Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome

Rio, Diego Fernando Garcia-del; Cardon, Tristan; Eyckerman, Sven; Fournier, Isabelle; Bonnefond, Amélie; Gevaert, Kris

doi:10.1016/j.isci.2023.105943

Cited by 4 publications

(12 citation statements)

References 68 publications

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“…A larger view on the proteomic landscape Subcellular fractionation is a validated approach to decrease sample complexity and to maximize resolution in LC-MS/MS analysis. In our previous works (17,30), such subcellular fractionation was proven bene cial for XL-MS work ows and provided better coverage of the proteome compared to analysing whole cell lysates (68). This enhanced the detection of low-abundant proteins (AltProts and crosslinked proteins).…”

Section: Discussionmentioning

confidence: 99%

“…In cellulo chemical cross-linking. The cross-linking methodology was described in Garcia-del Rio et al (17,30). To prepare a 50 mM stock solution of disuccinimidyl sulfoxide (DSSO, Thermo Fisher Scienti c), dry DMSO (Sigma-Aldrich) was used.…”

Section: Chemical Protein Cross-linking and Subcellular Fractionationmentioning

confidence: 99%

“…Protein subcellular fractionation. The subcellular fractionation methodology was also described in our previous work (17,30). In brief, three replicates of three million cells that underwent crosslinking were pelleted and the supernatant was removed.…”

Section: Chemical Protein Cross-linking and Subcellular Fractionationmentioning

confidence: 99%

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Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization

Tristan,

Rio,

Derhourhi

et al. 2024

Preprint

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Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has a high potential to unravel the characteristics, variants and expression levels of the alternative proteome, in addition to already annotated proteins (RefProts). To obtain a broader view of the proteome of ovarian cancer cells compared to ovarian epithelial cells, cell-specific total RNA-sequencing profiles and customized protein databases were generated. In total, 128 RefProts and 30 AltProts were identified exclusively in SKOV-3 and PEO-4 cells. Among them, an AltProt variant of IP_715944, translated from DHX8, was found mutated (p.Leu44Pro). We show high variation in protein expression levels of RefProts and AltProts in different subcellular compartments. The presence of 117 RefProt and two AltProt variants was described, along with their possible implications in the different physiological/pathological characteristics. To identify the possible involvement of AltProts in cellular processes, crosslinking-MS (XL-MS) was performed in each cell line to identify AltProt-RefProt interactions. This approach revealed an interaction between POLD3 and the AltProt IP_183088, which after molecular docking, was placed between POLD3-POLD2 binding sites, highlighting its possibility of the involvement in DNA replication and repair.

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Section: Discussionmentioning

confidence: 99%

Section: Chemical Protein Cross-linking and Subcellular Fractionationmentioning

confidence: 99%

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Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization

Tristan,

Rio,

Derhourhi

et al. 2024

Preprint

Self Cite

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“…42 New methodologies may improve the functional characterization of protein−protein interactomes. 43 Overall, iMOP aims to federate expertise to improve structural and functional knowledge of proteins to answer fundamental biological questions using the most relevant biological model.…”

Section: Initiative For Model Organism Proteomics (Imop)mentioning

confidence: 99%

“…Proteogenomics can identify and characterize the structure of new coding sequences to better define their function through short open reading frames and their possible PTMs . New methodologies may improve the functional characterization of protein–protein interactomes . Overall, iMOP aims to federate expertise to improve structural and functional knowledge of proteins to answer fundamental biological questions using the most relevant biological model.…”

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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New advances in cross-linking mass spectrometry toward structural systems biology

Huang

2023

Current Opinion in Chemical Biology

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Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome

Cited by 4 publications

References 68 publications

Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization

Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization

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

New advances in cross-linking mass spectrometry toward structural systems biology

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