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MassQC Benefits - Why Use MassQC?

From Rudnick (NIST)et el, 2010, Molecular and Cellular Proteomics:

  • First, is the analytical system performing optimally for the reproducible analysis of complex proteomes?
  • Second, can the sources of suboptimal performance and variability be identified and can the impact of changes or improvements be evaluated?
  • Third, can system performance metrics provide documentation to support the assessment of proteomic differences between biologically interesting samples?

This guide was designed to address the questions above


Metrics point to problem areas. The Control Charts, a history of the metrics, lets you find similar pattern of metrics in the past and use this knowledge to diagnose the present problems.

Optimize Lab Performance

Get better results when measuring real samples by making sure that the LC-MS system is working optimally.

Self Defense

Run standards before and after customer sample so that you can prove to the customer that the instrument was working. This is especially important if the customer’s samples don’t produce the results the customer expects when run through the mass spectrometer.

Support Strategic Planning

  • Decide if components need to be replaced
  • Localizing the largest sources of variation to help decide if replacing one component, for example a pump, would really improve the reproducibility of the LC-MS system
  • Decide which system to buy by comparing the reproducibility of various systems used in other labs

Peer Discussions

Talk with peers running similar instruments to ask for or give help. MassQC gives common vocabulary, metrics and scale for discussing LC-MS issues. And an on-line forum to facilitate finding and communicating with peers.

Train Instrument Operators

  • Check reproducibility to see if more careful procedures are required
  • Check to see that new employees are following protocols rigorously


Demonstrate to potential core lab clients the reproducibility of the LC-MS system.

Startup Protocols/Method Development

Run MassQC when new equipment is acquired and protocols are being worked out.

Check On Service Technician

Run MassQC after instrument has been tuned up by service tech as a check to see if the problem was really fixed.

Optimize Instrument Utilization

  • Use the LC-MS system better by checking that system maintenance brought the LC-MS into compliance
  • Identifying when tuning has changed how the system performs

Cross Lab Studies

Prove to your collaborators that your instruments are reproducible and will work for cross lab studies. Verify that the instruments in other labs are reproducible before agreeing to collaborate with them.


If you have questions, comments and/or insights about MassQC, you can share them on the MassQC Users Forum.

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