Organic Mass Spectrometry

Description

Organic/biological mass spectrometry data analysis.

http://OrgMassSpec.github.io/

Convert Concentration Basis

Description

Change the unit basis for a sample concentration, such as ng/g wet weight to ng/g dry weight, or pg/g lipid weight to pg/g wet weight.

Usage

ConvertConcentration(x, convert, percent)

Arguments

Details

The convert argument specifies the type of conversion, for example wet.to.dry is wet weight basis to dry weight basis.

Conversion between wet weight basis and dry weight basis requires percent to equal the percent moisture in the sample. Conversion between wet weight basis and lipid weight basis requires percent to equal the percent lipid in the sample. The following definitions for percent moisture and percent lipid are used.

percent moisture = \frac{wet weight - dry weight}{wet weight} * 100

percent lipid = \frac{lipid weight}{wet weight} * 100

The unit prefixes (for example ng/g or pg/g) are not changed by the conversion.

Value

Numeric vector of length 1. The unit prefixes are the same as for x, only the concentration basis is converted.

Author(s)

Nathan G. Dodder

Examples

## Convert a concentration of 15.3 ng/g wet weight,
## 5 percent lipid, to ng/g lipid weight.

ConvertConcentration(15.3, "wet.to.lipid", 5)

Convert peptide sequence.

Description

Convert single amino acid codes to an elemental formula or three letter codes.

Usage

ConvertPeptide(sequence, output = "elements", IAA = TRUE)

Arguments

Details

The amino acid residues must be specified by the one letter codes defined in the help for Digest.

The argument IAA specifies treatment of the protein with iodoacetamide to break the disulfide bonds. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S).

Value

If output = "elements", the value is a list specifying the number of each element. This list can be used as input to other functions, see the examples. If output = "3letter", the value is a vector of length 1, containing the amino acid sequence in three letter codes.

Author(s)

Nathan G. Dodder

Examples

ConvertPeptide("SEQENCE", output = "3letter")

# as input to MonoisotopicMass
MonoisotopicMass(formula = ConvertPeptide("SEQENCE"), charge = 1)

# as input to MolecularWeight
MolecularWeight(formula = ConvertPeptide("SEQENCE"))

Internal volume of tubing.

Description

Calculate the internal volume of a defined length of tubing.

Usage

DeadVolume(internalDiameterMicrometers = 24, tubeLengthCentimeters = 45)

Arguments

Value

Vector of the dead volume in microliters.

Author(s)

Nathan G. Dodder

See Also

FlowTime

Examples

DeadVolume(internalDiameterMicrometers = 47, tubeLengthCentimeters = 33)

Predict Peptides Resulting from Enzymatic Digest

Description

Cleave an amino acid sequence (a protein or peptide) according to enzyme specific rules and calculate the precursor ion m/z values.

Usage

Digest(sequence, enzyme = "trypsin", missed = 0, IAA = TRUE, 
       N15 = FALSE, custom = list())

Arguments

Details

The amino acid residues must be specified by one letter codes. The predefined residues are:

If "trypsin" is specified, the sequence is cleaved on the c-terminal side of K and R residues, except if K or R is followed by P. If "trypsin.strict" is specified, the sequence is cleaved on the c-terminal side of K and R residues. If "pepsin" is specified, the sequence is cleaved on the c-terminal side of F, L, W, Y, A, E, and Q residues. This rule is specific to pepsin at pH > 2, as used in hydrogen-deuterium exchange experiments.

When "trypsin" is specified, KP and RP are not considered missed cleavages when missed is > 0.

The argument IAA specifies treatment of the protein with iodoacetamide. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S).

If TRUE, the argument N15 specifies 100% nitrogen-15 incorporation. It is intended for proteins grown with a nitrogen-15 labeled food source. (Although the experiment itself may grow a protein with less than 100% nitrogen-15 incorporation). Setting N15 = TRUE does not modify the mass of a custom residue, or the mass of the nitrogen(s) added if IAA = TRUE.

If a custom residue code is identical to a predefined residue code, the custom residue mass will be used in place of the predefined mass.

The error message “object "mass" not found” indicates the input sequence contains an undefined residue(s).

Value

A data frame with the following column names.

Author(s)

Nathan G. Dodder

References

The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cuu/Constants/index.html.

See Also

MonoisotopicMass, FragmentPeptide

Examples

## digest human serum albumin with 0 and 1 missed cleavages
Digest(example.sequence, missed = 1)

## digest human serum albumin with a phosphoserine at position 58
## and all methionines oxidized
modifiedHsaSequence <- strsplit(example.sequence, split = "")[[1]]
modifiedHsaSequence[58] <- "s"   # insert code for phosphoserine  
modifiedHsaSequence <- paste(modifiedHsaSequence, collapse = "")
Digest(modifiedHsaSequence, custom = list(code = c("s","M"), 
       mass = c(MonoisotopicMass(list(C=3, H=6, N=1, O=5, P=1)),
                MonoisotopicMass(list(C=5, H=9, N=1, O=2, S=1)))))
                
## digest human serum albumin with strict rules
Digest(example.sequence, enzyme = "trypsin.strict")

Plot a Chromatogram

Description

Plot a chromatogram, color the area under specified peak(s), and calculate the peak area(s).

Usage

DrawChromatogram(time, intensity, range = list(start, stop), color = "blue", 
                 xlab = "retention time", ylab = "intensity", 
                 ylim = c(0, max(intensity) * 1.1), las = 1, ...)

Arguments

Details

The area under the peak(s) is rendered using the polygon function. The area calculation assumes that the polygon does not self-intersect.

Value

A data frame with the following column names.

Author(s)

Nathan G. Dodder

Examples

## single peak
x <- DrawChromatogram(example.chromatogram.single$time,  
                      example.chromatogram.single$intensity/100, 
                      range = list(start = 25.4, stop = 26.1), 
                      main = "example chromatogram 1",
                      ylab = "intensity x 100")
# label peak with retention time and area
text(x$retentionTime, x$apexIntensity + 1500, 
     labels = paste("RT = ", round(x$retentionTime, digits = 1),
                    ", Area = ", round(x$peakArea), sep = ""), cex = 0.9) 

## multiple peaks 
y <- DrawChromatogram(example.chromatogram.multiple$time, 
                      example.chromatogram.multiple$intensity / 1000, 
                      range = list(start = c(21.5, 21.925, 23.1, 25.5, 27.35), 
                        stop = c(21.925, 22.4, 23.6, 26.2, 28.0)),
                      color = c("blue", "red", "green", "yellow", "orange"), 
                      xlab = "retention time (min)", 
                      ylab = "intensity x 1000 (cps)", 
                      main = "Example Chromatogram")
## label peaks
text(y$retentionTime, y$apexIntensity + 50, labels = c("a", "b", "c", "d", "e"))

Determine the Number of Backbone Amide Hydrogens

Description

Determine the number of backbone amide hydrogens given a protein/peptide sequence. Used in hydrogen-deuterium exchange experiments.

Usage

ExchangeableAmides(sequence)

Arguments

Details

The number of backbone amide hydrogens in an amino acid sequence is the number of residues, minus the number of prolines, minus 1.

Value

A numeric vector containing the number of exchangeable hydrogens.

Author(s)

Nathan G. Dodder

See Also

IsotopicDistributionHDX

Examples

ExchangeableAmides(c("VDVMCTA", "VSTPTL"))

## find the number of exchangeable amides for 
## each peptide in a digest of human serum albumin
x <- Digest(example.sequence, enzyme = "pepsin", IAA = FALSE, missed = 4)
transform(x, exchange = ExchangeableAmides(x$peptide))

Solvent transit time.

Description

Calculate the time required for a liquid to flow through a defined length of tubing. Intended for conventional-flow or nano-flow liquid chromatography.

Usage

FlowTime(internalDiameterMicrometers = 24, tubingLengthCentimeters = 45, 
                flowRateMicrolitersPerMinute = 0.3)

Arguments

Details

The calculation assumes the viscosity of the liquid is negligible.

Value

Vector of the flow time in seconds.

Author(s)

Nathan G. Dodder

See Also

DeadVolume

Examples

FlowTime(internalDiameterMicrometers = 47, tubingLengthCentimeters = 33, 
                   flowRateMicrolitersPerMinute = 5)

Predict Peptide Fragment Ions

Description

Determine the b- and y-ions or c- and z-ions produced by the fragmentation of a peptide by tandem mass spectrometry.

Usage

FragmentPeptide(sequence, fragments = "by", IAA = TRUE, 
                N15 = FALSE, custom = list())

Arguments

Details

The amino acid residues must be specified by the one letter codes defined in the help for Digest.

The fragmentation rules can be set for collision induced dissociation (b- and y-ions) or electron transfer dissociation (c- and z-ions).

The argument IAA specifies treatment of the protein with iodoacetamide to break the disulfide bonds. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S).

If TRUE, the argument N15 specifies 100% nitrogen-15 incorporation. It is intended for proteins grown with a nitrogen-15 labeled food source. (Although the experiment itself may grow a protein with less than 100% nitrogen-15 incorporation). Setting N15 = TRUE does not modify the mass of a custom residue, or the mass of the nitrogen(s) added if IAA = TRUE.

If a custom residue code is identical to a predefined residue code, the custom residue mass will be used in place of the predefined mass.

Value

A data frame with the following column names. The data frame is arranged this way to facilitate selection of product-precursor ion pairs.

Author(s)

Nathan G. Dodder and Katharine M. Mullen

References

The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cgi-bin/cuu/Value?mmp.

See Also

MonoisotopicMass, Digest, PeptideSpectrum

Examples

## fragment unlabeled peptide
FragmentPeptide("NECFLQHK")

## fragment peptide with carbon-13 labeled lysine
k.mass <- MonoisotopicMass(formula = list(C = 6, H = 12, N = 2, O = 1),
                       isotopes = list(C = 13.0033548378)) 
FragmentPeptide("NECFLQHk", custom = list(code = "k", mass = k.mass))

## fragment peptide with two modifications
m.mass <- MonoisotopicMass(formula = list(C=5, H=9, N=1, O=2, S=1))
FragmentPeptide("NDmELWk", custom = list(code = c("m", "k"), mass = c(m.mass, k.mass)))

## fragment a vector of peptides produced by Digest
x <- Digest(example.sequence)
y <- subset(x, nchar(x$peptide) > 5 & nchar(x$peptide) < 12)
FragmentPeptide(y$peptide)

Isotopic Distribution of an Organic Molecule.

Description

Simulate the isotopic distribution of an organic molecule using the natural abundances of the isotopes.

Usage

IsotopicDistribution(formula = list(), charge = 1)

Arguments

Details

The elemental formula should be that of the charged molecule; i.e, the charge argument does not change the elemental formula.

The algorithm used in this function is based on sample, and will give a slightly different result each time it is run.

This function is intended for simulating the isotopic distributions of small molecules (< approximately 3000 amu and <= 3 charges) as measured on low resolution mass spectrometers.

Value

A data frame with the following column names.

Author(s)

Nathan G. Dodder

References

The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/.

See Also

IsotopicDistributionN, IsotopicDistributionHDX, sample

Examples

x <- IsotopicDistribution(formula = list(C = 9, H = 4, Br = 5, Cl = 1, N = 2))
library(lattice)
xyplot(percent ~ mz, data = x,
  type = "h",
  xlab = "m/z",
  ylab = "intensity (%)",
  main = "Isotopic Distribution, C9H4Br5ClN2")

Isotopic Distribution of a Peptide Undergoing H-D Exchange

Description

Simulates the isotopic distribution of a peptide undergoing hydrogen-deuterium exchange. Only the peptide backbone amides are labeled with deuterium.

Usage

IsotopicDistributionHDX(sequence, incorp, charge = 1, 
                        custom = list(code = NULL, elements = NULL))

Arguments

Details

The amino acid residues must be specified by the one letter codes defined in the help for Digest. If a custom residue code is identical to a predefined residue code, the custom residue mass will be used in place of the predefined mass.

The natural incorporation of deuterium is 0.000115.

The algorithm used in this function is based on sample, and will give a slightly different result each time it is run. IsotopicDistributionHDX has not been tested for sequences over approximately 3000 amu and charges greater that 3+.

Value

A data frame with the following column names.

Author(s)

Nathan G. Dodder

References

The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cuu/Constants/index.html.

See Also

IsotopicDistribution, IsotopicDistributionN, sample

Examples

## simulate a peptide with 0.0115 and 100 percent incorporation and plot
x <- IsotopicDistributionHDX("NECFLQHK", incorp = 0.000115)
x$t <- "incorp = 0.0115%"
y <- IsotopicDistributionHDX("NECFLQHK", incorp = 1)
y$t <- "incorp = 100%"
z <- rbind(x, y)
library(lattice)
print(xyplot(percent ~ mz | t, data = z,
       type = "h", main = "H-D exchange simulation",
       xlab = "m/z", ylab = "intensity (%)"))

Isotopic Distribution of a Nitrogen-15 Labeled Peptide.

Description

Simulates the isotopic distribution of a nitrogen-15 labeled peptide. Intended for peptides from proteins grown in media with, for example, nitrogen-15 labeled ammonium chloride as the only nitrogen source.

Usage

IsotopicDistributionN(sequence, incorp, IAA = TRUE, charge = 1, 
                      custom = list(code = NULL, elements = NULL))

Arguments

Details

The amino acid residues must be specified by the one letter codes defined in the help for Digest. If a custom residue code is identical to a predefined residue code, the custom residue will NOT be used in place of the predefined residue; doing so will cause errors.

The natural nitrogen-15 incorporation is 0.00368.

The argument IAA specifies treatment of the protein with iodoacetamide. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S). The nitrogen(s) added is not labeled.

The algorithm used in this function is based on sample, and will give a slightly different result each time it is run. It is similar to the algorithm used in reference 1. IsotopicDistributionN has not been tested for sequences over approximately 3000 amu and charges greater that 3+.

Value

A data frame with the following column names.

Author(s)

Nathan G. Dodder

References

1. "Method for Estimating the Isotopic Distributions of Metabolically Labeled Proteins by MALDI-TOFMS: Application to NMR Samples." Choudhary K, Spicer VL, Donald LJ, Duckworth HW, Ens W, Loewen PC, Standing KG, Analytical Chemistry, 2006, 78, 5419-5423.

2. "Perturbation and Interpretation of Nitrogen Isotope Distribution Patterns in Proteomics" Snijders APL, de Koning B, Wright PC, Journal of Proteome Research, 2005, 4, 2185-2191.

3. "Measurement of the Isotope Enrichment of Stable Isotope-Labeled Proteins Using High-Resolution Mass Spectra of Peptides" MacCoss MJ, Wu CC, Matthews DE, and Yates III JR, Analytical Chemistry, 2005, 77, 7646-7653.

The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cuu/Constants/index.html.

Note that in reference 3 "a biologically relevant 13C/12C isotope ratio of 1.096% was used instead of the more carbonate specific ratio of 1.112%." The 13C/12C ratio used by IsotopicDistributionN is 1.081%.

See Also

IsotopicDistribution, IsotopicDistributionHDX, sample

Examples

## simulate a peptide with 0.368 to 100 percent incorporation and plot
dn <- IsotopicDistributionN("NECFLQHK", incorp = 0.00368)
dn$t <- "incorp = 0.368%"
d50 <- IsotopicDistributionN("NECFLQHK", incorp = 0.5)
d50$t <- "incorp = 50%"
d99 <- IsotopicDistributionN("NECFLQHK", incorp = 0.99)
d99$t <- "incorp = 99%"
x <- rbind(dn, d50, d99)
library(lattice)
xyplot(percent ~ mz | t, data = x,
    type = "h", 
    xlab = "m/z", 
    ylab = "intensity (%)",
    main = "Isotopic distribution of peptide NECFLQHK with 
            varying nitrogen-15 incorporation")
## Not run:          
## simulate peptide DVFLGMFLYPYAR with oxidized methionine
IsotopicDistributionN("DVFLGmFLYPYAR", incorp = 0.5, 
                      custom = list(code = "m", 
                                    elements = c(C=5, H=9, N=1, O=2, S=1)))

## End(Not run)

Convert an Elemental Formula to a List

Description

Convert a character string representing an elemental formula to a list representing the elemental formula. The list can be used as input to other functions.

Usage

ListFormula(elemental.formula)

Arguments

Details

To maintain compatibility with MolecularWeight, MonoisotopicMass, and IsotopicDistribution the elemental formula can contain only C,H,N,O,S,P,Br,Cl,F,I,Si, and Sn (I and Sn are default elements in MolecularWeight only). Elements not in this set will be ignored and a warning will be generated. The function can handle repeated elements, but not element multiplication indicated by parenthesis.

Known issue: Lower case letters after numbers, such as the “o” in “C12oBr5H5” will not be caught with a warning and the resulting list will contain the incorrect number of elements.

Author(s)

Nathan G. Dodder

See Also

ConvertPeptide

Examples

ListFormula("C14H8Cl4")
ListFormula("C6H5OH")
ListFormula("C15H12I3NO4")

Calculate the molecular weight of an organic molecule.

Description

Given an elemental formula and the average relative atomic masses of the elements, determine the molecular weight.

Usage

MolecularWeight(formula = list(), amu = list())

Arguments

Details

The user defined x in the argument lists can be used to define an additional element, such as a metal. See example.

Due to apparent rounding differences at the elemental level, other sources of molecular weight information may vary in the second or third decimal place.

This function will accept values that do not correspond to known physical reality, such as a fractional number of elements or the wrong standard atomic mass for an element.

Value

The molecular weight of the molecule.

Author(s)

Nathan G. Dodder

References

The relative atomic masses of the elements are from the NIST Physical Reference Data Website https://www.nist.gov/pml/atomic-weights-and-isotopic-compositions-relative-atomic-masses.

See Also

MonoisotopicMass

Examples

MolecularWeight(formula = list(C=2, H=4))

## Molecular weight of cyanocobalamin (C63H88CoN14O14P) with user defined cobalt
MolecularWeight(formula = list(C=63, H=88, N=14, O=14, P=1, x=1),
                amu = list(x = 58.933200))
                
## Molecular weight of triiodothyronine (C15H12I3NO4) using output from ListFormula
MolecularWeight(formula = ListFormula("C15H12I3NO4"))               

Calculate the monoisotopic mass or monoisotopic m/z value of an organic molecule.

Description

Given an elemental formula, the relative atomic masses of the isotopes, and the charge state, determine the monoisotopic mass or monoisotopic m/z value.

Usage

MonoisotopicMass(formula = list(), isotopes = list(), charge = 0)

Arguments

Details

The elemental formula describes the uncharged molecule; the charge argument will add or remove hydrogens as needed. This assumes an electrospray or MALDI type ionization. In electron impact ionization a positive charge is generated by loss of an electron, not additon of H+, therefore to calculate the correct m/z, the charge should be set to zero as a workaround.

The relative atomic masses of the most abundant isotopes (carbon-12, hydrogen-1, nitrogen-14, and oxygen-16) are set as the default values. For reference, the relative atomic masses of some common isotopic labels are:

The user defined element x can be used to define an additional element, such as a metal, or to specify a certain number of isotopically labeled atoms in a molecule. See Examples.

This function will accept values that do not correspond to known physical reality, such as a fractional number of elements, a fractional charge, or the wrong relative atomic mass value for an isotope.

Value

The monoisotopic mass of the unchaged molecule or the monoisotopic m/z value of the charged molecule.

Author(s)

Nathan G. Dodder and Katharine M. Mullen

References

The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cuu/Constants/index.html.

See Also

Digest, FragmentPeptide, MolecularWeight

Examples

## monoisotopic m/z of creatinine (C4H7N3O), +1 charge
## unlabeled
MonoisotopicMass(formula = list(C=4, H=7, N=3, O=1), charge = 1)
## with all carbon-13 atoms
MonoisotopicMass(formula = list(C=4, H=7, N=3, O=1), 
                 isotopes = list(C = 13.0033548378),
                 charge = 1) 
## with 2 carbon-12 atoms and 2 carbon-13 atoms
MonoisotopicMass(formula = list(C=2, H=7, N=3, O=1, x=2), 
                 isotopes = list(x = 13.0033548378),
                 charge = 1)

## monoisotopic mass of cyanocobalamin (C63H88CoN14O14P)
MonoisotopicMass(formula = list(C=63, H=88, N=14, O=14, P=1, x=1),
                 isotopes = list(x = 58.9332002))

Plot Annotated Peptide Fragmentation Mass Spectrum

Description

Identify the b- and y-ions or c- and z-ions in a peptide fragmentation mass spectrum given the sequence. Generate a plot and table identifying the fragment ions.

Usage

PeptideSpectrum(expt, theory, t = 0.4, b = 5, label = "", xlim = c(100, 1500), 
                supress = FALSE)

Arguments

Details

A graphics window of width = 10 and height = 5.5 seems to work well. A crude attempt is made to prevent overlapping peak annotations. If this is unsuccessful, use supress = TRUE and then add the annotations using the text function. If two or more peak identifications are made within the set tolerance, all identifications will be printed, overlapping, on the plot.

Value

Generates an annotated spectrum and a data frame showing the matches between the experimental peaks and the theoretical fragment ions. The column names refer to the experimental m/z value (expt_mz), the experimental peak intensity (expt_int) and the error between the experimental and theoretical m/z values (error). The other column names are the same as for FragmentPeptide.

Author(s)

Nathan G. Dodder

See Also

FragmentPeptide

Examples

## plot spectrum of peptide NIDALSGMEGR
t <- FragmentPeptide("NIDALSGMEGR")   # generate theoretical fragment ions
PeptideSpectrum(example.spectrum.peptide, t, label = "CID", xlim = c(100, 1200))
mtext("Peptide fragmentation mass spectrum", line = 1)

Read in MSP Formatted Mass Spectra

Description

Reads in all .msp files within a directory and makes a single concatenated data frame of m/z values and intensities.

Usage

ReadMspDirectory(directory, skip = 2, comment.char = "", 
                 remove.placeholders = TRUE)

Arguments

Details

MSP is a National Institute of Standards and Technology (NIST) text format for centroid spectra. This format is exported by some instrument software.

The spectral files do not need to have the extension .msp. But an attempt will be made to process all files in the directory, regardless of the extension. The presense of other file types may cause errors.

ReadMspDirectory is a wrapper for ReadMspFile.

Value

A data frame with the following column names:

Author(s)

Nathan G. Dodder

See Also

ReadMspFile

Examples

## The package directory msp contains two .msp files 
ReadMspDirectory(paste(system.file(package = "OrgMassSpecR"), 
  "/extdata/msp", sep = ""))

Read in a MSP Formatted Mass Spectrum

Description

Reads in a .msp file and makes a data frame of m/z values and intensities.

Usage

ReadMspFile(file, skip = 2, comment.char = "", 
            remove.placeholders = TRUE)

Arguments

Details

MSP is a National Institute of Standards and Technology (NIST) ASCII format for centroid spectra. This format is exported by some instrument software.

The spectral file does not need to have the extension .msp.

Value

A data frame with the following column names:

Author(s)

Nathan G. Dodder

See Also

ReadMspDirectory

Examples

ReadMspFile(paste(system.file(package = "OrgMassSpecR"), "/extdata/msp/pentaBDE.msp", sep = ""))

Non-Isothermal Retention Index Calculation

Description

Determine the non-isothermal (temperature-programmed) gas chromatographic retention index of a target compound based on the retention times of adjacent n-alkanes.

Usage

RetentionIndex(n, target, preceding, following)

Arguments

Details

The retention time units can be either seconds or minutes, but should be consistent. The n-alkanes eluting before and after the target compound should differ by one carbon atom. This equation does not apply to isothermal separations or when the n-alkane series contains only odd or even carbon atoms.

Value

A vector giving the retention index.

Author(s)

Nathan G. Dodder

References

Van Den Dool H, Kratz PD, Journal of Chromatography, 1963, 11, 463-471.

Examples

RetentionIndex(8, 30, 28, 33)

Similarity Between Two Mass Spectra

Description

Generate a head-to-tail plot of the two mass spectra and calculate a similarity score.

Usage

SpectrumSimilarity(spec.top, spec.bottom, t = 0.25, b = 10, 
                   top.label = NULL, bottom.label = NULL, 
                   xlim = c(50, 1200), x.threshold = 0, 
                   print.alignment = FALSE, print.graphic = TRUE,
                   output.list = FALSE)

Arguments

Details

The mass spectral similarity score is calculated as (where \cdot is the dot product)

\cos \theta = \frac{u \cdot v}{\sqrt{u \cdot u} \sqrt{v \cdot v}}

where u and v are the aligned intensity vectors of the two spectra, as subsetted by the b and x.threshold arguments. The t argument is used to align the intensities. The bottom spectum is used as the reference spectrum, and the m/z values of peaks in the top spectrum that are within t of a reference m/z value are paired with that reference peak. Ideally, a single peak from the top spectrum should be paired with a single peak from the reference spectrum. Peaks without a match are paired with an intensity of zero.

Note that, although both are based on the cosine of the two intensity vectors, the spectral similarity score given by SpectrumSimilarity is not the same as that given by the NIST MS Search program, described in the reference below.

Value

A vector containing the similarity score. By default a base graphics head-to-tail plot of the two mass spectra is printed, and optionally the data frame showing the peak alignment is printed. Alternatively, if output.list = TRUE the function will return a list with the similarity score, alignment dataframe, and plot. In this case the plot is a gTree (grid graphics) object.

Author(s)

Nathan G. Dodder

References

"Optimization and Testing of Mass Spectral Library Search Algorithms for Compound Identification," Stein SE, Scott DR, Journal of the American Society for Mass Spectrometry, 1994, 5, 859-866.

See Also

PeptideSpectrum

Examples

## With output.list = FALSE (default)
SpectrumSimilarity(example.spectrum.unknown, example.spectrum.authentic,
                   top.label = "unknown, electron impact", 
                   bottom.label = "derivatized alanine, electron impact",
                   xlim = c(25, 350))
# label peaks
plot.window(xlim = c(25,350), ylim = c(-125, 125))
text(c(73, 147, 158, 232, 260), c(100, 23, 44, 22, 15) + 10,
     c(73, 147, 158, 232, 260), cex = 0.75)
text(c(73, 147, 158, 232, 260), -c(100, 47, 74, 33, 20) - 10, 
     c(73, 147, 158, 232, 260), cex = 0.75)
mtext("Spectrum similarity", line = 1)

## With output.list = TRUE
x <- SpectrumSimilarity(example.spectrum.unknown, example.spectrum.authentic,
                   top.label = "unknown, electron impact", 
                   bottom.label = "derivatized alanine, electron impact",
                   xlim = c(25, 350), output.list = TRUE)

print(x)
grid.newpage()
grid.draw(x$plot) # draw to device

Write Spectra to the NIST MSP Text Format

Description

Writes all spectra in the OrgMassSpecR data frame format to a single text file in NIST MSP format. The MSP files can be imported into the NIST MS Search program to make a custom seachable library.

Usage

WriteMspFile(spectra, metadata, filename = "library.msp", comment = "")

Arguments

Details

The spectra and metadata data frame format is specified in the help files for the LibraryReport functions in the spectral library packages, for example see SpecLibExample::LibraryReport. The spectra data frame must contain at least columns: filename, mz, and intensity. The metadata data frame must contain at least columns: filename and compound.

The NAME field for each spectrum in the MSP file is assigned based on compound in the metadata data frame.

Newlines are CR+LF since the NIST MS Search program is Windows based.

Value

An MSP file is written using a file connection.

Author(s)

Nathan G. Dodder

Examples

## Simple example to illustrate the input data formats. 

spectra <- data.frame(filename = c(rep("Spectrum A", 2), rep("Spectrum B", 2)),
                      mz = c(50, 51, 100, 101),
                      intensity = c(70, 71, 90, 91))

metadata <- data.frame(filename = c("Spectrum A", "Spectrum B"),
                       compound = c("Compound A", "Compound B"))

## Not run: 
WriteMspFile(spectra = spectra, 
             metadata = metadata,
             filename = "Test.txt",
             comment = "Test Comment")

## End(Not run)

## Example using SpecLibExample package located at http://OrgMassSpec.github.io/libraries.html.
## Not run: 
library(SpecLibExample)
WriteMspFile(spectra = spec,
             metadata = meta,
             comment = "example output")

## End(Not run)

Example Chromatograms

Description

Examples for DrawChromatogram.

Usage

example.chromatogram.single
example.chromatogram.multiple

Format

A data frame consisting of time (minutes) in the first column and intensity (counts per second) in the second.

Author(s)

Nathan G. Dodder

Human Serum Albumin Amino Acid Sequence

Description

Used in examples.

Usage

example.sequence

Format

Character sequence.

Source

Downloaded from the ExPASy Proteomics Server (P02768) on 2009-02-07. Residues 25-609.

Example MALDI-TOF Spectrum of Nitrogen-15 Labeled Peptide

Description

Example used in Vinegette.

Usage

example.spectrum.labeled

Format

A data frame consisting of m/z values in the first column and intensity in the second.

Author(s)

Protein expressed by Wei-Li Liao.

Source

Precursor ion spectrum of peptide YEVQGEVFTKPQLWP acquired on a MALDI-TOF/TOF. The peptide is labeled with approximately 99% nitrogen-15.

Example Peptide Fragmentation Spectrum

Description

Example for PeptideSpectrum.

Usage

example.spectrum.peptide

Format

A data frame consisting of (centroid) m/z values in the first column and peak intensities in the second.

Source

Peptide sequence NIDALSGMEGR. Acquired on a hybrid triple quadruploe/linear ion trap mass spectrometer in collision induced dissociation (CID) mode.

Example EI Fragmentation Spectra

Description

Examples for SpectrumSimilarity.

Usage

example.spectrum.unknown
example.spectrum.authentic

Format

A data frame consisting of (centroid) m/z values in the first column and peak intensities in the second.

Author(s)

Spectra acquired by Gauthier Eppe.

Source

Mass spectra of alanine derivatized with N-Methyl-N-[tert-butyldimethyl-silyl]trifluoroacetimide (MTBSTFA) collected in electron impact (EI) mode on a 2 dimensional gas chromatography time of flight (GCxGC-TOF) mass spectrometer. example.spectrum.unknown was acquired from a human plasma extract. example.spectrum.authentic was acquired from an authentic material.