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Organic/Biological Mass Spectrometry Data Analysis

OrgMassSpecR / Mass Spectral Libraries

Environmental Contaminant Mass Spectral Libraries

The mass spectral libraries below currently focus on electron impact (EI) spectra of anthropogenic environmental contaminants and halogenated natural products. The libraries document and organize the evidence for compound identifications, and may also contain interesting but unidentified mass spectra. Each library is provided as a PDF report containing the annotated spectra, a single text file containing all spectra in NIST MSP text format, and an R package. The PDF report allows the spectra to be viewed without specialized software. The MSP file can be used to import spectra into other software. The R package stores the mass spectra and associated metadata, and generates the PDF report and text file.

Bottlenose Dolphin Blubber: Rio de Janeiro Coast, Brazil

The original PDF version of this library appears as supporting information for the manuscript referenced below.

Report: SpecLibDolphin2016.pdf
NIST MSP: SpecLibDolphin2016.zip
R Package: SpecLibDolphin2016 Source Package
Reference: "Non-targeted screening of halogenated organic compounds in bottlenose dolphins (Tursiops truncatus) from Rio de Janeiro, Brazil" Environmental Science and Technology (accepted). [Link]
Authors: Mariana B. Alonso, Keith A. Maruya, Nathan G. Dodder, Jose Lailson Brito Jr., Alexandre Azevedo, Elitieri Santos-Neto, Joao Paulo M. Torres, Olaf Malm, Eunha Hoh
Samples: Blubber from common bottlenose dolphins (Tursiops truncatus) fatally stranded on the Rio de Janeiro coast from 2004 to 2011.
Instrument: GCxGC-TOF in EI mode.

DDT-Related Technical Mixture Library

The original PDF version of this library appears as supporting information for the manuscript referenced below. This project has two libraries, one for components of the DDT Technical Mixture, and the other for components of the Kelthane-Dicofol Technical Mixture. The PDF reports and MSP files are generated from a single R package.

Report: SpecLibDDT2015.pdf
SpecLibKelthane2015.pdf
NIST MSP: SpecLibDDT2015.zip
SpecLibKelthane2015.zip
R Package: SpecLibDDT2015 Source Package
Reference: "Newly Identified DDT-Related Compounds Accumulating in Southern California Bottlenose Dolphins" Environmental Science and Technology, 2016, 50, 12129-12137. [Link]
Authors: Susan A. Mackintosh, Nathan G. Dodder, Nellie J. Shaul, Lihini I. Aluwihare, Keith A. Maruya,Susan J. Chivers, Kerri Danil, David W. Weller, Eunha Hoh
Samples: DDT and Kelthane-Dicofol Technical Mixtures.
Instrument: GCxGC-TOF in EI mode.

Bottlenose Dolphin Blubber: Southern California, United States

The original PDF version of this library appears as supporting information for the manuscript referenced below.

Report: SpecLibDolphin2014.pdf
NIST MSP: SpecLibDolphin2014.zip
R Package: SpecLibDolphin2014 Source Package
Reference: "Nontargeted biomonitoring of halogenated organic compounds in two ecotypes of bottlenose dolphins (Tursiops truncatus) from the Southern California Bight" Environmental Science and Technology, 2015, 49, 1328-1338. [Link]
Authors: Nellie J. Shaul, Nathan G. Dodder, Lihini I. Aluwihare, Susan A. Mackintosh, Keith A. Maruya, Susan J. Chivers, Kerri Danil, David W. Weller, Eunha Hoh
Samples: Blubber from two ecotypes of common bottlenose dolphins (Tursiops truncatus) fatally stranded in the Southern California Bight from 1995 to 2010.
Instrument: GCxGC-TOF in EI mode.

Black Skimmer Bird Eggs: San Diego Bay, California, United States

The original PDF version of this library appears as supporting information for the manuscript referenced below.

Report: SpecLibBlackSkimmerEgg2014.pdf
NIST MSP: SpecLibBlackSkimmerEgg2014.zip
R Package: SpecLibBlackSkimmerEgg2014 Source Package
Reference: "Identifying Bioaccumulative Halogenated Organic Compounds Using a Nontargeted Analytical Approach: Seabirds as Sentinels" PLoS One, 10, e0127205. [Link]
Authors: Christopher Millow, Susan A. Mackintosh, Rebecca L. Lewison, Nathan G. Dodder, and Eunha Hoh
Samples: Contents of black skimmer (Rynchops niger) eggs collected in 2011 from San Diego Bay, California.
Instrument: GCxGC-TOF in EI mode.

Common Dolphin Blubber: Massachusetts, United States

The original PDF version of this library appears as supporting information for the manuscript referenced below. Note the PDF version here has different page numbers.

Report: SpecLibDolphin2011.pdf
NIST MSP: SpecLibDolphin2011.zip
R Package: SpecLibDolphin2011 Source Package
Reference: "Nontargeted Comprehensive Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry Method and Software for Inventorying Persistent and Bioaccumulative Contaminants in Marine Environments" Environmental Science and Technology, 2012, 46, 8001-8008. [Link]
Authors: Eunha Hoh, Nathan G. Dodder, Steven J. Lehotay, Kristin C. Pangallo, Christopher M. Reddy, and Keith A. Maruya
Sample: Blubber from a common dolphin (Delphinus delphis) fatally stranded January 2006 in Orleans, Massachusetts.
Instrument: GCxGC-TOF in EI mode.

Sea Lion Blubber (Example Library): Southern California, United States

This library was originally provided as proof-of-concept.

Report: SpecLibExample.pdf
NIST MSP: SpecLibExample.zip
R Package: SpecLibExample Source Package
Authors: Eunha Hoh and Nathan Dodder
Sample: Blubber from a male sea lion (Zalophus californianus) fatally stranded in the year 2000 in southern California.
Instrument: GCxGC-TOF in EI mode. A description of the analytical method is in the package help.