Immunopeptidomics / neoantigen

26 workflows · 2012–2026

Immunopeptidomics / neoantigen: HLA-presented peptides, where non-specific processing makes the search space too large for a database and the interesting peptides are the ones not in it. 26 catalogued workflows and 32 papers.

HLA-presented peptides, where non-specific processing makes the search space too large for a database and the interesting peptides are the ones not in it.

Workflows 26
Papers 32
Authors 248
Active 2012-09-01 to 2026-10-16

Workflows (26)

  • Melanoma HLA peptidome immunogenicity (2012): HLA class I peptidomes of four melanoma cell lines, extracted from isolated HLA, separated by two-dimensional HPLC and sequenced by MALDI post-source-decay MS. Spectra were interpreted twice over, by database-dependent Mascot search and by database-independent de novo sequencing in Sequit!, with synthetic peptides used to confirm assignments and to measure immunogenicity. Overlap between the four peptidomes was small, indicating highly individual HLA peptidomes, yet they were broadly immunogenic both in the patients the lines came from and in unrelated patients, and that cross-patient immunogenicity was only exceptionally attributable to individual peptides. Most epitopes came from low to medium abundance proteins in sensitive processes such as cell cycle control, DNA replication and tumour suppression.
  • Proteasomal spliced peptide estimation (2018): Uses de novo sequencing of HLA-I peptide spectra, filtered against UniProt and matched to spliced candidates, to estimate how many ligands are proteasome-spliced.
  • DeepNovoAA (2019): Immunopeptidome neoantigen discovery
  • Bat MHC I peptidome (2019): Crystal structures of Pteropus alecto MHC I plus de novo LC-MS/MS of peptides eluted from a random library exchange show a bat-specific three-residue insertion promotes high-affinity peptide binding.
  • DIA immunopeptidomics with PEAKS database and de novo search (2019): Combines database search and de novo sequencing on DIA immunopeptidomics data, so HLA peptides can be identified without a DDA-built spectral library.
  • CRC liver metastasis neoantigen discovery (2020): Proteogenomics and de novo sequencing of the immunopeptidomes of patient colorectal cancer liver metastases to find HLA peptides that database search misses.
  • Proteasome-catalysed peptide splicing signatures (2020): In vitro proteasomal digests of viral and self polypeptides were analysed with a tailored mass-spectrometry de novo sequencing workflow to define the residue and length signatures of forward and reverse cis-splicing.
  • Swine SLA-I immunopeptidome (RPLD-MS) (2021): Random peptide library plus MS de novo sequencing (RPLD-MS) defined the peptides bound by swine SLA-I variants, linked to crystal structures of the binding pockets.
  • Melanoma and EGFR lung cancer HLA-I proteogenomics (2021): Proteogenomic HLA class I immunopeptidomics in melanoma and EGFR-mutant lung adenocarcinoma, using de novo search to find variant, PTM and lncRNA-encoded peptides.
  • MHC I PTM and spliced peptide immunopeptidome (2021): MHC class I immunopeptidomics of Loucy and A375 cells where PEAKS de novo sequencing identified spliced peptides making up about 5 to 7% of the MHC-bound repertoire, validated with synthetic peptides.
  • sORF noncanonical MHC-I peptides (2021): Combines Ribo-seq-derived sORF databases with database search and de novo sequencing to identify 308 noncanonical MHC class I peptides from two tumor cell lines.
  • Unsupervised HLA-I peptidome mining with SMSNet (2021): Applies the SMSNet hybrid de novo approach to mono-allelic HLA-I peptidomics data to find new ligands, refine binding motifs and flag likely contaminant peptides in community databases.
  • Swine SLA-I peptide length preference (RPLD-MS) (2022): Random peptide library binding plus LC-MS/MS de novo sequencing (RPLD-MS) showed that swine SLA-1*13:01 binds more long peptides than SLA-1*04:01, explained by crystal structures.
  • Proteasome-spliced HLA ligand discovery (2022): De novo sequencing of HLA class I ligands from a colorectal cancer line found genome-untemplated proteasome-spliced peptides that CD8+ T cells recognise.
  • DeepNovo Peptidome (2022): Immunopeptidomics pipeline
  • MARS (2022): Non-canonical antigen selection
  • CRC cryptic peptide T-cell stimulation (2022): Characterises the HLA ligandome of two hypermutated colorectal cancers, finding 97 cryptic tumour-specific candidates with the de novo-based Peptide-PRISM, and shows patients’ T cells stimulated with them recognise autologous tumour cells.
  • Noncanonical MAP atlas (2023): A proteogenomic pipeline based on deep-learning de novo sequencing plus open search mapped 8,601 noncanonical MHC class I peptides from noncoding regions across 11 cancer types.
  • Noncanonical HLA-I tumour ligand immunogenicity (2023): A de novo sequencing-based proteogenomic search found noncanonical HLA-I ligands in nine patient tumour cell lines; none was recognized by autologous T cells, though some elicited TCRs from donor blood.
  • pXg (2024): MHC-I noncanonical peptides
  • pSILAC quantitative immunopeptidomics with Peptide-PRISM (2025): Pulsed SILAC labelling combined with Peptide-PRISM de novo-based identification and MaxQuant quantification tracks how MAPK inhibition reshapes the melanoma immunopeptidome, revealing cryptic HLA peptides.
  • IFN-alpha beta-cell HLA-I immunopeptidome (2025): A de novo sequencing-based immunopeptidomics pipeline showed that interferon-alpha expands the beta-cell HLA-I repertoire toward HLA-B and toward non-canonical peptides from alternative and cis-splicing.
  • Neoantigen proteomics survey (2025): Surveys database search and deep learning de novo sequencing for cancer neoantigen discovery and compares tools on HepG2 and HCC samples.
  • HCC non-canonical neoantigen discovery (2026): Finds non-canonical neoantigens in hepatocellular carcinoma by mass spectrometry-based de novo sequencing and then tests them, addressing the gap that de novo proposes cryptic antigens whose immunogenicity goes unverified.
  • TIPs (2026): Deep-learning-guided proteogenomic framework that uses de novo sequencing to refine the search space for transposable-element-derived HLA antigens, finding 20-fold more than conventional searches.
  • Thai RCC personalised immunopeptidomics (2026): Profiles the personalised immunopeptidomes of 13 Thai renal cell carcinoma patients, whose HLA allotypes are underrepresented in public reference data. Builds a personalised proteome from whole-exome sequencing and searches it alongside de novo peptide sequencing, so de novo produced part of the result.

Papers (32)

Sequencing tools these papers used

Casanovo, PEAKS, Peptide-PRISM, PointNovo, SMSNet, Sequit

Authors (248)

Ajitha Rajan, Akhilesh Pandey, Aleksander Palkowski, Alena Gros, Alexander Laird, Alexia Carré, Amanda Anderson, Amol Prakash, Andrea Garcia-Garijo, Andreas Schlosser, Andrzej Dzionek, Anil K. Madugundu, Ankur Dhanik, Anna Rye-Weller, Anna Yuste-Estevanez, Annalisa Nicastri, Anne Rech, Anne Wendt, Annette Paschen, Anthony Manganaro, Arun Tailor, August Vidal, Baohua Zou, Baozhen Shan, Barbara Brandao, Basak Arslan, Bastian Schilling, Carolina Barra, Catherine Ade, Catia Pesquita, Cenk Sahinalp, Chao Peng, Chatchapon Sricharoensuk, Chloe Chong, Christian Iseli, Christiana Lekka, Christina S Mullins, Christophe Battail, Chun Xia, Chungong Yu, Constance M. Cultraro, Darshit shah, David Gfeller, David J. Harrison, David Milewski, David R. Goodlett, Decio L. Eizirik, Deep Patel, Dominika Bedran, Dongbo Bu, Elena Garralda, En Hu, Eunok Paek, Eva Muñoz-Couselo, Evgenia Olshvang, Fabio Massimo Zanzotto, Farah Kobaisi, Fatoumata Samassa, Florian Erhard, Francesc Canals, Geng Meng, George Coukos, Georges Bedran, German Leonov, Gourav Dey, Guojiao Feng, Haicang Zhang, Haiming Qin, Hanqing Liao, Hans-Christof Gasser, Hans-Georg Rammensee, Haofei Miao, Hieu Tran, Hirofumi Chiba, Hiroki Takahashi, Hongwei Wang, Hui Peng, Hui-Song Pak, Huihui Li, Håkan Axelson, Ignacio Matos, Ilan Beer, Ioannis Xenarios, Irene Brana, Isaac Woodhouse, J. Robert O’Neill, Jahnavi Aluri, James C. Yang, Jan-Niklas Herbel, Jane A. Peterson, Jara Palomero, Jared J. Gartner, Javed Khan, Javier A. Alfaro, Javier Perez-Hernandez, Jiahe Ouyang, Jiaxin Cai, Jiayi Shen, Jingxiang Lang, Jinyan Li, Jirapat Techachakrit, Johanna Schmitz, Josep Maria Piulats, Juan Martín-Liberal, Julin Opanuraks, Kamil Cygan, Kapil Dev Kampe, Ken-ichi Hanada, Kenji Murata, Kenneth Weke, Kevin Litchfield, Khoa D. Nguyen, Kiran K. Mangalaparthi, Kishore Garapati, Koji Kato, Laurence C. Eisenlohr, Laurie Landry, Lei Chen, Lei Xin, Lijie Zhang, Lizhen Ma, Lorella Marselli, Maciej Parys, Maciej Pawlik, Maikel L. Colli, Maki Nakayama, Marcus Göransson, Maria Lozano-Rabella, Maria Ochoa-de-Olza, Marion Berthold, Markus Müller, Markus W Löffler, Marvin Markel, Masaya Oshima, Melina Lappe, Melissa Bernhardt, Michael Ghosh, Michael J. Hogan, Michael Linnebacher, Michal Bassani-Sternberg, Ming Li, Mingxin Liu, Mohammad H. Ebrahimabadi, Morten Nielsen, Munehide Nakatsugawa, Nadine Mockel-Tenbrinck, Naoto Hirano, Nattiya Hirankarn, Ngoc Hieu Tran, Nianzhi Zhang, Nicola Ternette, Ningyi Shao, Olav Olsen, Orlando Burgos Morales, Parunya Chaiyawat, Paul M. Brennan, Paul Shan, Persephone Borrow, Peter Bauer, Peter Walden, Phijitra Muanwien, Piero Marchetti, Ping Wu, Piriya Wongkongkathep, Poorichaya Somparn, Qian Wu, Qian Zhao, Qing Zhang, Qingyang Lei, Qizhen Feng, Raphael Scharfmann, Robert Parker, Robert Salzler, Roberto Mallone, Robin Fahraeus, Roc Farriol-Duran, Roman Mylonas, Rui Qiao, Ruijing Tang, Ruiying Liang, Sachin Kote, Saharat Nanthawong, Sally C. Kent, Sandra Schwarz, Sarah J. Richardson, Saulius Jarmalavicius, Serina Tokita, Seunghyuk Choi, Shanji Zhang, Shanop Shuangshoti, Shaojian Gao, Shen Li, Shifu Luo, Sine R. Hadrup, Sira Sriswasdi, Song Wang, Songming Zhang, Stefan N. Symeonides, Suqiu Wang, Susann Krake, Sutpirat Moonmuang, Sylvaine You, Takayuki Kanaseki, Tanupat Boonchalermvichien, Tanyaluck Kampoun, Tapan K. Maity, Tatchapon Apinan, Ted R. Hupp, Terufumi Kubo, Thomas Partridge, Tomohide Tsukahara, Tongjie Wang, Toshihiko Torigoe, Trairak Pisitkun, Udayan Guha, Vikram Misra, Wayne Paes, Wenguang Shao, Wenting Li, William Olson, Xavier Matías-Guiu, Xiaobing Liu, Xiaohua Xing, Xiaohui Wei, Xiaoli Xie, Xiaolong Liu, Xiaoxiang Huang, Xin Chen (Waterloo), Xinyue Zhou (Shanghai Jiao Tong University), Xu Peng, Xu Zhang, Xuan Dong, Yang Yang (Hong Kong Polytechnic University), Yaxin Tang, Yi Zhang, Ying Shi, Ying Yang, Yoshihiko Hirohashi, Yuanliang Zhang, Yue A. Qi, Yvonne Welte, Zachary C. Ryan, Zehui Qu, Zhi Xie, Zhicheng Zhou, Zhuolin Li, Zibin Li, Zixiang Shang

Where the work happened

Belgium, Canada, China, Denmark, France, Germany, India, Italy, Japan, Macao, Netherlands, Poland, Portugal, Singapore, South Korea, Spain, Sweden, Switzerland, Thailand, UK, USA

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