Proteomics FAQ

Sample Preparation and Submittal

Can the sample be submitted in either gel or liquid form?

Samples can be submitted in either gel or liquid form for all services with the exception of intact protein molecular weight determination.

  • Samples for intact protein molecular weight analysis should be in liquid form (i.e. in buffer solution). The buffer should not contain any detergent. Gel samples are not suitable because the intact protein cannot be extracted from gels efficiently.
  • Gel bands submitted for other services should be cut into approximately 1 mm cubes. View schematic.
  • Liquid samples for all other services can contain up to 4% SDS. If a liquid sample contains SDS, an additional fee for a FASP procedure will be added.

What is the sample submittal process?

Fill out the online project request form, and then hand samples directly to core staff in LTL 016 during business hours, 8:00 a.m. to 6:00 p.m. or drop off in proteomics sample drop-off fridge/freezer in front of LTL 017 near IDT pickup table. Please include the sample transmittal iLAB request form.

Where is the sample drop-off place?

There are two (2) proteomics sample drop-off fridge/freezers in front of LTL 017 near the IDT pickup table.

  1. For a gel sample, put it in an Eppendorf tube with dH2O (along with the iLAB form and labeled with iLAB request number) in the 4°C fridge near the IDT pickup table. Be certain NOT to confuse this location with the DNA sequencing drop-off.
  2. For a liquid sample, put it (along with the iLAB form and labeled with iLAB request number) in -20°C freezer near the IDT pickup table. Be certain NOT to confuse this location with the DNA sequencing drop-off.

How much does it cost and how long will it take to get the results?

An estimated cost will be displayed in iLAB request form and turn around time is about a week.  We will try our best to speed up the process.

    Is it possible to discuss the project before submitting the sample?

    You are always welcome to discuss the project with us. Please contact Saw Kyin, [email protected], 609-258-2210, or stop by the facility (LTL 016) at any time.


    Which database search engine do you use for protein identification?

    We use the Proteome Discoverer software with the built-in Sequest HT search engine and Scaffold software.

    Which database do you use?

    We use the database. If you have a specific database for your project, provide the database in fasta format.

    Can we get a copy of Proteome Discoverer and Scaffold?

    Proteome Discoverer can be downloaded from the Thermo Proteome Discoverer Software portal. After the free trial period of 60 days, it can be used as Proteome Discoverer Viewer to analyze results in .msf files.

    Scaffold software viewer can be downloaded from Proteome Software Inc.

    How will the results be reported?

    Results will be provided in a Scaffold (.sf3) file. A free fully functional viewer is available for download. Users may filter and manipulate their data as they see fit.

    Where will the result be stored?

    Your raw MS data and Scaffold results files will be uploaded to the OIT file server "lowrie". For external collaborators, the Scaffold results file will be sent to you using SecureSend.

    Where is "lowrie"?

    The file server "lowrie" can be accessed at the locations show below, using your Princeton netID and password. If you have not yet been given access to "lowrie" please contact the IT Helpdesk at 609-258-4357 (609-258-HELP) or [email protected].


    1. Right-click on My Computer, and choose "Map network drive"
    2. Enter: "\\\molbio5\corefacilities\proteomics\lab-folder-name*"


    1. In Finder, select Go => Connect to Server
    2. Enter: "cifs://*"

    * Lab folders are named with the PI name followed by "lab", e.g. basserlab, schwarzbauerlab

    Can raw data files be accessed?

    Yes. Raw data files will be uploaded to the file server "lowrie".