fragmentSeq: Fragment Protein Or Peptide Sequence

In wrTopDownFrag: Internal Fragment Identification from Top-Down Mass Spectrometry

Fragment Protein Or Peptide Sequence

Description

Makes internal/terminal fragments of a SINGLE peptide/protein input (as single letter amino-acid code) and returns list of all possible sequences ($full, $Nter, $Cter, $inter).

Usage

fragmentSeq(
  sequ,
  minSize = 3,
  maxSize = 300,
  internFragments = TRUE,
  separTerm = FALSE,
  keepRedSeqs = TRUE,
  prefName = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

sequ	(character, length=1) sequence used for fragmenting, as as mono-aminoacid letter code (so that cuting will be perfomed between all the letters/characters)
minSize	(integer) min number of AA residues for considering peptide fragments
maxSize	(integer) max number of AA residues for considering peptide fragments
internFragments	(logical) logical (return only terminal fragments if 'FALSE')
separTerm	(logical) if 'TRUE', separate N-terminal, C-terminal and internal fragments in list
keepRedSeqs	(logical) if 'FALSE' remove fragments with redundant content (but my be from different origin in 'sequ'); remove redundant so far only when no separation of Nterm/Cterm/intern as list
prefName	(logical) alternative name for all fragments (default the sequence itself), avoid separators '.' and '-'
silent	(logical) suppress messages
debug	(logical) additional messages for debugging
callFrom	(character) allow easier tracking of messages produced

Details

Note: Thus function can handle only 1 sequence at each run ! Note: The mass values returned correspond to neutral peptides. If you are looking for ions, you need to adjust masses to the repsective ion-charcteriostics (adding H+, etc).

Value

This function returns a numeric vector with the (neutral) mass of fragmented peptides

See Also

makeFragments; convAASeq2mass

Examples

fragmentSeq("ABCDE")
fragmentSeq("ABCDE", minSize=3, internFragments=FALSE)
fragmentSeq("ABCDE", minSize=3, internFragments=TRUE)

## Run multiple peptides/proteins
twoPep <- cbind(c("a","ABCABCA"), c("e","EFGEFGEF"))
apply(twoPep, 2, function(x) fragmentSeq(x[2], mi=3, kee=FALSE, sep=TRUE, pre=x[1]))

## Ubiquitin example
P0CG48 <- "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"  
system.time( fra1 <- (fragmentSeq(P0CG48, mi=5, kee=FALSE)))      # < 0.5 sec  

wrTopDownFrag documentation built on June 8, 2025, 1:34 p.m.