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A mzIdentML file only contains the identification information: Protein information, peptide information, ion fragments, identification software and other information related with the identification process. One mzIdentML can be related with more than one Mass Spectrum files (mzXML, mzML, mzData, pkl, mgf, dta, ms2). See also mzIdentML specifications.

To add the ms files, you can use two options: Once selected one of these options you can add files with the Add Spectra Files Button. This method will try to find MS annotations in the mzIdentML file and match selected files using the location in the SpectraData object (See also mzIdentML specifications.).

Load spectrum files before mzIdentML loading

If you know the folder and the MS files associated with your mzIdentML you can add them before loading the mzIdentML file.

Load spectrum files before mzIdentML loading

Click on Add spectra files button to associate to each mzIdnetML files the spectra files.

The table below gives a short description for every column in the Spectrum File Table.

Column Description
File Name The name of the File added
Size(M) The size of experiment file to download in megabyte.
Type MS File Type: pkl, mgf, dta, ms2, mzML, mzData
Remove Button to remove the added file
You can choose Set Button to continue with the loading process.

Load spectrum files after mzIdentML loading

After mzIdentML loading you can add the MS files associated with your mzIdentML. Click the Ms information on the Assays Panel

Load spectrum files after mzIdentML loading

Click on Add spectra files button to associate to each mzIdentML files the spectra files. Also you can add manually (Click the Ms Add) for each SpectraData object (See also mzIdentML specifications.) the file associated if the annotated ms name do not match with the actual name of your file.

The table below gives a short description for every column in the Spectrum File Table.

Column Description
File ID SpectraData MS File ID annotated in mzIdentML
Spectra File Source SpectraData MS File Name annotated in mzIdentML
No. Spectra Number of Spectra identified in the mzIdentML file associated with the MS File
MS File Location of the MS File Added
Type MS File Type: pkl, mgf, dta, ms2, mzML, mzData
Add/Remove Button to add manually the file or remove the added file
You can choose Set Button to continue with the loading process.

See Also

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