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Comparison of efficacy in immunopeptide identification from HCT116 by "without" FAIMS

ABSTRACT: HLA class I immunopeptides were affinity purified by W6/32 antibody and analyzed by Orbitrap Fusion Lumos without FAIMS. Customized database which includes somatic mutations of HCT116 obtained from COSMIC database was used for database search. Identification results were filtered at 1% FDR thresholds by searching against a randomized decoy database using Proteome Discoverer 2.4 (Sequest HT).

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Koji UEDA

PROVIDER: PXD023770 | JPOST Repository | Sat Aug 20 00:00:00 BST 2022

REPOSITORIES: jPOST

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Differential ion mobility mass spectrometry in immunopeptidomics identifies neoantigens carrying colorectal cancer driver mutations.

Minegishi Yuriko Y Kiyotani Kazuma K Nemoto Kensaku K Inoue Yoshikage Y Haga Yoshimi Y Fujii Risa R Saichi Naomi N Nagayama Satoshi S Ueda Koji K

Communications biology 20220818 1

Understanding the properties of human leukocyte antigen (HLA) peptides (immunopeptides) is essential for precision cancer medicine, while the direct identification of immunopeptides from small biopsies of clinical tissues by mass spectrometry (MS) is still confronted with technical challenges. Here, to overcome these hindrances, high-field asymmetric waveform ion mobility spectrometry (FAIMS) is introduced to conduct differential ion mobility (DIM)-MS by seamless gas-phase fractionation optimal ...[more]

PMID: 35982173

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Global identification of HCT116 immunopeptides by FAIMS-assisted immunopeptidomics

Project description:HLA Class I immunopeptides were affinity purified by W6/32 antibody and analyzed by Orbitrap Fusion Lumos with FAIMS. Customized database which includes somatic mutations of HCT116 obtained from COSMIC database was used for database search. Identification results were filtered at 1% FDR thresholds by searching against a randomized decoy database using Proteome Discoverer 2.4 (Sequest HT).

2022-08-20 | PXD023773 | JPOST Repository

Comparison of efficacy in immunfopeptide identification from HCT116 by "with" FAIMS

Project description:HLA class I immunopeptides were affinity purified by W6/32 antibody and analyzed by Orbitrap Fusion Lumos with FAIMS. Customized database which includes somatic mutations of HCT116 obtained from COSMIC database was used for database search. Identification results were filtered at 1% FDR threshold by searching against a randomized decoy database using Proteome Discoverer 2.4 (Sequest HT).

2022-08-20 | PXD023771 | JPOST Repository

Identification of HLA class I immunopeptide from human colon tissue (Tumor)

Project description:HLA Class I immunopeptides were affinity purified by W6/32 antibody and analyzed by Orbitrap Fusion Lumos with FAIMS. Personalized database which includes patient-specific somatic mutations obtained from whole exome sequencing (WES) data was used for database search. Identification results were filtered at 1% FDR thresholds by searching against a randomized decoy database using Proteome Discoverer 2.4 (Sequest HT).

2022-08-20 | PXD023805 | JPOST Repository

Identification of HLA class I immunopeptide from human colon tissue (Normal)

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Transcription profiling of human colorectal cell line HCT116 DICER Exon5 knockout cells

Project description:The experiment was to study the gene expression changes in human colorectal cell HCT116 DICER Exon5 knockout cells comparing to that in parental HCT116 cellls. Experiment Overall Design: Experiment includes using of two Agilent human 44K microarrays with dye-swap replication.

2008-06-14 | E-GEOD-6427 | biostudies-arrayexpress

Gene expression profiling of HCT116 cells with or without PHGDH knockout

Project description:HCT116 cells (WT or PHGDH KO) were harvested and mRNA were extracted for high-throughput sequencing

2021-10-31 | GSE150261 | GEO

Microarray analysis of HCT116 cells with and without a 1.4kb deletion

Project description:One of the strongest associated type 2 diabetes (T2D) loci reported to date resides within the TCF7L2 gene. Previous studies point to the T allele of rs7903146 in intron 3 as the causal variant at this locus. To aid in the identification of the actual gene(s) under the influence of this variant, we first generated a CRISPR/Cas9 mediated 1.4kb deletion of the genomic region harboring rs7903146 in the HCT116 cell line followed by global gene expression analysis. HCT116 cells with or without a CRISPR/Cas9 mediated1.4kb deletion of the genomic region harboring the SNP rs7903146 were analyzed for expression, with 3 replicates per condition (DEL vs WT). We observed 99 genes with significant differential expression (FDR cut-off=10%) and an effect size of at least two-fold. We then carried out high-throughput chromosome conformation capture assays in the HCT116 and NCM460 cell lines and in colon tissue (see experiment E-MTAB-4845) in order to ascertain which of these perturbed genesâ promoters made consistent physical contact with the genomic region harboring the variant. This revealed just one gene, ACSL5, which resides in the same topologically associating domain as TCF7L2.

2016-08-16 | E-MTAB-4839 | biostudies-arrayexpress

Charecterization of RBM42 interacting proteins in HCT116 cells with and without DNA damage

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2023-11-22 | PXD034854 | Pride

microRNA expression of K562, Me45 and HCT116, with or without p53 knock-out, treated with ionizing radiation.

Project description:MicroRNA expression was assessed in human cancer cells (K562, Me45, HCT116 wt and HCT116 p53-/-) treated with 4Gy of ionizing radiation. RNA was extracted from the cells 12 hours after irradiation and after 1h from non-treated controls.

2016-12-01 | E-MTAB-5197 | biostudies-arrayexpress

Next Generation DNA sequencing of telomere fusion events isolated from HCT116 LIG3-/-:mL3, HCT116 LIG4-/-, WT HCT116 and MRC5HPVE6E7 cells

Project description:We characterized the DNA sequences spanning telomere fusion junctions focusing on XpYp:17p inter-chromosomal events in HCT116 LIG3-/-:mL3, HCT116 LIG4-/-, WT HCT116 and MRC5HPVE6E7 cells.

2014-07-30 | E-MTAB-2769 | biostudies-arrayexpress

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