Immunopeptidomics / neoantigen

6 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. 6 catalogued workflows and 8 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 6
Papers 8
Authors 53
Active 2012-09-01 to 2026-09-04

Workflows (6)

  • 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.
  • DeepNovoAA (2019): Immunopeptidome neoantigen discovery
  • MARS (2022): Non-canonical antigen selection
  • DeepNovo Peptidome (2023): Immunopeptidomics pipeline
  • pXg (2024): MHC-I noncanonical peptides
  • 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 (8)

Sequencing tools these papers used

Sequit

Authors (53)

Alexia Carré, Arun Tailor, Baozhen Shan, Carolina Barra, Chao Peng, Chungong Yu, Dongbo Bu, Eunok Paek, Haicang Zhang, Haiming Qin, Hanqing Liao, Haofei Miao, Isaac Woodhouse, Jingxiang Lang, Jirapat Techachakrit, Julin Opanuraks, Laurence C. Eisenlohr, Lei Xin, Michael J. Hogan, Ming Li, Morten Nielsen, Nattiya Hirankarn, Ngoc Hieu Tran, Nicola Ternette, Parunya Chaiyawat, Persephone Borrow, Peter Walden, Phijitra Muanwien, Ping Wu, Piriya Wongkongkathep, Poorichaya Somparn, Qing Zhang, Qingyang Lei, Robert Parker, Roberto Mallone, Rui Qiao, Saharat Nanthawong, Saulius Jarmalavicius, Seunghyuk Choi, Shanop Shuangshoti, Sira Sriswasdi, Sutpirat Moonmuang, Tanyaluck Kampoun, Tatchapon Apinan, Trairak Pisitkun, Wayne Paes, Wenting Li, Xiaolong Liu, Xin Chen (Waterloo), Xu Peng, Yi Zhang, Yvonne Welte, Zhicheng Zhou

Where the work happened

Canada, China, Denmark, France, Germany, Netherlands, South Korea, Thailand, UK, USA

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