Literature DB >> 31420320

Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands".

Zach Rolfs1, Markus Müller2, Michael R Shortreed1, Lloyd M Smith3, Michal Bassani-Sternberg4,5.   

Abstract

There is still no convincing evidence for the frequent occurrence of posttranslationally spliced HLA-I peptides.
Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2019        PMID： 31420320      PMCID： PMC7039048          DOI： 10.1126/sciimmunol.aaw1622

Source DB:  PubMed          Journal:  Sci Immunol        ISSN： 2470-9468


  10 in total

1.  Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets.

Authors:  Arun Devabhaktuni; Joshua E Elias
Journal:  J Proteome Res       Date:  2016-01-25       Impact factor: 4.466

2.  Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS.

Authors:  Oleg V Krokhin; Stephen Ying; John P Cortens; Dhiman Ghosh; Victor Spicer; Werner Ens; Kenneth G Standing; Ronald C Beavis; John A Wilkins
Journal:  Anal Chem       Date:  2006-09-01       Impact factor: 6.986

3.  Production of spliced peptides by the proteasome.

Authors:  Nathalie Vigneron; Vincent Stroobant; Violette Ferrari; Joanna Abi Habib; Benoit J Van den Eynde
Journal:  Mol Immunol       Date:  2018-04-09       Impact factor: 4.407

4.  A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands.

Authors:  Pouya Faridi; Chen Li; Sri H Ramarathinam; Julian P Vivian; Patricia T Illing; Nicole A Mifsud; Rochelle Ayala; Jiangning Song; Linden J Gearing; Paul J Hertzog; Nicola Ternette; Jamie Rossjohn; Nathan P Croft; Anthony W Purcell
Journal:  Sci Immunol       Date:  2018-10-12

5.  Comet: an open-source MS/MS sequence database search tool.

Authors:  Jimmy K Eng; Tahmina A Jahan; Michael R Hoopmann
Journal:  Proteomics       Date:  2012-12-04       Impact factor: 3.984

6.  De novo peptide sequencing by deep learning.

Authors:  Ngoc Hieu Tran; Xianglilan Zhang; Lei Xin; Baozhen Shan; Ming Li
Journal:  Proc Natl Acad Sci U S A       Date:  2017-07-18       Impact factor: 11.205

7.  Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion.

Authors:  Zach Rolfs; Stefan K Solntsev; Michael R Shortreed; Brian L Frey; Lloyd M Smith
Journal:  J Proteome Res       Date:  2018-10-31       Impact factor: 4.466

8.  A large fraction of HLA class I ligands are proteasome-generated spliced peptides.

Authors:  Juliane Liepe; Fabio Marino; John Sidney; Anita Jeko; Daniel E Bunting; Alessandro Sette; Peter M Kloetzel; Michael P H Stumpf; Albert J R Heck; Michele Mishto
Journal:  Science       Date:  2016-10-20       Impact factor: 47.728

9.  PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification.

Authors:  Jing Zhang; Lei Xin; Baozhen Shan; Weiwu Chen; Mingjie Xie; Denis Yuen; Weiming Zhang; Zefeng Zhang; Gilles A Lajoie; Bin Ma
Journal:  Mol Cell Proteomics       Date:  2011-12-20       Impact factor: 5.911

10.  Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome.

Authors:  Roman Mylonas; Ilan Beer; Christian Iseli; Chloe Chong; Hui-Song Pak; David Gfeller; George Coukos; Ioannis Xenarios; Markus Müller; Michal Bassani-Sternberg
Journal:  Mol Cell Proteomics       Date:  2018-08-31       Impact factor: 5.911
  10 in total
  16 in total

1.  The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases.

Authors:  Juan Antonio Vizcaíno; Peter Kubiniok; Kevin A Kovalchik; Qing Ma; Jérôme D Duquette; Ian Mongrain; Eric W Deutsch; Bjoern Peters; Alessandro Sette; Isabelle Sirois; Etienne Caron
Journal:  Mol Cell Proteomics       Date:  2019-11-19       Impact factor: 5.911

Review 2.  Identification of tumor antigens with immunopeptidomics.

Authors:  Chloe Chong; George Coukos; Michal Bassani-Sternberg
Journal:  Nat Biotechnol       Date:  2021-10-11       Impact factor: 54.908

3.  Peptide-Spectrum Match Validation with Internal Standards (P-VIS): Internally-Controlled Validation of Mass Spectrometry-Based Peptide Identifications.

Authors:  Timothy Aaron Wiles; Laura M Saba; Thomas Delong
Journal:  J Proteome Res       Date:  2020-09-29       Impact factor: 4.466

Review 4.  A few good peptides: MHC class I-based cancer immunosurveillance and immunoevasion.

Authors:  Devin Dersh; Jaroslav Hollý; Jonathan W Yewdell
Journal:  Nat Rev Immunol       Date:  2020-08-20       Impact factor: 53.106

Review 5.  Spliced HLA-bound peptides: a Black Swan event in immunology.

Authors:  P Faridi; M Dorvash; A W Purcell
Journal:  Clin Exp Immunol       Date:  2021-03-28       Impact factor: 4.330

Review 6.  Towards new horizons: characterization, classification and implications of the tumour antigenic repertoire.

Authors:  Sebastian P Haen; Markus W Löffler; Hans-Georg Rammensee; Peter Brossart
Journal:  Nat Rev Clin Oncol       Date:  2020-06-22       Impact factor: 66.675

7.  A large peptidome dataset improves HLA class I epitope prediction across most of the human population.

Authors:  Siranush Sarkizova; Susan Klaeger; Phuong M Le; Letitia W Li; Giacomo Oliveira; Hasmik Keshishian; Christina R Hartigan; Wandi Zhang; David A Braun; Keith L Ligon; Pavan Bachireddy; Ioannis K Zervantonakis; Jennifer M Rosenbluth; Tamara Ouspenskaia; Travis Law; Sune Justesen; Jonathan Stevens; William J Lane; Thomas Eisenhaure; Guang Lan Zhang; Karl R Clauser; Nir Hacohen; Steven A Carr; Catherine J Wu; Derin B Keskin
Journal:  Nat Biotechnol       Date:  2019-12-16       Impact factor: 54.908

8.  An in silico-in vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients.

Authors:  Michele Mishto; Artem Mansurkhodzhaev; Ge Ying; Aruna Bitra; Robert A Cordfunke; Sarah Henze; Debdas Paul; John Sidney; Henning Urlaub; Jacques Neefjes; Alessandro Sette; Dirk M Zajonc; Juliane Liepe
Journal:  Front Immunol       Date:  2019-11-15       Impact factor: 7.561

9.  Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics.

Authors:  Mathias Wilhelm; Daniel P Zolg; Michael Graber; Siegfried Gessulat; Tobias Schmidt; Karsten Schnatbaum; Celina Schwencke-Westphal; Philipp Seifert; Niklas de Andrade Krätzig; Johannes Zerweck; Tobias Knaute; Eva Bräunlein; Patroklos Samaras; Ludwig Lautenbacher; Susan Klaeger; Holger Wenschuh; Roland Rad; Bernard Delanghe; Andreas Huhmer; Steven A Carr; Karl R Clauser; Angela M Krackhardt; Ulf Reimer; Bernhard Kuster
Journal:  Nat Commun       Date:  2021-06-07       Impact factor: 14.919

10.  Is the Immunopeptidome Getting Darker?: A Commentary on the Discussion around Mishto et al., 2019.

Authors:  Anthony W Purcell
Journal:  Front Immunol       Date:  2021-07-13       Impact factor: 7.561
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