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Reference Reagents for Mass Spectrometry

Adequate monitoring of instrument performance for proteomic studies requires complex protein reference materials. Whole-cell protein extracts provide the needed complexity. We offer mass spec-compatible whole-cell reference protein extracts from yeast and human cells in a convenient, pre-digested lyophilized form.

For routine reporting on MS instrument sensitivity and dynamic range as well various LC parameters, we recommend use of the 6 x 5 LC-MS/MS Peptide Reference Mix. The product is a mixture of 30 peptides: 6 sets of 5 isotopologues of the same peptide sequence differing only in the number of stable, heavy labeled amino acids incorporated into the sequence. Chromatographically, each of the isotopologues is indistinguishable; however, since they differ in mass, they are clearly resolved by mass spectrometry.

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What are Reference Reagents for Mass Spectrometry?

Obtaining the sensitivity and accuracy that makes mass spec analysis such a highly accurate and valuable technique requires sophisticated, well-maintained instrumentation and careful sample preparation. MS instruments can be negatively affected by compounds from biological samples, particularly salts and detergents used in sample prep. These compounds can cause loss of sensitivity of the mass spec analysis.
Regular monitoring of Mass Spec instrument performance and careful validation of sample preparation methods are essential to generating reliable MS data. Such monitoring requires reference materials of high complexity that generate reproducible results. Protein extracts for LC/MS performance monitoring must have:
  • Compatibility with LC/MS (lack detergents, salts, etc.)
  • High integrity (minimal degradation and non-biological PTMs)
  • Compatibility with common sample preparation methods such as proteolysis, PTM enrichment and mass-tag labeling
  • Reproducible lot-to-lot protein composition and quantity
The yeast and human whole cell protein extracts and the 6 × 5 LC-MS/MS Peptide Reference Mixture are predigested protein and peptide mixes designed specifically to meet the above parameters for monitoring LC/MS instrument performance.