After installing PatternLab for Proteomics, the user is able for analysing proteomics data. Follow step-by-step below to perform the first analysis.
Performing an analysis labeled with iTRAQ®
Note: The images below summarize how PatternLab for proteomics 4.0 works.
Figure 1 shows the Comet search engine's window. Comet will perform a search using the Peptide Spectrum Matching approach. Set all parameters according to this figure changing the directory with RAW files and the sequence database directory reflecting where your files are.
Figure 2 shows the SEPro's window. It is responsible for filtering all data generated by Comet. After filtering the data, SEPro provides a dynamic report containing all identified proteins (Figure 3). The user can visualize the protein coverage, as well as, the spectrum of all identified peptides.
Figure 4 shows the Isobaric Analyzer's window. This module will analyse isotopically labeled data, like TMT® or iTRAQ®. Set all parameters as you can see and click on Generate Report button. For analysing two conditions experiment by click on Two conditions experiment button and then, by click on Go button. The results will be displayed on Result Browser tab, as you can see in (Figure 5). You can visualize a graph showing the intensity signal of each channel from the specific peptide (Figure 6).
⇒ A search engine tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). SIM-XL introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. SIM-XL is the first tool to support XL data in the mzIdentML format.
⇒ A software tool that can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). [YADA 1.0 is available here.]