Fixing mz calculation for multiply-charged ions and negative atoms

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: RMassBank
 Type: Package
 Title: Workflow to process tandem MS files and build MassBank records
-Version: 3.5.2
+Version: 3.5.2.1
 Authors@R: c(
     person(given = "RMassBank at Eawag", email = "[email protected]",
     role=c("cre")),

R/formulaCalculator.R

@@ -358,6 +358,7 @@ split.formula.posneg <- function(f, as.formula = TRUE, as.list=FALSE)
 	if(!is.list(f)) f <- formulastring.to.list(f)
 	pos <- f[which(f > 0)]
 	neg <- f[which(f < 0)]
+	neg <- multiply.formula(neg, -1, as.list = TRUE)
 	if(as.formula & !as.list)
 		return(list(pos=list.to.formula(pos), neg=list.to.formula(neg)))
 	else

R/leCsvAccess.R

@@ -541,22 +541,26 @@ findMz.formula <- function(formula, mode="pH", ppm=10, deltaMz=0)
 	formula <- add.formula(formula, mzopt$addition)
 	# Since in special cases we want to use this with negative and zero number of atoms, we account for this case
 	# by splitting up the formula into positive and negative atom counts (this eliminates the zeroes.)
+	# Note: the previous implementation was incorrect, since 
 	formula.split <- split.formula.posneg(formula)
 	m <- 0
 	if(formula.split$pos != "")
 	{
-		formula.pos <- get.formula(formula.split$pos, charge = mzopt$charge)
+		formula.pos <- get.formula(formula.split$pos, charge = 0)
 		m = m + formula.pos@mass
 	}
 	if(formula.split$neg != "")
 	{
-		formula.neg <- get.formula(formula.split$neg, charge = -mzopt$charge)
+		formula.neg <- get.formula(formula.split$neg, charge = 0)
 		m = m - formula.neg@mass
 	}
-	if((nchar(formula.split$pos)==0) & (nchar(formula.split$neg)==0))
-	{
-		m <- get.formula("H", charge = mzopt$charge)@mass - get.formula("H", charge = 0)@mass
-	}
+	m <- m + get.formula("H", charge = mzopt$charge)@mass - get.formula("H", charge = 0)@mass
+
+	# get.formula only takes "charge" into account to add the electrons - not to 
+	# divide by z to get m/z. therefore, we do it ourselves
+	if(mzopt$charge != 0)
+	  m <- m / abs(mzopt$charge)
+	# Note: technically there is no m/z for charge=0
 	delta <- ppm(m, ppm, l = TRUE)
 	return(list(mzMin = delta[[2]] - deltaMz, mzMax = delta[[1]] + 
 							deltaMz, mzCenter = m))

inst/tests_wip/test_leCsvAccess.R

@@ -0,0 +1,35 @@
+# Test correct results of findMz.formula wiht positive and negative charge,
+# single and multiple charge, no charge, and fictitious negative atoms
+expect_equal(findMz.formula("C6", "")$mzCenter, 72)
+expect_equal(
+  findMz.formula("C6", "mH")$mzCenter, 
+  72 - 1.0078 + RMassBank:::.emass,
+  tolerance = 0.00001 )
+expect_equal(
+  findMz.formula("C6", "pH")$mzCenter, 
+  72 + 1.0078 - RMassBank:::.emass,
+  tolerance = 0.00001 )
+expect_equal(
+  findMz.formula("C6H-1", "")$mzCenter, 
+  72 - 1.0078,
+  tolerance = 0.00001 )
+expect_equal(
+  findMz.formula("C6H-1", "mM")$mzCenter, 
+  72 - 1.0078 + RMassBank:::.emass,
+  tolerance = 0.00001 )
+expect_equal(
+  findMz.formula("C6H-1", "pM")$mzCenter, 
+  72 - 1.0078 - RMassBank:::.emass,
+  tolerance = 0.00001 )
+expect_equal(
+  findMz.formula("C6", "m2H_c2")$mzCenter, 
+  (72 - (2*1.0078) + 2*RMassBank:::.emass) / 2,
+  tolerance = 0.00001 )
+expect_equal(
+  findMz.formula("C6H-1", "m2H_c2")$mzCenter, 
+  (72 - (3*1.0078) + 2*RMassBank:::.emass) / 2,
+  tolerance = 0.00001 )
+
+
+
+