AA: AA - amino acid table

In protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

AA - amino acid table

Description

Among other attributes it contains '1-letter code', 'monoisotopic mass' and 'average mass' of each amino acids.

Format

contains a table

Value

returns a data.frame

Author(s)

Christian Panse 2013

See Also

• https://www.matrixscience.com/help/aa_help.html

• https://education.expasy.org/student_projects/isotopident/htdocs/aa-list.html

• https://www.unimod.org

Examples

    data(AA)
    AA
    AA.lm<-lm(AA$Monoisotopic ~ AA$Average)

    plot(AA$Monoisotopic, AA$Average); 
    abline(AA.lm, col='grey')
    text(AA$Monoisotopic, AA$Average, AA$letter1, pos=3)

    plot(AA$Average-AA$Monoisotopic)  
    axis(3,1:20,AA$letter1); 
    abline(v=1:20,col='grey')

	
	
    # computes monoisotopic mass out of formula using the CDK package
    ## Not run: 
    	if (require(rcdk)){
	plot(AA$Monoisotopic, 
	     sapply(AA$formula, function(x){
		     get.formula(as.character(x), charge = 1)@mass
	     }))
	}
    
## End(Not run)
    ## Not run: 
	    if (require(XML)){
	unimodurl <- url("http://www.unimod.org/xml/unimod_tables.xml")
	unimod.list <- XML::xmlToList(
	  XML::xmlParse(
	    scan(unimodurl, what = character())))
	unimod.AA <- data.frame(
	  do.call('rbind', unimod.list$amino_acids))
	rownames(unimod.AA) <- unimod.AA$one_letter
	    }
    
## End(Not run)

protViz documentation built on May 29, 2024, 8:21 a.m.