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Using Clarity LabLink LIMS

In order for Penn State College of Medicine’s Mass Spectrometry core to archive and distribute the eventual data from investigator experiments, investigators need to set up a (free) account in Clarity LabLink Laboratory Information Management System (LIMS), which takes a few days to get approved by IT.

For External Users Only

For external users – that is, those who do not have an or email address – the external user or someone in their lab needs to create a Penn State Access ID account following the instructions here.

After Getting a Penn State Access ID

Investigators then need to set up a LabLink Clarity LIMS account, and once this LIMS account is approved (which comes with an email confirmation), the investigator can go into the LabLink site and import the appropriate Excel sample submission spreadsheet for the sample into Clarity LabLink.

Submitting Samples in Clarity LabLink LIMS

  • Select “Submit Samples” on the left of the entry screen.
  • Choose “Create a new project”, enter the project name, and select project type “Proteomics & Mass Spectrometry” then use the other drop-down boxes and/or type in all needed information to create the project under which this and similar samples will be organized.
  • Select “Import a sample spreadsheet” and then click “Choose File” to find the completed Excel spreadsheet, then select “Next.”
  • If there are any errors with the Excel sample submission sheet, an error message will show up in red type, and they will need to be corrected on the sample submission sheet and resubmitted. Investigators who cannot figure out how to correct the sample submission sheet should email Dr. Bruce Stanley at, attaching the “problem” Sample Submission Sheet to the email.
  • Once the sample submission sheet has all the required information in it, another screen will appear displaying important terms and conditions. Investigators must indicate agreement by clicking “Agree.”
  • This will then bring up a screen that should be printed, signed and included with the physical sample submission, along with a hard-copy printout of the original sample submission sheet. This allows the core to know exactly what the sample is called, what type of sample it is, where the information for the sample is located in the LabLink Clarity LIMS system, and what is to be done with the sample. All this information is then permanently archived in the LabLink Clarity LIMS system as well for future reference, e.g., when preparing manuscripts etc.
  • After printing, clicking “Done” will return the user to the top level of the LabLink Clarity LIMS system, where investigators can either submit additional sample or project information or log out.

Delivering Physical Samples

Physical samples and the printed information from above (signed LIMS sheet, and printed sample submission Excel sheets) should be delivered to Room C1734 at Penn State College of Medicine, notifying Anne Stanley, Suja Maddukuri, Bruce Stanley or Dongxiao Sun that samples are being dropping off so that they can be stored properly (Freezer B) and the paperwork properly noted.

Researchers from University Park can send samples using the campus shuttle if the Mass Spectrometry and Proteomics Core is notified of exactly when delivery can occur. (Check by calling 717-531-6087.) Note that no dry ice containers are accepted.

The package must have the address and contact information below clearly marked on it, and must also be accompanied a completed University Shuttle Transport Form.

Address for All Shipments

Anne Stanley
Section of Research Resources
Room C1734
Penn State College of Medicine
500 University Dr.
Hershey, PA 17033-2390

Telephone: 717-531-6087


Researchers from other universities and companies can ship samples to the above address using FedEx, UPS, USPS, etc., being certain to ship in conditions that will maintain sample quality during the time required to deliver the samples to the College of Medicine. No Saturday or Sunday deliveries can be accepted.