Proteinpilot 4.5 beta

Tandem mass spectrometric analysis was carried out using AB SCIEX TripleTOF 5600+ instrument (AB SCIEX, Redwood City, CA, USA) coupled to Eksigent expert nano-LC 400 system (AB SCIEX). MS and MS/MS data was acquired using Analyst^® TF v.1.6 (AB SCIEX).
Mass spectrometry data was analyzed by using ProteinPilot 4.5 Beta (AB SCIEX) for the peptide identifications. Detailed protocol in Supplementary File S5. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [33 ] via the PRIDE partner repository with the dataset identifier PXD003018.

Tandem mass spectrometric analysis was carried out using an AB SCIEX TripleTOF 5600+ instrument (AB SCIEX, Redwood City, CA, USA) coupled to an Eksigent expert nano-LC 400 system (AB SCIEX). MS and MS/MS data were acquired using Analyst® TF v.1.6 (AB SCIEX).
Mass spectrometry data was analyzed using ProteinPilot 4.5 Beta (AB SCIEX) for peptide identification.

Shotgun proteomic analyses have been performed with AB SCIEX TripleTOF^® 5600+ integrated to Eksigent ekspert™ nanoLC 400 System (AB Sciex, USA). Trap column (3 μm, ChromXP C18CL) and nanoAQUITY UPLC^® NanoLC column (1.8-μm HSS T3, 75 μm × 150 mm) were used in the trap-elute mode for the separation of peptides. Within the 310-min analysis, Data Dependent Acquisition Top 20 tandem MS was performed. Raw data analysis and multiple analytical measurements in a single sample were done using Analyst^® TF v.1.6 (AB Sciex, USA) software. Precursor and product ion evaluations were completed with PeakView (1.2, AB Sciex). Generated peak lists containing MS and MS/MS spectra were used to identify proteins, protein isoforms, and their modifications with ProteinPilot 4.5 Beta (AB Sciex, USA). Identification was made using the UniProtKB-based reference library of resistant strain A. baumannii BAA 1710 (UP000002446) and non-resistant strain A. baumannii 17978 (UP000006737). During identifying proteins, the false discovery rate was determined to be 1%, and proteins containing at least two identified peptide fragments were considered correct identification.

LC–MS/MS analysis was performed with a Triple ToF 5600+ (AB Sciex, Framingham, MA, USA) that was associated with an LC–MS/MS Eksigent Ekspert NanoLC 400 System (AB Sciex). The peptide mixture was separated by a nanoACQUITY UPLC 1.8 μM HSS T3 C18 column (Thermo Fisher, Waltham, MA, USA) in the trap‐elute mode. A 4–40% ACN gradient was used for 240 min to separate the peptides. Data dependent acquisition (DDA) MS/MS analysis of separated peptides was performed after electrospray ionization. For each sample, the raw data analysis and multiple analytical data measurements were performed with Analyst TF v.1.6 (AB Sciex). The peptides and the ion‐product of the MS and MS/MS data were evaluated with PeakView (AB Sciex). Generated peak‐lists were evaluated in consideration of the UniProtKB‐based reference library of the Homo sapiens species on our server with ProteinPilot 4.5 Beta (AB Sciex).