MassSpec Directory Structure


Link to the NEW Microchem group storage on new EMC.

You can load RAW files from this location into PD, move Mascot results to this location, store PD results, store fasta databases and load fasta databases into PD from here.

This is Microchem group future location after the old EMC goes away, but can be used already for the purpose of testing the new system. Since it's on the SEER domain, there's no authentication / permission issues.


Similarly, link to any storage on the new EMC.

This should be used for the input RAW data files, user-specific FASTA databases and the final destination for the result data files for user / group. Mascot and PD results should be moved here.


Points to small 1TB area on the network storage that is used to support the MassSpec apps.

Subdirs contain applications, application data, configuration, global FASTA DB repository, scratch / temp files for applications, temporary result data.

Users should NOT store their permanent data there, this is only for TEMPORARY files (not all applications support configuration of the output data path).

Watch your result data and move it regularly to your group storage. Filling up of MassSpec application storage will cause malfunction of the applications, at some point admins will need to start deleting the user data -- it is user responsibility to move their data on regular basis.


Do not touch, applications, apps configs, scratch, etc.

 C:\MassSpec\storage\data\pd, C:\MassSpec\storage\data\mascot

Place for temporary Mascot and PD data -- move your files to your user/group storage when data is ready.


Temporary / scratch space for user data -- use this only if really needed and for short periods of time.

Use your group storage whenever possible (e.g. c:\MassSpec\Microchem2, c:\MassSpec\) instead for your input data and result data (e.g. result data generated by Mascot or PD).


Global, controlled fasta repository for PD and Mascot. Limited privileges here. Users can load custom FASTA databases into PD from user/group storage as needed.


Scripts and tools for any data processing. Directory subtree will be created here for specific projects, groups, researchers, etc.

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