Discovering Mercury Protein Modifications in Whole Proteomes Using Natural Isotope Distributions Observed in Liquid Chromatography-Tandem Mass Spectrometry

Journal Article · Mon Aug 01 00:00:00 EDT 2011 · Molecular & Cellular Proteomics. MCP, 10(8):Art. No. 10: M110.004853

DOI:https://doi.org/10.1074/mcp.M110.004853· OSTI ID:1023723

Polacco, Benjamin J; Purvine, Samuel O; Zink, Erika M; LaVoie, Stephen P; Lipton, Mary S; Summers, Anne O; Miller, Susan M

The identification of peptides that result from post-translational modifications is critical for understanding normal pathways of cellular regulation as well as identifying damage from, or exposures to xenobiotics, i.e. the exposome. However, because of their low abundance in proteomes, effective detection of modified peptides by mass spectrometry (MS) typically requires enrichment to eliminate false identifications. We present a new method for confidently identifying peptides with mercury (Hg)-containing adducts that is based on the influence of mercury’s seven stable isotopes on peptide isotope distributions detected by high-resolution MS. Using a pure protein and E. coli cultures exposed to phenyl mercuric acetate, we show the pattern of peak heights in isotope distributions from primary MS single scans efficiently identified Hg adducts in data from chromatographic separation coupled with tandem mass spectrometry with sensitivity and specificity greater than 90%. Isotope distributions are independent of peptide identifications based on peptide fragmentation (e.g. by SEQUEST), so both methods can be combined to eliminate false positives. Summing peptide isotope distributions across multiple scans improved specificity to 99.4% and sensitivity above 95%, affording identification of an unexpected Hg modification. We also illustrate the theoretical applicability of the method for detection of several less common elements including the essential element, selenium, as selenocysteine in peptides.

• Research Organization: Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1023723
• Report Number(s): PNNL-SA-80519; 34915; KP1504010; TRN: US201120%%1059
• Journal Information: Molecular & Cellular Proteomics. MCP, 10(8):Art. No. 10: M110.004853, Vol. 10, Issue 8
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
ADDUCTS
DAMAGE
DETECTION
ELEMENTS
ENRICHMENT
FRAGMENTATION
ISOTOPES
ISOTOPE RATIO
LIQUID COLUMN CHROMATOGRAPHY
MASS SPECTROSCOPY
MERCURY
MODIFICATIONS
PEPTIDES
PROTEINS
SELENIUM
SENSITIVITY
SPECIFICITY
STABLE ISOTOPES
XENOBIOTICS
POSTTRANSLATIONAL MODIFICATIONS
PEPTIDE IDENTIFICATIONS
SOFTWARE PACKAGE
MS
THROUGHPUT
STRATEGY
DATABASE
IONIZATION
SEARCH
GENOME
Environmental Molecular Sciences Laboratory