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TRACK INSTRUMENT VARAIBILITY

 

Isolating Sources of Variability in Proteomics

 

There are many possible sources of variation in the protein identification process. MassQC helps isolate the three major areas:

 

• Upstream variability
• LC-MS variability
• Analysis variability

 

Upstream variability includes factors such as variance in the biological samples, sample preparation, protein separation, and digestion.

Analysis variability arises from software settings. MassQC eliminates that source by exactly replicating the calibration analysis process every time.

 

A SUBSYSTEM APPROACH

 

To aid effective analysis, MassQC breaks down the performance of LC-MS systems by subsystem metrics, developed by NIST:

 

• Chromatography
• Ion Source
• MS1
• Dynamic Sampling
• MS2
• Identification

 

Each subsystem has several metrics that characterize performance. You can see each metric at a glance.

 

A SIMPLE PROCESS

 

MassQC uses a three-step process to build a foundation for reproducibility:

 

• First run a standard protein sample, usually something like a Bovine Serum Albumin (BSA) tryptic digest, run on an LC-MS/MS system, using a Data Dependent method
• Next you upload the Thermo® Data Dependent Analysis (DDA) MS/MS *.RAW data to MassQC
• And, finally, compare the newest results to a historic record using the Control Charts