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Genome Specific Proteomics

This page lists the available genome-specific FASTA files we have created for a panel of commonly used cancer cell lines, based on accompanying DNA exome sequencing experiments conducted on the Illumina HiSeq platform. The detected mutations were mapped onto the Ensembl reference human genome to detect the protein altering mutations, which can subsequently be used for searching Mass Spectrometry data originating from proteomics experiments. The exact experimental and computational procedures are described in Schoof, Creixell, Pasculescu et al., Nat. Meth. under review. The purpose of these FASTA files are to allow the proteomics community to conduct cell line specific Mass Spectrometry searches on raw data originating from the respective cell lines, facilitating the investigation of how mutations are propagated at the proteome level. This page will be updated with additional cell lines as data becomes available. The files are presented in 2 versions: 1) Only the mutant variants and their wild-type counterparts, or 2) all the mutant variants and wild-type proteins contained in the human v68 Ensembl database.
File AR archive HeLa_STDFILT_mut+wt.fasta
HeLa_STDFILT_mut+wt.fasta
File AR archive HeLa_STDFILT_mut.fasta
HeLa_STDFILT_mut.fasta
File AR archive HT29_STDFILT_mut+wt.fasta
HT29_STDFILT_mut+wt.fasta
File AR archive HT29_STDFILT_mut.fasta
HT29_STDFILT_mut.fasta
File AR archive MCF7_STDFILT_mut+wt.fasta
MCF7_STDFILT_mut+wt.fasta
File AR archive MCF7_STDFILT_mut.fasta
MCF7_STDFILT_mut.fasta

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