Computational protocol: Variation and Genetic Control of Protein Abundance in Humans

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Protocol publication

[…] Lymphoblastoid cell lines (LCLs) from 95 HapMap individuals were obtained from the Coriell Institute for Medical Research. All trypsin-digest mixtures were analyzed on an LTQ Orbitrap Velos (Thermo Scientific) equipped with an online 2D nanoACQUITY UPLC System (Waters) as previously described with modifications. The acquired mass spectrometry raw data were searched against a human International Protein Index (IPI) database, version 3.75, concatenated with a decoy database with all the protein sequences in reverse order, using SEQUEST algorithm (Proteome Discoverer software, version 1.2, Thermo Scientific). The correspondence between proteins, genes (Ensembl gene IDs) and genomic loci was established based on the protein and gene cross-reference tables of IPI database version 3.87 and transcript sequences of Ensembl database release 62. Screening of peptides overlapping with protein coding changes was based on genotypes and annotations releases by the HapMap and 1000 Genomes Project,,. To estimate the false discovery rate for sex, population and pQTL analyses, the QVALUE Bioconductor package was used. For full methods, see . […]

Pipeline specifications

Software tools Comet, Proteome Discoverer
Databases IPI
Application MS-based untargeted proteomics
Organisms Homo sapiens