Computational protocol: Evaluating the use of HILIC in large-scale, multi dimensional proteomics: Horses for courses?

Similar protocols

Protocol publication

[…] The raw MS data from the Q-Exactive Orbitrap (Thermo Scientific) were processed with the MaxQuant software package (version 1.3.0.5). Proteins and peptides were identified against the UniProt reference proteome database (August 2013) using the Andromeda search engine , . The following search parameters were used: mass deviation of 6 ppm on the precursor and 0.5 Da on the fragment ions; Tryp/P for enzyme specificity; two missed cleavages. Carbamidomethylation on cysteine was set as a fixed modification. Oxidation on methionine; phosphorylation on serine, threonine, and tyrosine; hydroxylation on proline and acetylation at the protein N-terminus were set as variable modifications. Thresholds for the identification of phosphopeptides were Delta Score = 6 and Andromeda score = 40. The false discovery rate was set to 5% for positive identification of proteins, peptides, and phosphorylation sites.Most of the subsequent data analysis was done in R version 3.1.3 using Rstudio 0.98.1091 and the package ggplot2 ; the sequence coverage analysis was done using Perseus 1.5.1.6 and the GO-terms enrichment analysis using the Cytoscape , app BiNGO. […]

Pipeline specifications

Software tools MaxQuant, Andromeda, Ggplot2, Perseus, BiNGO
Applications Miscellaneous, MS-based untargeted proteomics
Organisms Equus caballus