ArticleJournal of proteome research2017
Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach.
Article in Journal of proteome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Artificial Intelligence and Machine Learning in Mass Spectrometry-Based Proteomics and Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- The State of Peptide Detectability in Computational Proteomics and Guidelines for AI Applications.Computational and structural biotechnology journal · 2026Article
- To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry.Journal of proteome research · 2025Article
- DeepPD: A Deep Learning Method for Predicting Peptide Detectability Based on Multi-feature Representation and Information Bottleneck.Interdisciplinary sciences, computational life sciences · 2025Article
- PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models.Scientific reports · 2024Article
- DbyDeep: Exploration of MS-Detectable Peptides via Deep Learning.Analytical chemistry · 2023Article
- PD-BertEDL: An Ensemble Deep Learning Method Using BERT and Multivariate Representation to Predict Peptide Detectability.International journal of molecular sciences · 2022Article
- Prediction of Peptide Detectability Based on CapsNet and Convolutional Block Attention Module.International journal of molecular sciences · 2021Article
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Authors and funding
11 authors.
Funding
Abstract
The Human Proteome Project (HPP) aims deciphering the complete map of the human proteome. In the past few years, significant efforts of the HPP teams have been dedicated to the experimental detection of the missing proteins, which lack reliable mass spectrometry evidence of their existence. In this endeavor, an in depth analysis of shotgun experiments might represent a valuable resource to select a biological matrix in design validation experiments. In this work, we used all the proteomic experiments from the NCI60 cell lines and applied an integrative approach based on the results obtained from Comet, Mascot, OMSSA, and X!Tandem. This workflow benefits from the complementarity of these search engines to increase the proteome coverage. Five missing proteins C-HPP guidelines compliant were identified, although further validation is needed. Moreover, 165 missing proteins were detected with only one unique peptide, and their functional analysis supported their participation in cellular pathways as was also proposed in other studies. Finally, we performed a combined analysis of the gene expression levels and the proteomic identifications from the common cell lines between the NCI60 and the CCLE project to suggest alternatives for further validation of missing protein observations.
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Registered trials
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