processMS2 — processMS2 • RHermes

processMS2 processes the MSMS files generated for a given IL and performs compound identification using an MSMS reference spectra database. Only the struct id and MS2files parameters are mandatory.

processMS2(
  struct,
  id,
  MS2files,
  sstype = "regular",
  useDB = FALSE,
  referenceDB = "D:/sp_MassBankEU_20200316_203615.RData",
  mincos = 0.8,
  minhits = 1,
  method = "cosine"
)

# S4 method for RHermesExp,numeric,character,character
processMS2(
  struct,
  id,
  MS2files,
  sstype = "regular",
  useDB = FALSE,
  referenceDB = "D:/sp_MassBankEU_20200316_203615.RData",
  mincos = 0.8,
  minhits = 1,
  method = "cosine"
)

Arguments

struct	The RHermesExp object to add the processed data.
id	Numeric, the id of the inclusion list to process.
MS2files	Character vector of the MS2 files address.
sstype	How to "process" the MS2 scans. Defaults to assuming you have acquired in continuous MS2 mode (sstype = "regular"). You can also take the most intense scan (sstype = "onescan") or even all acquired scans (sstype = "all"). Beware that "all" takes substantially longer.
useDB	Whether to use an MS2 DB to match the spectra.
referenceDB	Character, where to find the MSMS database to query against.
mincos	Numeric, between 0 and 1, the minimum spectral cosine between query and reference spectrum for a match to be reported (see the paper for more detail on this).
minhits	Numeric, minimum number of matching fragments to calculate the similarity score. If there are fewer, the match is not considered.
method	Character, the similarity algorithm to use. Defaults to "cosine", but it can be changed to other metrics included in the package Philentropy.

Value

An RHermesExp object with the identifications set in the used MS2Exp slot.

Examples

if(FALSE){
processMS2(myHermes, 1, c('C:/myFolder/File1.mzML',
                         'C:/myFolder/File2.mzML'))
}