A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics

Li, Xiaokang; Pak, Hui Song; Huber, Florian; Michaux, Justine; Taillandier-Coindard, Marie; Altimiras, Emma Ricart; Bassani-Sternberg, Michal

doi:10.1016/j.crmeth.2023.100479

Cited by 9 publications

(6 citation statements)

References 75 publications

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“…An additional study on the Astral from the Olsen lab demonstrates the identification of around 5200 proteins from single HeLa cells, which is again the highest number of protein IDs for a single HeLa cell that the authors are aware of [62]. [1,29,36,49,63,64].…”

Section: Evolution Of Mass Spectrometers For Scp and Immunopeptidomicsmentioning

confidence: 96%

“…Similar to chip-based approaches in SCP and low-input proteomics [23,[33][34][35], the group of Bassani-Sternberg very recently developed a chip-based system for immunopeptidomics sample preparation. This system uses micropillar arrays to demonstrate unsurpassed sensitivity in immunopeptidomics with around 4000 MHC class I peptides identified for only 200,000 RA957 cells, while only 2700 peptides were identified in comparison via the column-based method [36]. They could also identify more than 5000 immunopeptides from as little as 5 mg of melanoma tissue.…”

Section: Miniaturization and Acceleration Of Immunopeptidomics Sample...mentioning

confidence: 99%

“…They also show that still around 3000 peptides can be identified with their method when using only the equivalent of 1 × 10 6 cells. As mentioned earlier in the manuscript, the team of Bassani-Sternberg showed that a high number of IDs can be still attained using even less starting material (2 × 10 5 cells) with a less sensitive instrument, that is, the Q Exactive HF-X in their case [36]. However, they utilized data-independent acquisition (DIA) and recorded libraries including larger cell quantities to circumvent the reduced sensitivity of the instrument.…”

Section: Evolution Of Mass Spectrometers For Scp and Immunopeptidomicsmentioning

confidence: 99%

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Immunopeptidomics in the Era of Single-Cell Proteomics

Mayer,

Mechtler

2023

Biology

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Immunopeptidomics, as the analysis of antigen peptides being presented to the immune system via major histocompatibility complexes (MHC), is being seen as an imperative tool for identifying epitopes for vaccine development to treat cancer and viral and bacterial infections as well as parasites. The field has made tremendous strides over the last 25 years but currently still faces challenges in sensitivity and throughput for widespread applications in personalized medicine and large vaccine development studies. Cutting-edge technological advancements in sample preparation, liquid chromatography as well as mass spectrometry, and data analysis, however, are currently transforming the field. This perspective showcases how the advent of single-cell proteomics has accelerated this transformation of immunopeptidomics in recent years and will pave the way for even more sensitive and higher-throughput immunopeptidomics analyses.

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Section: Evolution Of Mass Spectrometers For Scp and Immunopeptidomicsmentioning

confidence: 96%

Section: Miniaturization and Acceleration Of Immunopeptidomics Sample...mentioning

confidence: 99%

Section: Evolution Of Mass Spectrometers For Scp and Immunopeptidomicsmentioning

confidence: 99%

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Immunopeptidomics in the Era of Single-Cell Proteomics

Mayer,

Mechtler

2023

Biology

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“…cThe HIPP has organized several high-profile webinars. The second HUPO-HIPP Summer School in Oxford, UK, in September 2022 addressed HLA-antibody specificities and their impact on sample quality, optimized workflows for improved identification of PTMs, advantages in automating sample preparation now emerging in specialized laboratories, − improved HLA-peptide acquisition technology, , and the importance of accurate and improved spectral annotation and validation strategies, , specifically in the context of tumor-specific, noncanonical peptide discovery. , The third HUPO-HIPP Summer School will take place in Montreal in August 2024. The HIPP organized a pre-HUPO Congress workshop in Korea on the noncanonical proteomea novel class of clinically targetable T cell antigens in conjunction with genome annotation and Ribo-Seq experts.…”

Section: Biology and Disease-driven Hppmentioning

confidence: 99%

The 2023 Report on the Proteome from the HUPO Human Proteome Project

Omenn,

Lane,

Overall

et al. 2024

J. Proteome Res.

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Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1–4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

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“…On the other side, the amount of biological material required for these studies is usually higher than that used for gene sequencing, although in recent years these methodologies are being improved. 49 , 50 …”

Section: Neoantigens Originated From Mutationsmentioning

confidence: 99%

Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies

Aparicio,

Theunissen,

Hervas-Stubbs

et al. 2024

Human Vaccines & Immunotherapeutics

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Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.

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A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics

Cited by 9 publications

References 75 publications

Immunopeptidomics in the Era of Single-Cell Proteomics

Immunopeptidomics in the Era of Single-Cell Proteomics

The 2023 Report on the Proteome from the HUPO Human Proteome Project

Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies

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