Computational protocol: Integrated proteomics and metabolomics analysis of rat testis: Mechanism of arsenic-induced male reproductive toxicity

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Protocol publication

[…] Details of protein sample preparation, tryptic digestion and proteomic profiling acquisition were described in . The acquired LC-MS/MS data were analyzed using the MaxQuant software (, version for protein identification and quantification. The Andromeda search engine was used for matching the peak lists against a concatenated forward and reverse database including the complete UniProt-SwissProt rat database (reviewed, with a total of 9638 entries) and the standard MaxQuant contaminant database. The following settings were chosen for the MaxQuant software analysis: Carbamidomethyl (C) was set as a fixed modification; Oxidation of methionine and N-terminal acetylation were set as variable modifications. Peptide tolerance was set to 20 ppm for the first and 4.5 ppm for the main search. The maximum number of peptide modifications was set to 5. Trypsin/P was selected as the digestive enzyme and the maximum number of missed cleavages was 2. Peptide and protein false discovery rate (FDR) were set to 0.01. The minimum number of peptide counts was 1 and peptide intensity threshold was set to 500. Quantification was achieved using the LFQ (Label-Free Quantification) algorithms. Protein identification and quantification data were obtained from an output file named proteinGroups (txt format). Protein fold changes were calculated by normalizing the LFQ intensity of treatment groups to that of control (treatment/control ratio, control = 1). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium ( via the PRIDE partner repository with the dataset identifier PXD004364. […]

Pipeline specifications

Software tools MaxQuant, Andromeda
Application MS-based untargeted proteomics
Organisms Rattus norvegicus, Homo sapiens
Chemicals Arsenic, Testosterone