Antibodyomics

50 workflows · 2006–2026

Antibodyomics: Antibody and antibody-repertoire sequencing, where the variable regions are by definition absent from any reference proteome. 50 catalogued workflows and 62 papers.

Antibody and antibody-repertoire sequencing, where the variable regions are by definition absent from any reference proteome.

Workflows 50
Papers 62
Authors 361
Active 2006-05-01 to 2026-09-01

Workflows (50)

  • Anti-OX40L mAb de novo sequencing (2006): Full-length de novo sequencing of a monoclonal antibody raised against OX40 ligand, from overlapping proteolytic and chemical digests read by mass spectrometry and cross-checked by Edman degradation.
  • Automated mAb de novo (Bandeira SPS) (2008): Landmark Nat Biotech 2008 paper by Bandeira, Pham, Pevzner, Arnott & Lill: applies Shotgun Protein Sequencing (SPS), that is MS/MS spectral assembly, end-to-end to a monoclonal antibody, recovering both chains without any prior sequence.
  • Camelid VHH top-down sequencing (2010): Determines the primary structure of a 13.6 kDa camelid single heavy chain antibody by MALDI-TOF/TOF top-down analysis, recovering most of the sequence from the intact protein rather than from peptides.
  • ABRF-PSRG 2010 antibody top-down de novo sequencing (2010): Sequenced the N- and C-terminal regions of both chains of the ABRF-PSRG 2010 study antibody by MALDI in-source decay top-down de novo sequencing.
  • Immunoglobulin peptide biomarker profiling (2010): Immunoglobulin peptides themselves used as biomarkers of an immune response, rather than the antigens they bind. Rats were immunised with one of two purified antigens and immunoglobulins from pre- and post-immune sera were profiled by nano-LC on an LTQ-Orbitrap with top-5 data-dependent fragmentation, giving 684 peptides differentially present between the treatment groups and cluster separation of the two. Sequences were obtained for 44% of spectral features by combining Mascot database search with de novo sequencing in PEAKS Studio 5.1, merged in Progenesis, which keeps the best-scoring sequence per feature. The authors state the de novo half was essential, because immunoglobulins are poorly represented in sequence databases. The shared peptides found across animals indicate that repertoire development is not fully random but under selection pressure favouring the best-binding sequences.
  • CDR peptide biomarker sequencing (2011): Tests detection of specific antibody CDR peptides in serum IgG backgrounds by Orbitrap MS, de novo sequencing half of the detectable adalimumab CDR peptides at attomole levels.
  • Template proteogenomic antibody resurrection (2011): Recovers the sequence of an anti-lymphotoxin-alpha mouse hybridoma antibody whose genetic material was lost after a decade in storage, by template proteogenomic de novo sequencing of the stored ascites, then reverse-engineers the gene.
  • Anti alpha-synuclein mAb sequencing (2012): The primary sequence of a monoclonal antibody against alpha-synuclein was determined de novo by mass spectrometry combining ion-trap CID and HCD fragmentation.
  • High-mass light chain germline phenotype (2015): De novo bottom-up sequencing of a monoclonal light chain showed that a subset of kappa and lambda germline sequences with CDR insertions explains a higher-mass light-chain phenotype in serum.
  • Phage display plus de novo mAb reverse engineering (2016): Combines mass-spectrometry de novo sequencing of antibody variable domains with small phage-displayed libraries and antigen-binding selection to resolve ambiguous CDR residues, recovering functional Fabs for two anti-CD137 antibodies.
  • Astrovirus-neutralizing antibody resurrection (2016): Sequences a human astrovirus-neutralizing monoclonal antibody de novo and re-expresses it, addressing the common case where a useful antibody exists as protein but its sequence and cell line do not.
  • Native antibody de novo MS/MS (2017): De novo MS/MS sequencing workflow for native human antibodies.
  • SpotLight proteomics (2017): Combines de novo MS/MS sequencing of enriched antibodies and co-extracted proteins with label-free quantification of the new peptides, uncovering a hidden blood proteome useful for patient stratification.
  • Anti-CD34 mAb sequencing and humanization (2017): De novo protein sequencing of QBEND/10, a mouse monoclonal against the haematopoietic progenitor antigen CD34, followed by humanization and in vitro testing of the resulting antibody on endothelial tube formation.
  • Antibody de novo sequencing chapter (2017): Book chapter on proteomic de novo sequencing of monoclonal antibodies when the hybridoma or its DNA sequence is unavailable or unreliable.
  • CHO C-terminal Fc-extension discovery (2018): De novo sequencing of a 1177 Da Fc impurity revealed an unexpected splicing-derived extension, fixed by changing the glycine codon.
  • GM-CSF autoantibody proteogenomics (2020): Analyses GM-CSF autoantibodies from an autoimmune alveolar proteinosis patient by TIMS-TOF proteogenomics, confirming CDR3 to FR4 peptides by de novo sequencing.
  • Capillary-electrophoresis mAb sequencing (2020): Reaches complete monoclonal antibody sequence coverage by pairing the usual LC-MS/MS with capillary electrophoresis, on the argument that one separation chemistry alone leaves gaps no amount of searching can fill.
  • CDR3 sequence-ladder IgG de novo sequencing (2020): Favours selective, high-quality fragmentation over sequence coverage to produce sequence ladders through IgG CDR3 regions, so the variable regions can be read de novo.
  • Multi-protease dual-fragmentation antibody sequencing (2021): Direct de novo sequencing of monoclonal IgG from the purified product with a panel of complementary proteases and both stepped HCD and EThcD on every precursor, demonstrated on the anti-FLAG-M2 antibody.
  • Non-canonical myeloma protein analysis (2021): Characterises non-canonical myeloma proteins with an adapted immunofixation electrophoresis, native top-down mass spectrometry and middle-down de novo sequencing.
  • Myeloma light chain proteoform sequencing (2021): De novo sequencing of patient-derived monoclonal immunoglobulin light chains in multiple myeloma by combining bottom-up and top-down proteomics without a database.
  • Patient light chain amyloidogenicity (2021): Sequences of nine multiple myeloma and one AL amyloidosis light chains were solved by de novo mass spectrometry sequencing and used to show all have comparable amyloidogenic potential.
  • M-protein de novo sequencing and tracking (2021): De novo sequencing of the patient-specific M-protein followed by a targeted MS/MS assay tracks multiple myeloma in serum far more sensitively than SPEP or IFE.
  • EasyM M-protein monitoring (2021): Personalized assay that de novo sequences each multiple myeloma patient’s M-protein, then quantifies its unique peptides by targeted MS to predict relapse earlier than standard tests.
  • Human plasma IgG1 repertoire profiling (2021): De novo MS workflow (LC-MS coupled with Stitch / native MS) for profiling the circulating human plasma IgG1 antibody repertoire, demonstrating individual-specific dynamics: landmark application of de novo to clinical antibodyomics.
  • Multi-enzyme template-assisted mAb sequencing (2022): Complete monoclonal-antibody sequencing from multiple enzyme digests read by HCD and EThcD, with the de novo calls made template-assisted in Supernovo. Refined on an antibody of known sequence, then applied to 25 anti-haemagglutinin influenza antibodies of unknown sequence, recovering high-confidence sequence for over 99% of the CDRs; the resulting heavy and light chains were cloned and expressed, and the recombinant antibodies reproduced the original binding curves. Distinguishes Ile from Leu correctly on the known-sequence controls.
  • Myeloma M-protein monitoring from SPEP gels (2022): Monitors multiple myeloma M-protein retrospectively by mass spectrometry of archived serum protein electrophoresis gels, using de novo sequencing to find each patient’s clonotypic peptides.
  • Anti-AFB1 mAb de novo assisted assembly (2022): Two-protease digestion and de novo-assisted assembly gave full sequence coverage of an aflatoxin B1 monoclonal antibody, with all CDRs correct.
  • Conformation-specific cytochrome c antibody (2022): Sequences de novo an antibody that recognises an alternative conformer of cytochrome c, so that conformational states can be detected in cells and tissue, and rebuilds it from that sequence.
  • COVID-19 IgG1/IgA1 repertoire profiling (2022): Longitudinal intact-mass profiling of IgG1 and IgA1 clonal repertoires in severe COVID-19 patients, with dominant clones sequenced de novo by combined top-down, middle-down and bottom-up proteomics.
  • Endogenous antibody de novo sequencing (perspective) (2022): Perspective on reading antibody sequences at the protein level rather than from B-cell receptor repertoires at the nucleotide level, surveying what mass spectrometry can already do for therapeutic antibodies and what endogenous, polyclonal ones still demand.
  • Antibody proteomics review (Biomeditsinskaya Khimiya) (2023): Russian-language review of proteomic and proteogenomic approaches to antibodies, centred on determining variable-region sequences by de novo sequencing, plus PTM evaluation and bioinformatics tools.
  • SARS-CoV-2 hybrid immunity CDR profiling (2023): LC-MS/MS profiling of complementarity determining regions of anti-RBD antibodies, partly by de novo sequencing, separates hybrid-immunity CDR profiles from vaccination-only ones.
  • Anti-Ro52 autoantibody sequencing in Sjogren’s syndrome (2023): De novo sequencing of purified anti-Ro52 autoantibodies, matched to IMGT, showed that isolated anti-Ro52 patients have less isotype switching, narrower variable-region usage and less somatic hypermutation.
  • Anti-MUC1 139H2 reverse engineering (2023): Reverse-engineers the anti-MUC1 antibody 139H2 by mass spectrometry-based de novo sequencing, MUC1 being a mucin whose aberrant expression and glycosylation matter in adenocarcinoma.
  • MGUS M-protein sequencing from serum (2023): Detected a monoclonal gammopathy in patient serum and sequenced the full Fab-glycosylated M-protein by multi-protease bottom-up de novo sequencing with template assembly, validated by top-down MS.
  • Streptolysin O epitope de novo workflow (2023): Multi-modal MS workflow combining three deep-learning de novo sequencers (PointNovo, Casanovo, InstaNovo) with antibody profiling to identify a conserved protective epitope in Streptococcus pyogenes Streptolysin O.
  • Polyclonal IgG neutralizing antibody discovery (2024): Sequencing the circulating antibody repertoire itself rather than the B cells that make it. Human plasma-derived polyclonal IgG is sequenced by combining mass spectrometry with B-cell sequencing, applied to the IgG response to the Moderna Spikevax COVID-19 vaccine. Twelve recombinant antibodies were generated from the natural polyclonal response; six of them, including four derived by de novo protein sequencing, bound at least as well as the original polyclonal antibody, and all six neutralised the target antigen. The argument for the approach is that sequencing peripheral B cells may not represent the complete receptor repertoire, so the circulating IgG pool has to be examined directly. Notable as antibody discovery carried out end to end by a commercial de novo sequencing service.
  • Light chain cast nephropathy FLC sequencing (2024): Bottom-up de novo workflow with PEAKS and assembly that recovers full-length monoclonal free light chain sequences from patients with light chain cast nephropathy, identical to repertoire sequencing.
  • Serum immunoglobulin variable-region detection (2024): FAIMS or 2D chromatography increased detection of antibody variable-region peptides in serum, matched by combining de novo sequencing with BLAST.
  • SP-MEGD antibody sequencing (2024): Single-Pot and Multi-Enzymatic Gradient Digestion: a bottom-up-only workflow for faster, cheaper de novo sequencing of COVID-19 neutralizing antibodies.
  • SUMO-remnant antibody paratope mapping (2025): A SUMO-remnant antibody was sequenced de novo by mass spectrometry and its paratope and epitope were mapped by cross-linking MS and molecular docking.
  • RSV postfusion F antibody 131-2a sequencing (2025): De novo MS sequencing of the widely used anti-RSV-F antibody 131-2a enabled a recombinant version and a structure explaining its postfusion specificity.
  • Anti-PfEMP1 plasma antibody MS sequencing (2025): Identifies broadly inhibitory human monoclonal antibodies against PfEMP1 CIDRalpha1 from a malaria-exposed child by mass spectrometry sequencing of antigen-purified plasma IgG combined with Ig transcript sequencing.
  • Rheumatoid factor CDR peptide profiling (2025): Rheumatoid factor autoantibodies were captured, digested and profiled by LC-MS/MS; de novo sequenced variable-region peptides not in the human proteome were among those discriminating RF-positive rheumatoid arthritis patients.
  • PolySeq.AI (2025): An automated workflow that integrates de novo bottom-up, middle-down and intact mass spectrometry to sequence polyclonal antibody mixtures without germline databases or B-cell sequencing, validated by expressing recombinant antibodies.
  • MS-based antibody sequencing technologies review (2026): Chinese-language review of mass-spectrometry antibody sequencing, covering database-dependent strategies, multi-enzyme digestion, hybrid fragmentation and AI-assisted de novo sequencing.
  • Goat ApoA-I antibody de novo sequencing (2026): Replaces a polyclonal reagent with defined monoclonals by de novo sequencing goat antibodies: 15 candidate sequences were recovered, four mixtures formulated, and the four-antibody mixture benchmarked against the polyclonal in an ApoA-I immunoturbidimetric assay over 105 human sera.
  • AL amyloid light-chain proteoform sequencing (2026): Pipeline for systemic AL amyloidosis that combines intact-mass Q-TOF measurement before and after deglycosylation with multi-protease digestion and de novo peptide sequencing, linking urinary N-glycosylated light-chain proteoforms to in situ renal amyloid deposits.

Papers (62)

Sequencing tools these papers used

ALPS, Novor, PEAKS, Shotgun Protein Sequencing, Stitch, Supernovo

Authors (361)

A. Broijl, A.N. Tintu, Adrian Guthals, Adrian Y. S. Lee, Agustín Correa, Ailee Aihemaiti, Akira Yamagata, Albert Bondt, Albert J. R. Heck, Alberto Papi, Alena Bensussan, Alexander K. Buell, Alicia Sanchez-Fauquier, Allen Nguyen, Amber L. Couzens, Amelie Boquoi, Anders Eklund, Andrew B. Ward, Anja Resemann, Ari Zeida, Arjan Barendregt, Arjan D. van Zuilen, Atsushi Hashimoto, Bao-Tran Truong, Baozhen Shan, Bas Calcoen, Bastiaan de Graaf, Beatrix Ueberheide, Bert JC Janssen, Bettina Warscheid, Bin Ma, Bin Ma (KuaiXu), Birthe Michiels, Bo Zhang, Bohong Li, Brian D. Soriano, Camellia Adams, Carlo Alberto Volta, Carlos Gueto-Tettay, Celia Quijano, Ceri Zwart, Changrui Xing, Chao Peng, Chelsea Reitzel, Chenyu Yao, Chia-Yu Fan, Chongjing Liu, Chongyang Li, Christian Malosse, Christian W. Wang, Christoph Stingl, Christopher S. Spahr, Cornelis A. M. de Haan, Craig M. Rive, Dag Aarsland, Dan Suan, Daniel T. R. Minja, Danique M.H. van Rijswijck, David Arnott, David Barnidge, David D. Y. Chen, David Morgenstern, David Murray, David S. Gibson, Davinder Gill, Detlev Suckau, Di Tang, Dirk Wunderlich, Donna Reece, Doreen Dillaerts, Dorothea Rutishauser, Douwe Schulte, Elisabeth Hjortswang, Emil Wiklundh, Emma Beadle, Eric Brouwer, Eric Lyimo, Eric Sousa, Eshetu G. Atenafu, Ewen Berube, Feargal P. McNicholl, Florencia Tomasina, Florian Platten, Florian Tucholski, Francesca Fortini, Franziska Völlmy, Fu–de Zhou, Gang Liu, Gerald Nakamura, Gianluca Campo, Giovanni Piza, Giuseppe A. Sautto, Glynis Frans, Gregg B. Morin, Gregory C. Ippolito, Guanglei Li, H. Denis Alexander, H. Russcher, Hamssika Chandrasekaran, Heather H. Shih, Heinrich Leonhardt, Henry Lowman, Ikhlaq Hussain Kana, J Wouter Beugelink, J.F.M. Jacobs, Jacqueline van Rijswijk, Jan Hansen, Jan Van Elslande, Jane L. Grogan, Janet Paulsen, Jean-François Greisch, Jennie R. Lill, Jennitte L. Stevens, Jennyfer Martínez, Jens Fuchser, Jeremy Stinson, Jian Yuan, Jianhui Cheng, Jin Duan, Jin Xiao, Jing Jing Wang, Jing Wang, Jingyi Wang, Joanne H. Reed, Joel Ströbaek, Johan Grunewald, Johan Malmström, Johannes R. Loeffler, John Hilkens, John P. A. Lusingu, John P. McGee, Jonas De Leeuw, Joost Snijder, Joseph McLaughlin, Judy Young, Julia Chamot-Rooke, Jun Ma, Junmei Wan, Kai Chen, Kaidong Wei, Karin Strijbis, Kathleen Gorospe, Katja Kuhlmann, Keith W. Rickert, Kelly Dingess, Kevin C. Graham, Khadija Tejjani, Kim Marquette, Koen CAP Giesbers, Koh Nakata, Krista McCutcheon, Kristin Harden, Kurt Schroeder, Kusay Arat, Kyle Annibale, Kyle Hoffman, L. Zeneyedpour, L.Sh. Kazieva, Lars Malmström, Laura Castro, Laura Murray, Lei Xin, Lennard J. M. Dekker, Li Yang, Lin Wu, Lina Ancheva, Lingyu Wang, Linting Li, Linzhu Li, Liqiang Yang, Lise Boon, Lissa C. Anderson, Lotta Happonen, Louise Turner, Luba Grinberg, Luciana Hannibal, Lucía Piacenza, Luis F. Schachner, Luitgard Nagel-Steger, Lulai Xu, M. Zajec, Maaike Cockx, Magalie Duchateau, Maik Hüttemann, Manuel Baca, Marc J.M. Bonten, Marco Contoli, Maria D. Person, Marit J. van Gils, Mariya Liyasova, Mark E. Daris, Marko Jovic, Marloes Grobben, Marshall Bern, Marta Šiborová, Martial Rey, Martijn M. VanDuijn, María Laura Chiribao, Mathieu Dupré, Matt Goff, Matthew J. Smith, Matti F Pronker, Maurits A. den Boer, Max Hoek, Meri R.J. Varkila, Michael A. Bowen, Michael J. Deery, Michelle V. Gadush, Min-Yuan Chou, Ming Li, Ming Zhu, Ming-Wei Lin, Ming–hui Zhao, Minyoung Park, Mirjam Damen, Monica Lisa Fernández-Quintero, Monique C. Minnema, Nadia J. Mokiem, Natalie Castellana, Neil L. Kelleher, Ngoc Hieu Tran, Nick Geukens, Nico Callewaert, Ning-Shao Xia, Nuno Bandeira, Olaf L. Cremer, Paige Vinson, Paola Rizzo, Patrick Verschueren, Paul M. Thomas, Paul T. Morse, Paul Taylor, Pavel A. Pevzner, Peifeng Ji, Peng Li, Peng XUE, Peter A. E. Sillevis Smitt, Pierre Thibault, Pieter Vermeersch, Pieter-Jan Haas, Ping-Chiang Lyu, Qiang Li, Qingfang Bu, Qitao Song, Qixin Liu, Quan Yuan, Rafael D. Melani, Rafael Radi, Rainer Haas, Rasmus K. Norrild, Rasmus W. Jensen, Rebecca M. DuBois, Rebecca Sternke-Hoffmann, Rita Derua, Robert A. Holt, Robert H. Carnahan, Robert M. Woods, Robert Martone, Rogier M. Thurlings, Roland Fenk, Roman A. Zubarev, Ronald Jemmerson, Rongshan Yu, Rosalin M. Dubois, Ryo Kajita, Ryota Kakui, S. Noori, Sabine Metzger, Sai Li, Sai Sundar Rajan Raghavan, Sanjay Swaminathan, Sarah Hymowitz, Savino Spadaro, Sebastiaan C. de Graaf, Sebastien Carpentier, Sem Tamara, Sheng-Mei LIU, Sheng-Yu Huang, Shiho Takeuchi, Shuang Wang, Shuyang Zhang, Simon Comtois-Marotte, Simon Ekström, Sjors P. A. van der Lans, Stefan U. Egelhaaf, Stephane Olland, Stone D.-H. Shi, Surendra Dasari, Susan Wilson, Susanna L. Lundström, Suxia Wang, Suzan H. M. Rooijakkers, Suzanne Trudel, T.E. Farafonova, Takahiro Tanaka, Tao He, Ted M. Ross, Teresa Nunez de Villavicencio Diaz, Theo M. Luider, Thierry Le Bihan, Thomas Dejoie, Thomas Lavstsen, Thomas Pauly, Thor G. Theander, Tim Chataway, Tina Heyder, Tom Dehaemers, Tom P. Gordon, Tracy Cooper, Trishni Putty, Ulrich Rothbauer, V.G. Zgoda, Valerie J. Winton, Verónica Demicheli, Victoria Lange, Victoria Pham, Vineet Bafna, Vineet Pham, W. Hayes McDonald, W. Ian Deighan, Walter A. Bogdanoff, Wei Zhao, Weijing Yi, Weiping Sun, Weiwei Peng, Wenbin Jiang, Wendy Sandoval, Wenjing Yan, Wenjuan Du, Wenting Li, William J. Henzel, Wim Maes, Xavier Bossuyt, Xiao-Jian WANG, Xiaobing Han, Xiaojuan Yu, Xiaoqing Chen, Xiao–juan Yu, Xin Wang, Xin Xu, Xin Yang, Xinyue Zhou, Xiyue Zhang, Xuesheng Wu, Y.B. de Rijke, Yangtao Wu, Yi Liu (Wuhan), Yongmei Chen, Yueting Xiong, Yueyue Zhu, Yun Xie, Yutian Gan, Zac McDonald, Zheng Chen, Zhengzhong Song, Zhijian Lu, Zhikang Kong, Zi-hao Yong, Zidi Yan, Zihao Wang, Éric Bonneil

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Australia, Belgium, Brazil, Canada, China, Denmark, France, Germany, Italy, Japan, Mexico, Netherlands, Norway, Russia, Sweden, Switzerland, Tanzania, UK, USA

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