The intuitive and unbiased workflow of Progenesis LC-MS makes the labor-intense data evaluation much more efficient. The support of the mz-XML data format enables the analysis of datasets acquired on many different MS instruments, eliminating the dependency on specialized vendors' software.
How do "same peptide" outlines work in Progenesis LC-MS?
Each run is aligned and the aligned runs are used to find a common set of peptide outlines. All of the runs are used during the peptide detection process so, even if a peptide is missing from one or more runs, its outline will still be found. This set of outlines is then applied to all aligned runs. If a peptide ion is absent from a particular run, an outline is placed were it would be. This means Progenesis LC-MS only measures a zero abundance if the peptide is truly missing.
