Computational protocol: Quantifying extracellular matrix turnover in human lung scaffold cultures

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Protocol publication

[…] Raw files were analyzed in MaxQuant (version 1.5.3.30). The resulting peak lists were searched in Andromeda against a reviewed UniProt human database (Swiss-prot downloaded 2015-11-17), complemented with the standard MaxQuant contaminant database. Enzyme specificity was set to trypsin and a maximum of two missed cleavages. Precursor mass tolerance was set to 4.5 ppm and fragment ion mass tolerance to 20 ppm. Carbamidomethylation of cysteine was used as fixed modification and methionine oxidation as variable modifications. The false discovery rate (FDR) was set to 0.01 for both peptides and proteins. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD007995. […]

Pipeline specifications

Software tools MaxQuant, Andromeda
Databases UniProt
Application MS-based untargeted proteomics
Organisms Homo sapiens
Chemicals Amino Acids