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Mass Spec Data Menu
The MassSpec main menu contains the following options:
Import MZML Data...
The 3D mass spectrometry data in PeakLab is maintained separately from the main 2D chromatography and
spectroscopy data sets. Use this Import MZML data... option to import the 3D data matrices from
MZML files. Because these files can be very large, the number of mass spec data sets you can import may
be limited by the RAM on your machine:
Installed RAM Maximum Mass Spec Data Sets that Can Be Imported
64 25
48 16
32 12
24 9
16 4
Note that you may need to increase Windows' virtual (paged) memory if your data sets are especially
large. PeakLab only imports MS1 data so the count of imported points will be much smaller without the
MS2 data. Still, for HRMS data, you should expect in the vicinity to 5-15 million data points in the MS1
matrix for each data set.
Except for the Agilent data.ms option described below, you must use your instrument's software to
convert the data to the MZML standard in order to import the data in PeakLab.
These data will remain in memory until you the Clear Mass Spec Data menu item to free this memory or until you reinvoke this option to load different data sets.
Import Agilent data.ms Data...
If you have the Agilent data.ms mass spectra data format available, you can use this Import Agilent data.ms Data... option to directly import Agilent mass spectra without first converting the data to an MZML file. Here you specify the .d data folders where the data.ms resides.
Filter Background/Spikes in MS Data...
PeakLab offers this Filter Background/Spikes in MS Data... option to clean noisy MS backgrounds. In this option, PeakLab fits a Whittaker baseline to each MS1 extracted ion chromatogram. For many HRMS data sets, this will consist of thousands of baseline subtractions which are reassembled to produce a background filtered MS data matrix. You must first import MS data using the MassSpec | Import MZML data... or the MassSpec | Import Agilent data.ms Data... option.
View Mass Spec Data [time,m/z,intensity]...
Use this View Mass Spec Data [time,m/z,intensity] option to see a 3D visualization of your MS data matrix. You must first import MS data using the MassSpec | Import MZML data... or the MassSpec | Import Agilent data.ms Data... option.
Fitting the Mass Spec XICs to PeakLab Peak Models and Creating a Overall "Peak Fit"
There are two options for extracting and modeling the XICs in a PeakLab style peak-fit. These options automatically produce a peak fit, except that the XICs are individual fitted and reassembled, and for each peak there is a neutral mass. If you are interested in serious quantification, you should use the first IRD option. You must first import MS data using the MassSpec | Import MZML data... or the MassSpec | Import Agilent data.ms Data... option.
Extract and Fit Quantitative HRMS XICs (IRD)...
Extract and Fit Qualitative HRMS XICs (OpenMS)...
Extract TIC (Total Ion Chromatograms) as CSV Files
You can use the Save TIC CSV files to Original Locations... option to save the TICs of the currently loaded MS data. These will be saved to the same folders as the mzml or mdata.ms files. To use this option, you must be certain those folders are not read only. You must first import MS data using theMassSpec | Import MZML data... or the MassSpec | Import Agilent data.ms Data... option.
Save Current Mass Spec Data to MZML Files...
You can use the Save Current Mass Spec Data to MZML Files... option to save the loaded MS data. These will be saved to the same folders as the original mzml or Agilent mdata.ms files. To use this option, you must be certain those folders are not read only. The files will be written with a (1), (2) suffix. Your original data files will not be overwritten. You must first import MS data using the MassSpec | Import MZML data... or the MassSpec | Import Agilent data.ms Data... option.
Clear Mass Spec Data
Use the Clear Mass Spec Data option to clear all of the MS data stored in memory. Note that the existing MS loaded data will be cleared if new data are imported.