Computational protocol: Exploring the Antimicrobial Action of Quaternary Amines against Acinetobacter baumannii

Similar protocols

Protocol publication

[…] Protein identification was provided by the Proteomics Facility at the University of Texas at Austin following previously published procedures (). Scaffold (version Scaffold_4.8.2; Proteome Software Inc., Portland, OR) was used to validate tandem mass spectrometry (MS/MS)-based peptide and protein identifications. Tandem and Sequest were set up to search acinetobacter_07-15.fasta (unknown version; 3,798 entries), assuming the presence of the digestion enzyme trypsin. Peptide identifications were accepted if they could be established at greater than 89.0% probability to achieve an FDR of less than 1.0%. Peptide probabilities evaluated using Sequest software were assigned by the Scaffold Local FDR algorithm. Peptide probabilities evaluated using X! Tandem software were assigned by the Peptide Prophet algorithm () with Scaffold delta-mass correction. Protein identifications were accepted if they could be established to achieve an FDR of less than 5.0% at greater than 99.0% probability and contained at least 2 identified peptides. Protein probabilities were assigned by the Protein Prophet algorithm (). Proteins that contained similar peptides and that could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony. Proteins were annotated with Gene Ontology (GO) terms from gene_association.goa_uniprot (downloaded 14 January 2015) (). Relative abundances were quantified by the use of normalized exponentially modified protein abundance index (emPAI) values, with a minimal value setting of 0. […]

Pipeline specifications

Software tools Comet, X! Tandem
Application MS-based untargeted proteomics
Organisms Acinetobacter baumannii, Bacteria, Homo sapiens, Staphylococcus aureus, Clostridioides difficile
Diseases Blood Protein Disorders, Proteostasis Deficiencies, Drug-Related Side Effects and Adverse Reactions
Chemicals Amines, Benzalkonium Compounds