Computational protocol: eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs

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Protocol publication

[…] Samples were analyzed by LC-MS/MS using an UltiMate 3000 RSLC nano HPLC (Dionex) in-line connected to a Q-Exactive HF mass spectrometer (Thermo Fisher Scientific Inc.). Spectra identification was performed with MaxQuant (version 1.5.3.30) using the Andromeda search engine () with false discovery rate (FDR) set at 1% on peptide and protein level. Spectra were searched against the ‘aTIS database’ or ‘custom database’. Proteins were quantified by the MaxLFQ algorithm integrated in the MaxQuant software (). For details, see . […]

Pipeline specifications

Software tools MaxQuant, Andromeda
Application MS-based untargeted proteomics
Chemicals Nucleotides