To upload spectral files to the existing or new experiment, click the “+ Upload spectral files” link in the experiment view page. Then the uploading box will appear to choose spectral files to upload.

Spectral file formats can be ms1/ms2 files or Thermo raw file with “convert raw file” check box selected. ms1/ms2 files can be generated from RawConverter, RawXtractor, ProteoWizard, etc. (We recommend RawConverter for better precursor ion detection). If you have raw files from different vendors, you can try IP2Daemon or contact us. For batch file uploading, users can use IP2Daemon described in next chapter.

For ABSciex wiff file, Users can convert wiff files to mzML by using AB SCIEX MS Data Converter (http://www.absciex.com/downloads/software-downloads) Then, use RawConverter to convert mzML to MS1/MS2

Figure 5.1.1 Click “ Plus.png” to display the upload interface

Figure 5.1.2 spectra file type to upload

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