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D283 MED, a cell line derived from peritoneal metastatic medulloblastoma — a good choice for missing protein discovery

ABSTRACT: Our goal is the identification of more and more missing proteins from cancer cell lines. This project focuses on D283 med and U-118mg cell lines which contribute to 12 missing protein identification.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Siqi Liu

PROVIDER: MSV000087678 | MassIVE | Mon Jun 21 23:47:00 BST 2021

SECONDARY ACCESSION(S): PXD021482

REPOSITORIES: MassIVE

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Publications

D283 Med, a Cell Line Derived from Peritoneal Metastatic Medulloblastoma: A Good Choice for Missing Protein Discovery.

Zhang Yuanliang Y Zhang Keren K Bu Fanyu F Hao Piliang P Yang Huanming H Liu Siqi S Ren Yan Y

Journal of proteome research 20201119 12

Since the Chromosome-Centric Human Proteome Project (C-HPP) was launched in 2010, many techniques have been adopted for the discovery of missing proteins (MPs). Because of these efforts, only 1481 MPs remained as of July 2020; however, by relying only on technique optimization, researchers have reached a bottleneck in MP discovery. Protein expression is tissue- or cell-type-dependent. The tissues of the human testis and brain have been reported to harbor a large number of tissue-specific genes a ...[more]

PMID: 33210925

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D283 MED, a cell line derived from peritoneal metastatic medulloblastoma — a good choice for missing protein discovery

Project description:Our goal is the identification of more and more missing proteins from cancer cell lines. This project focuses on D283 med and U-118mg cell lines which contribute to 12 missing protein identification.

2020-11-26 | PXD021482 | Pride

The exploration of Missing Proteins by a combination approach to enrich the low abundance membrane proteins from several cancer cell lines

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Mining Missing Membrane Proteins by High-pH Reverse Phase StageTip Fractionation and Validation by Multiple Reaction Monitoring Mass Spectrometry

Project description:Several significant efforts have been made in the past decade to map all human proteome. However, more than 3000 proteins are grouped as missing having no evidence of translation. Membrane protein annotation of the current missing proteins list showed 34%to be missing membrane proteins, which are challenging even in standard shotgun proteomics. So as to find missing membrane proteins, we employed a highly sensitive and efficient peptide pre-fractionation of membrane enriched sample from 11 non-small cell lung cancer (NSCLC) cell lines of different EGFR mutation status by High-pH Reverse Phase StageTip. Besides, we analyzed 20 tumor and adjacent normal lung cancer tissue membrane samples to enhance identification coverage. With the use of multiple search engines and FDR analysis: X!Tandem and Comet followed by MAYU through TPP as well as Mascot followed PeptideShaker for FDR estimation, we were able to confidently identify 7701 proteins from which 5120 (66%) were annotated to be membrane proteins with below 1% FDR at protein, peptide and PSMs level having at least one unique peptide of 7 or more amino acid residues. Of this 181 proteins belong to the missing proteins in neXtProt (09-2014 release) and 75 are annotated to be missing membrane proteins. Furthermore we were able to validate 8 selected missing proteins (7 membrane proteins with TMH domain) using 10 synthetic peptides assisted multiple reaction monitoring (MRM) mass spectrometry. This study indicates membrane sub-proteome focus with efficient pre-fractionation and bioinformatics filtering followed by targeted validation by MRM is useful approach to assist mapping of all human proteome.

2015-07-27 | PXD002224 | Pride

Finding missing proteins from epigenetically manipulated human cells

Project description:We performed transcriptome sequencing to assess the genes turn on in the cell under epigenetically manipulation. MHCC97H, A549 and HCT116 were treated by GSK126, S2101 and TSA respectively. We detected the missing proteins in the cells under epigenetically manipulation.

2016-05-23 | GSE69420 | GEO

Utility of Intra-operative Image Guidance System for Missing Metastases

Project description:Intraoperatively, the surgeon will interrogate the liver with ultrasound. The time spent by the surgeon using the ultrasound is recorded. If all lesions seen on pre-op imaging were found, the patient does not have the Pathfinder Explorer system applied. If one or more lesions cannot be found, then the Pathfinder Explorer system is calibrated and a tracking device is attached to the ultrasound probe, which the surgeon will use to reattempt localization of the missing tumor. The Pathfinder Explorer system operates in real-time in conjunction with the ultrasound.

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A shot to missing protein from an aneuploidy cell line

Project description:With fast development of proteomic technology, the scale of missing proteins (MPs) has being continuously shrunk, approximately 1,470 MPs not explored yet. Discovery of MPs, on the other hand, is appearing more difficult. In some aneuploid cells, the abundance changes are proportional to the additional chromosome(s), while several MPs were found within them. Herein, we hypothesize that a stable aneuploid cell line with the increased chromosomes was a useful material that assists MP exploration. Ker-CT cell line with trisomy at chromosome 5 and 20 was selected. With a combination strategy of RNA-Seq and LC-M/MS, a total of 22,178 transcripts and 8,846 proteins were identified in Ker-CT. Although the transcripts corresponding to 31 and 32 MP genes located at chromosome 5 and 20 were detected, none of MPs was found in Ker-CT. Surprisingly, 3 MPs containing at least two unique non-nest peptides of length ≥9 amino acid were identified in Ker-CT, whose genes are located in chromosome 3 and 10. Furthermore, the 3 MPs were verified using the method of parallel reaction monitoring (PRM).

2021-11-25 | PXD028647 | Pride

Chr18 Consortium MS-data for missing proteins mining

Project description:Despite direct or indirect efforts of proteomic community, the fraction of blind spots on the protein map is still significant. Almost 10% (?) of human master protein has no experimental validation up to now. Apparently, proteomics has reached the stage where all easy scores are achieved (?), and every next identification requires more intension and curiosity in expansion of unusual types of biomaterial and/or conditions. In this article we discuss the current state of missing proteins search conducted by eclectic Russian Consortium in frame of C-HPP. We accumulated various data, obtained by Russian Proteomic Consortium.

2020-06-03 | PXD014300 | Pride

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