrared light-controlled proximity labeling in vitro and in vivo
Wang, W.; Guo, H.; Yan, X.; et al., Nature Communications. 2025.
https://doi.org/10.1038/s41467-025-63496-x
Near-infrared light-controlled proximity labeling chemistry applied in vitro and in vivo. FragPipe was used for mass-offset-based identification and quantification of probe-derived modifications, enabling localization and comparison of proximity-labeled proteins across experimental conditions.
Spatiotemporally resolved mapping of extracellular proteomes via in vivo-compatible TyroID
Zhang, Z.; Wang, Y.; Lu, W.; et al., Nature Communications. 2025.
https://doi.org/10.1038/s41467-025-57767-w
Tyrosine-based proximity labeling strategy for extracellular proteome mapping. FragPipe supported peptide identification and label-free quantification of TyroID-labeled proteins, enabling spatiotemporal comparison of extracellular proteomes in complex biological contexts.
DIA-Enabled and High-Throughput Chemoproteomics Workflows
TMT-based multiplexed (chemo)proteomics on the Orbitrap Astral Mass Spectrometer
He, Y.; Yang, K.; Li, S.; Zelisko, M.; Zhu, Y.; Gurdal, S.; Li, L.; Molecular & Cellular Proteomics. 2025.
https://doi.org/10.1016/j.mcpro.2025.100968
Workflow-focused chemoproteomics study demonstrating high-throughput analysis on the Orbitrap Astral platform. FragPipe was used as the primary analysis environment for identification and quantitative reporting in large-scale chemoproteomics datasets acquired with DIA-style strategies.
Chemoenzymatic and Enzyme-Driven PTM Chemoproteomics
Dynamic in vivo mapping of the methylproteome using a chemoenzymatic approach
Farhi, J.; et al., Journal of the American Chemical Society. 2025.
https://doi.org/10.1021/jacs.4c08175
Chemoenzymatic chemoproteomics strategy for proteome-wide mapping of protein methylation in cells and in vivo. FragPipe was used for modification-centric database searching with variable mass shifts corresponding to chemically installed methylation handles, enabling unbiased discovery and residue-level localization of methylated peptides.
Cellular consequences, citrullination substrates, and antigenicity resulting from wild-type and targeted PAD4 on cell surfaces
Kong, S.; Peters-Clarke, T.M.; Delaveris, C.S.; Phojanakong, P.; Steri, V.; Wells, J.A.; bioRxiv. 2026.
https://doi.org/10.64898/2026.01.05.696859
Chemoenzymatic profiling of protein citrullination driven by PAD4 activity. FragPipe was used for modification-aware identification and quantification of citrullinated peptides, enabling site-resolved mapping of citrullination substrates and their biochemical consequences.
Affinity-Based and Molecular Glue Interactomics
ProxiCapture reveals context-dependent CRBN interactome landscape of molecular glue degraders
Kazi, R.; et al., bioRxiv. 2026.
https://doi.org/10.64898/2026.01.05.697692
Affinity-based chemoproteomics approach for molecular glue-dependent interactome profiling. FragPipe label-free quantification workflows with match-between-runs were used to quantify CRBN-associated proteins across biological contexts, enabling identification of context-dependent molecular glue interactions.