get_matched_peaks: Matches Calculated Fragments to the Experimental Spectrum and...

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

Matches Calculated Fragments to the Experimental Spectrum and creates the "Matched Peak" object

Description

Returns the "matched_peaks" object with experimental spectrum annotated with matches to calculated fragments.

Usage

get_matched_peaks(
  ScanMetadata = NULL,
  PeakData = NULL,
  PPMThreshold = 10,
  IonGroups = c("a", "b", "c", "x", "y", "z"),
  CalculateIsotopes = TRUE,
  MinimumAbundance = 1,
  CorrelationScore = 0,
  MatchingAlgorithm = "closest peak",
  IsotopeAlgorithm = "Rdisop",
  AlternativeIonGroups = NULL,
  AlternativeSequence = NULL,
  AlternativeSpectrum = NULL,
  AlternativeCharge = NULL,
  AlternativeGlossary = NULL,
  ...
)

Arguments

ScanMetadata	Object of the scan_metadata class from get_scan_metadata. Required, unless an alternative spectrum, sequence, and charge is provided.
PeakData	Object of the peak_data class from get_peak_data. Required, unless an alternative spectrum, sequence, and charge is provided.
PPMThreshold	The ppm error threshold between calculated fragments. Default is 10. Required.
IonGroups	Determine which ion types to calculate. a, b, c, x, y, z are supported. Default is c("a", "b", "c", "x", "y", "z"). Required.
CalculateIsotopes	A logical which indicates whether isotopes should be calculated. FALSE = Faster Calculations. Default is TRUE. Required.
CorrelationScore	A minimum correlation score to filter isotopes by. Range is 0 to 1. Default is 0. There is a 3 peak minimum to calculate a correlation score. Required.
MatchingAlgorithm	Either "closest peak" or "highest abundance" where the "closest peak" implementation chooses the peak closest to the true M/Z value within the PPM window and "highest abundance" chooses the highest intensity peak within the PPM window. "closest peak" is recommended for peaks that have been peak picked with an external tool, and "highest abundance" is recommended for noisy datasets or those with many peaks.
IsotopeAlgorithm	"isopat" uses the isopat package to calculate isotopes, while "Rdisop" uses the Rdisop package. Though more accurate, Rdisop has been known to crash on Windows computers when called iteratively more than 1000 times. Default is Rdisop, though isopat is an alternative.
AlternativeIonGroups	A "modified_ion" object from "make_mass_modified ions." Default is NULL.
AlternativeSequence	A proforma-acceptable string to calculate the literature fragments. The default is the sequence matched in the ScanMetadata file. Default is NULL.
AlternativeSpectrum	An alternative "peak_data" spectrum to use instead of the default PeakData. Mostly used by other packages. Default is NULL.
AlternativeCharge	A different charge value to test besides the one in the PeakData spectrum.
AlternativeGlossary	Try a different glossary. See system.file("extdata", "Unimod_v20220602.csv", package = "pspecterlib) for formatting.
MinAbundance	Minimum abundance for calculating isotopes. Default is 0.1.

Details

The data.table outputted by this function contains 17 columns.

M/Z	The calculated M/Z value of the fragment
Ion	The ion's type (a, b, c, x, y, or z) with the ion's position, oriented by terminus: N-terminus (a-c) or C-terminus (x-z)
Type	The ion's type (a, b, c, x, y, or z) with modified ion annotations (z*) if applicable
Position	The ion's position, oriented by terminus
Z	The charge of the fragment
Sequence	The peptide sequence of the fragment
N Position	The ion's position, oriented by only the N-terminus
General Type	The ion's type, removing modified ion annotation (z* would be z)
Modifications	Any PTMs assigned to this fragment. If none, the string will be ""
M/Z Tolerance	Based on the inputted PPM Tolerance, this value indicates how far off the calculated M/Z and Experimental M/Z can be.
M/Z Experimental	The experimental M/Z value that was matched to the calculated M/Z value for that fragment.
Intensity Experimental	The experimental intensity for the experimental M/Z value
PPM Error	A calculated value to indicate how far off the experimental and calculated value are from each other, in parts per million (PPM)
Molecular Formula	The formula of the sequence at that fragment. Used to determine isotopic percentages
Isotope	Annotation of isotopes in the M+n format, where M+0 is the non-isotope peak, and each successive isotope is M+1, M+2, etc.
Isotopic Percentage	The calculated intensity, proportional to M+0. For example, if M+1 has an isotopic percentage of 0.5, it is half the size of M+0.
Correlation Score	If at least two isotopes are recorded, a cosine correlation score of calculated and experimental intensities is determined for these 3+ fragments.
Residue	Name of the C-terminal residue. Used in downstream functions.

Objects of the class "matched_peaks" contain attributes that are referenced by downstream functions. The attributes are the input parameters as well as coverage (number of residues with an ion annotation, over the length of the peptide minus 1), and the median ppm error for all the fragments in the spectra.

Examples

## Not run: 

# Test bottom up data
BU_Peak <- get_peak_data(ScanMetadata = BU_ScanMetadata, ScanNumber = 31728)
BU_Match <- get_matched_peaks(ScanMetadata = BU_ScanMetadata, PeakData = BU_Peak)

# Test bottom up data with a PTM
BU_Match2 <- get_matched_peaks(
  ScanMetadata = BU_ScanMetadata,
  PeakData = BU_Peak,
  AlternativeSequence = "M.IGAV[Acetyl]GGTENVSLTQSQMPAHNHLVAASTVSGTVKPLANDIIG[20.1]AGLNK" 
)

# Test bottom up data with a mass modified ion 
BU_Match3 <- get_matched_peaks(
 ScanMetadata = BU_ScanMetadata,
 PeakData = BU_Peak, 
 IonGroups = "b",
 AlternativeIonGroups = make_mass_modified_ion(Ion = "y", Symbol = "^", AMU_Change = 1.00727647)
)


# Test with top down data
TD_Peak <- get_peak_data(ScanMetadata = TD_ScanMetadata, ScanNumber = 5709)
TD_Match <- get_matched_peaks(ScanMetadata = TD_ScanMetadata, PeakData = TD_Peak)


## End(Not run)

EMSL-Computing/pspecterlib documentation built on Jan. 28, 2024, 8:13 p.m.