Xcalibur columbus software#
Results from standards are manually inspected and/or searched by peptide identification software to determine system performance. Standard protein digests or peptide mixtures are routinely used to calibrate the LC-MS/MS system. In some cases, the LC retention times for peptides are also used as complementary information for peptide identification and characterization (Shinoda et al., 2008). The experimental MS/MS spectra are most commonly transformed by use of database search software into peptide and protein identifications (Sadygov et al., 2004). Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) is one of the most commonly used methods to identify and characterize peptides and proteins in complex samples (Aebersold and Mann, 2003). A basic implementation of the approach based on the MassMatrix database search and LC retention time analysis programs is presented.Īvailability: An open source implementation of the LC-MS/MS system diagnosis software based on the MassMatrix database search program is freely available to non-commercial users and can be downloaded at Contact: information: Supplementary data are available at Bioinformatics online. Furthermore, the results from system diagnosis can provide feedback to the workflow to stop batch analysis if system performance falls below prescribed thresholds. The implementation of a standard approach for assessing LC-MS/MS system performance enables researchers to apply reliable metrics to assess their workflows performance over different batch experiments. This schematic consists of four main software components: (i) data conversion, (ii) peptide identification, (iii) LC retention time analysis and (iv) system performance evaluation. The proposed software scheme provides a robust framework for establishing automated diagnosis of LC-MS/MS system performance for a variety of instruments and experiments. Summary: We report a software scheme for automated diagnosis of liquid chromatography tandem mass spectrometry (LC-MS/MS) system performance.