Download PEAKS Studio 3.1 User Manual - Bioinformatics Solutions Inc.

Select a file (in .ANZ, .pkl, .mgf, .dta, or .txt format). Click the Open button.
Usually, PEAKS Studio 3.1 will then ask us if we want to merge together MS/MS
scans of the same peptide, thereby reducing the amount of data to process, and at the
same time, improving the data quality. To do so, choose a mass range, and press the
OK button. MS/MS spectra whose parent ions are within this mass range of eachother will be merged together. If the data file also contains retention time information, we can
merge spectra whose parent ions’ mass and retention time are closer together than the specified mass
range and retention time range.
If we don’t want to
merge peaks, we
can enter 0.00, or
press the Cancel
button.
The data file we just opened appears in the Peptide Data Frame on the left. It is
represented by its file name. Each spectrum contained in the data file is represented by
its precursor ion information (m/z value followed by the charge of the precursor ion
that generated the spectrum).
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