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Human N-terminal proteome using TMPP labelling and dN-TOP approach

ABSTRACT: The present study describes the free N-terminome analysis of human mitochondria-enriched samples using trimethoxyphenylphosphonium (TMPP) labelling approaches and dN-TOP validation of the proteomics data acquired with an Orbitrap mass spectrometer. The doublet N-terminal oriented proteomics (dN-TOP) strategy is based on a double light/heavy TMPP labelling which enable fast, efficient and reliable high throughput N-terminome data validation

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Monocyte, Cell Culture

SUBMITTER: Magali Rompais

LAB HEAD: Christine CARAPITO

PROVIDER: PXD064426 | Pride | 2026-03-23

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Energiome_Mascot_24b_TMPP_search.mzid	Mzid
	Ho_DCpSP_AVJ-2015_20150212.fasta	Fasta
	QE02854.mgf	Mgf
	QE02854.raw	Raw
	QE02855.mgf	Mgf

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Publications

Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups.

Bouwmeester Robbin R Nameni Alireza A Declercq Arthur A Devreese Robbe R Velghe Kevin K Gorshkov Vladimir V Penanes Pelayo A PA Kjeldsen Frank F Rompais Magali M Carapito Christine C Gabriels Ralf R Martens Lennart L

Nature communications 20260210 1

While LC retention time prediction of peptides and their modifications has proven useful, widespread adoption and optimal performance are hindered by variations in experimental parameters. These variations can render retention time prediction models inaccurate and dramatically reduce the value of predictions for identification, validation, and DIA spectral library generation. To date, mitigation of these issues has been attempted through calibration or by training bespoke models for specific exp ...[more]

PMID: 41667442

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Human “free-N-terminome” analysis

Project description:The high throughput characterization of protein N-termini is becoming an emerging challenge in the proteomics and proteogenomics fields. The present study describes the N-terminal oriented analysis of human mitochondria enriched samples by the trimethoxyphenyl phosphonium (TMPP) labeling approach (N-TOP and dN-TOP approaches (Gallien et al, 2009, Bertaccini et al. 2013)). The dN-TOP strategy based on a double light/heavy TMPP labeling has been optimized in order to improve and automate the workflow for efficient, fast and reliable high throughput N-terminome analysis.

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Project description:Epitranscriptomic reader, writer and eraser (RWE) proteins are involved in the recognition, installation, and removal, respectively, of chemical modifications in RNA, and aberrant expressions of some of these proteins were found to be associated with cancer initiation and progression. Here, we our recently established parallel-reaction monitoring (PRM)-based targeted proteomic method, in conjunction with stable isotope labelling by amino acids in cell culture (SILAC), to investigate the differential expression of epitranscriptomic RWE proteins in a matched pair of primary/metastatic colorectal cancer (CRC) cells (i.e., SW480/SW620) derived from the same patient. We were able to detect 113 non-redundant epitranscriptomic RWE proteins in these two lines of cells. We found that 48 and 5 proteins were respectively up- and down-regulated by at least 1.5-fold in SW620 over SW480 cells. Particularly, NAT10, HNRNPC, and DKC1 were markedly up-regulated, and their potential roles in driving CRC metastasis were supported by recent studies. Interrogation of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data revealed that the elevated expressions of these and other RWE proteins are also accompanied with CRC initiation, suggesting the roles of these proteins in both the initiation and metastatic transformation of CRC. It can be envisaged that the established PRM method can be further utilized to examine the roles of epitranscriptomic RWE proteins in the metastatic transformations of other types of cancer.

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