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Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories.

ABSTRACT: Mass spectrometry (MS) measurements are not inherently calibrated. Researchers use various calibration methods to assign meaning to arbitrary signal intensities and improve precision. Internal calibration (IC) methods use internal standards (IS) such as synthesized or recombinant proteins or peptides to calibrate MS measurements by comparing endogenous analyte signal to the signal from known IS concentrations spiked into the same sample. However, recent work suggests that using IS as IC introduces quantitative biases that affect comparison across studies because of the inability of IS to capture all sources of variation present throughout an MS workflow. Here, we describe a single-point external calibration strategy to calibrate signal intensity measurements to a common reference material, placing MS measurements on the same scale and harmonizing signal intensities between instruments, acquisition methods, and sites. We demonstrate data harmonization between laboratories and methodologies using this generalizable approach.

SUBMITTER: Pino LK

PROVIDER: S-EPMC6854904 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories.

Pino Lindsay K LK Searle Brian C BC Huang Eric L EL Noble William Stafford WS Hoofnagle Andrew N AN MacCoss Michael J MJ

Analytical chemistry 20181023 21

Mass spectrometry (MS) measurements are not inherently calibrated. Researchers use various calibration methods to assign meaning to arbitrary signal intensities and improve precision. Internal calibration (IC) methods use internal standards (IS) such as synthesized or recombinant proteins or peptides to calibrate MS measurements by comparing endogenous analyte signal to the signal from known IS concentrations spiked into the same sample. However, recent work suggests that using IS as IC introduc ...[more]

PMID: 30350613

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Project description:PubChem serves as a comprehensive repository, housing over 100 million unique chemical structures representing the breadth of our chemical knowledge across numerous fields including metabolism, pharmaceuticals, toxicology, cosmetics, agriculture, and many more. Rapid identification of these small molecules increasingly relies on electrospray ionization (ESI) paired with tandem mass spectrometry (MS/MS), particularly by comparison to genuine standard MS/MS data sets. Despite its widespread application, achieving consistency in MS/MS data across various analytical platforms remains an unaddressed concern. This study evaluated MS/MS data derived from one hundred molecular standards utilizing instruments from five manufacturers, inclusive of quadrupole time-of-flight (QTOF) and quadrupole orbitrap "exactive" (QE) mass spectrometers by Agilent (QTOF), Bruker (QTOF), SCIEX (QTOF), Waters (QTOF), and Thermo QE. We assessed fragment ion variations at multiple collisional energies (0, 10, 20, and 40 eV) using the cosine scoring algorithm for comparisons and the number of fragments observed. A parallel visual analysis of the MS/MS spectra across instruments was conducted, consistent with a standard procedure that is used to circumvent the still prevalent issue of mischaracterizations as shown for dimethyl sphingosine and C20 sphingosine. Our analysis revealed a notable consistency in MS/MS data and identifications, with fragment ions' m/z values exhibiting the highest concordance between instrument platforms at 20 eV, the other collisional energies (0, 10, and 40 eV) were significantly lower. While moving toward a standardized ESI MS/MS protocol is required for dependable molecular characterization, our results also underscore the continued importance of corroborating MS/MS data against standards to ensure accurate identifications. Our findings suggest that ESI MS/MS manufacturers, akin to the established norms for gas chromatography mass spectrometry instruments, should standardize the collision energy at 20 eV across different instrument platforms.

Dataset Information

Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories.

Publications

Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories.

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