R/MSMS2.R
In ManuelPerisDiaz/CysMpro: Mass Spectrometry-Based Structural Analysis of Metalloproteins
MSMS2<-function (sequence, fragments = "by", IAA = TRUE, N15 = FALSE,
custom = list(),Metal,Nmetal,Adduct
)
{
results_list <- vector("list")
for (sequence_number in 1:length(sequence)) {
peptide_vector <- strsplit(sequence[sequence_number],
split = "")[[1]]
peptide_length <- length(peptide_vector)
if (peptide_length < 2)
stop("sequence must contain two or more residues")
C <- 12
H <- 1.0078250321
O <- 15.9949146221
S <- 31.97207069
N <- ifelse(N15 == TRUE, 15.0001088984, 14.0030740052)
proton <- 1.007276466
Zn=63.928047
Cd=113.903358
Hg=201.970596
Cu=62.929600
Pb=207.976593
NH4=18.033823
Na=23
K=39
NH3=17
H20=18
#Nmetalseq<-seq(0,Nmetal)
if (Metal== "Zn"){
element<-Zn*Nmetal
}
if (Metal=="Cd"){
element<-Cd* Nmetal}
if (Metal=="Hg"){
element<-Hg* Nmetal}
if (Metal=="Cu"){
element<-Cu* Nmetal}
if (Metal=="Pb"){
element<-Pb* Nmetal}
if(length(Metal)==0){
element<-0
}
if(Nmetal==0){
element<-0
}
electron <- 0.00054857990943
residueMass <- function(residue) {
if (residue == "A")
mass = C * 3 + H * 5 + N + O
if (residue == "R")
mass = C * 6 + H * 12 + N * 4 + O
if (residue == "N")
mass = C * 4 + H * 6 + N * 2 + O * 2
if (residue == "D")
mass = C * 4 + H * 5 + N + O * 3
if (residue == "E")
mass = C * 5 + H * 7 + N + O * 3
if (residue == "Q")
mass = C * 5 + H * 8 + N * 2 + O * 2
if (residue == "G")
mass = C * 2 + H * 3 + N + O
if (residue == "H")
mass = C * 6 + H * 7 + N * 3 + O
if (residue == "I")
mass = C * 6 + H * 11 + N + O
if (residue == "L")
mass = C * 6 + H * 11 + N + O
if (residue == "K")
mass = C * 6 + H * 12 + N * 2 + O
if (residue == "M")
mass = C * 5 + H * 9 + N + O + S
if (residue == "F")
mass = C * 9 + H * 9 + N + O
if (residue == "P")
mass = C * 5 + H * 7 + N + O
if (residue == "S")
mass = C * 3 + H * 5 + N + O * 2
if (residue == "T")
mass = C * 4 + H * 7 + N + O * 2
if (residue == "W")
mass = C * 11 + H * 10 + N * 2 + O
if (residue == "Y")
mass = C * 9 + H * 9 + N + O * 2
if (residue == "V")
mass = C * 5 + H * 9 + N + O
if (residue == "C" )
mass = C * 3 + H * 5 + N + O + S
if (residue == "X" & IAA == TRUE)
mass <- ifelse(N15 == FALSE, C * 5 + H * 8 +
N * 2 + O * 2 + S, C * 5 + H * 8 + N + 14.0030740052 +
O * 2 + S)
if (length(custom) != 0)
for (i in 1:length(custom$code)) if (residue ==
custom$code[i])
mass = custom$mass[i]
return(mass)
}
masses <- sapply(peptide_vector, residueMass)
pm <- sum(masses,element)
if (is.null(Adduct)){
p1 <- round(pm + H * 2 + O + proton, digits = 3)
p2 <- round((pm + H * 2 + O + (2 * proton))/2, digits = 3)
p3 <- round((pm + H * 2 + O + (3 * proton))/3, digits = 3)
p4 <- round((pm + H * 2 + O + (4 * proton))/4, digits = 3)
p5 <- round((pm + H * 2 + O + (5 * proton))/5, digits = 3)
p6 <- round((pm + H * 2 + O + (6 * proton))/6, digits = 3)
if (fragments == "by") {
b1 <- vector(mode = "numeric", length = 0)
b2 <- vector(mode = "numeric", length = 0)
b3 <- vector(mode = "numeric", length = 0)
b4 <- vector(mode = "numeric", length = 0)
b5 <- vector(mode = "numeric", length = 0)
bs <- vector(mode = "character", length = 0)
bi <- vector(mode = "integer", length = 0)
y1 <- vector(mode = "numeric", length = 0)
y2 <- vector(mode = "numeric", length = 0)
y3 <- vector(mode = "numeric", length = 0)
y4 <- vector(mode = "numeric", length = 0)
y5 <- vector(mode = "numeric", length = 0)
ys <- vector(mode = "character", length = 0)
yi <- vector(mode = "integer", length = 0)
for (i in 1:(peptide_length - 1)) {
mass <- sum(masses[1:i], element)
b1[i] <- round(mass + proton, digits = 3)
b2[i] <- round((b1[i] + proton)/2, digits = 3)
b3[i] <- round((b1[i] + proton)/3, digits = 3)
b4[i] <- round((b1[i] + proton)/4, digits = 3)
b5[i] <- round((b1[i] + proton)/5, digits = 3)
bs[i] <- paste(peptide_vector[1:i], collapse = "")
bi[i] <- i
}
for (j in 2:peptide_length) {
mass <- sum(masses[j:peptide_length],element)
y1[j - 1] <- round(mass + H * 2 + O + proton,
digits = 3)
y2[j - 1] <- round((y1[j - 1] + proton)/2, digits = 3)
y3[j - 1] <- round((y1[j - 1] + proton)/3, digits = 3)
y4[j - 1] <- round((y1[j - 1] + proton)/4, digits = 3)
y5[j - 1] <- round((y1[j - 1] + proton)/5, digits = 3)
ys[j - 1] <- paste(peptide_vector[j:peptide_length],
collapse = "")
yi[j - 1] <- peptide_length - j + 1
}
ms1seq <- rep(sequence[sequence_number], times = ((5 *
(length(bi))) + (5 * (length(yi)))))
ms1z1 <- rep(p1, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z2 <- rep(p2, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z3 <- rep(p3, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z4 <- rep(p4, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z5 <- rep(p5, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z6 <- rep(p6, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms2seq <- c(rep(bs, times = 5), rep(ys, times = 5))
b1.type <- paste("[b", bi, "]1+", sep = "")
b2.type <- paste("[b", bi, "]2+", sep = "")
b3.type <- paste("[b", bi, "]3+", sep = "")
b4.type <- paste("[b", bi, "]4+", sep = "")
b5.type <- paste("[b", bi, "]5+", sep = "")
y1.type <- paste("[y", yi, "]1+", sep = "")
y2.type <- paste("[y", yi, "]2+", sep = "")
y3.type <- paste("[y", yi, "]3+", sep = "")
y4.type <- paste("[y", yi, "]4+", sep = "")
y5.type <- paste("[y", yi, "]5+", sep = "")
ms2type <- c(b1.type, b2.type,b3.type,b4.type,b5.type, y1.type, y2.type,y3.type,y4.type,y5.type)
ms2mz <- c(b1, b2,b3,b4,b5, y1, y2,y3,y4,y5)
}
####
if (fragments == "cz") {
c1 <- vector(mode = "numeric", length = 0)
c2 <- vector(mode = "numeric", length = 0)
cs <- vector(mode = "character", length = 0)
ci <- vector(mode = "integer", length = 0)
z1 <- vector(mode = "numeric", length = 0)
z2 <- vector(mode = "numeric", length = 0)
zs <- vector(mode = "character", length = 0)
zi <- vector(mode = "integer", length = 0)
for (i in 1:(peptide_length - 1)) {
mass <- sum(masses[1:i],element)
c1[i] <- round(mass + 3 * H + N + proton, digits = 3)
c2[i] <- round((c1[i] + proton)/2, digits = 3)
cs[i] <- paste(peptide_vector[1:i], collapse = "")
ci[i] <- i
}
for (j in 2:peptide_length) {
mass <- sum(masses[j:peptide_length],element)
z1[j - 1] <- round(mass + O - N, digits = 3)
z2[j - 1] <- round((z1[j - 1] + proton)/2, digits = 3)
zs[j - 1] <- paste(peptide_vector[j:peptide_length],
collapse = "")
zi[j - 1] <- peptide_length - j + 1
}
ms1seq <- rep(sequence[sequence_number], times = ((2 *
(length(ci))) + (2 * (length(zi)))))
ms1z1 <- rep(p1, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms1z2 <- rep(p2, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms1z3 <- rep(p3, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms2seq <- c(rep(cs, times = 2), rep(zs, times = 2))
c1.type <- paste("[c", ci, "]1+", sep = "")
c2.type <- paste("[c", ci, "]2+", sep = "")
z1.type <- paste("[z", zi, "]1+", sep = "")
z2.type <- paste("[z", zi, "]2+", sep = "")
ms2type <- c(c1.type, c2.type, z1.type, z2.type)
ms2mz <- c(c1, c2, z1, z2)
}
results_list[[sequence_number]] <- data.frame(ms1seq,
ms1z1, ms1z2, ms1z3,ms1z4,ms1z5,ms1z6, ms2seq, ms2type, ms2mz,Nmetal)
}else{
proton<-18.033823
p1 <- round(pm + H * 2 + O + proton, digits = 3)
p2 <- round((pm + H * 2 + O + (2 * proton))/2, digits = 3)
p3 <- round((pm + H * 2 + O + (3 * proton))/3, digits = 3)
if (fragments == "by") {
b1 <- vector(mode = "numeric", length = 0)
b2 <- vector(mode = "numeric", length = 0)
bs <- vector(mode = "character", length = 0)
bi <- vector(mode = "integer", length = 0)
y1 <- vector(mode = "numeric", length = 0)
y2 <- vector(mode = "numeric", length = 0)
ys <- vector(mode = "character", length = 0)
yi <- vector(mode = "integer", length = 0)
for (i in 1:(peptide_length - 1)) {
mass <- sum(masses[1:i], element)
b1[i] <- round(mass + proton, digits = 3)
b2[i] <- round((b1[i] + proton)/2, digits = 3)
bs[i] <- paste(peptide_vector[1:i], collapse = "")
bi[i] <- i
}
for (j in 2:peptide_length) {
mass <- sum(masses[j:peptide_length],element)
y1[j - 1] <- round(mass + H * 2 + O + proton,
digits = 3)
y2[j - 1] <- round((y1[j - 1] + proton)/2, digits = 3)
ys[j - 1] <- paste(peptide_vector[j:peptide_length],
collapse = "")
yi[j - 1] <- peptide_length - j + 1
}
ms1seq <- rep(sequence[sequence_number], times = ((2 *
(length(bi))) + (2 * (length(yi)))))
ms1z1 <- rep(p1, times = ((2 * (length(bi))) + (2 *
(length(yi)))))
ms1z2 <- rep(p2, times = ((2 * (length(bi))) + (2 *
(length(yi)))))
ms1z3 <- rep(p3, times = ((2 * (length(bi))) + (2 *
(length(yi)))))
ms2seq <- c(rep(bs, times = 2), rep(ys, times = 2))
b1.type <- paste("[b", bi, "]1+", sep = "")
b2.type <- paste("[b", bi, "]2+", sep = "")
y1.type <- paste("[y", yi, "]1+", sep = "")
y2.type <- paste("[y", yi, "]2+", sep = "")
ms2type <- c(b1.type, b2.type, y1.type, y2.type)
ms2mz <- c(b1, b2, y1, y2)
}
if (fragments == "cz") {
c1 <- vector(mode = "numeric", length = 0)
c2 <- vector(mode = "numeric", length = 0)
cs <- vector(mode = "character", length = 0)
ci <- vector(mode = "integer", length = 0)
z1 <- vector(mode = "numeric", length = 0)
z2 <- vector(mode = "numeric", length = 0)
zs <- vector(mode = "character", length = 0)
zi <- vector(mode = "integer", length = 0)
for (i in 1:(peptide_length - 1)) {
mass <- sum(masses[1:i],element)
c1[i] <- round(mass + 3 * H + N + proton, digits = 3)
c2[i] <- round((c1[i] + proton)/2, digits = 3)
cs[i] <- paste(peptide_vector[1:i], collapse = "")
ci[i] <- i
}
for (j in 2:peptide_length) {
mass <- sum(masses[j:peptide_length],element)
z1[j - 1] <- round(mass + O - N, digits = 3)
z2[j - 1] <- round((z1[j - 1] + proton)/2, digits = 3)
zs[j - 1] <- paste(peptide_vector[j:peptide_length],
collapse = "")
zi[j - 1] <- peptide_length - j + 1
}
ms1seq <- rep(sequence[sequence_number], times = ((2 *
(length(ci))) + (2 * (length(zi)))))
ms1z1 <- rep(p1, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms1z2 <- rep(p2, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms1z3 <- rep(p3, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms2seq <- c(rep(cs, times = 2), rep(zs, times = 2))
c1.type <- paste("[c", ci, "]1+", sep = "")
c2.type <- paste("[c", ci, "]2+", sep = "")
z1.type <- paste("[z", zi, "]1+", sep = "")
z2.type <- paste("[z", zi, "]2+", sep = "")
ms2type <- c(c1.type, c2.type, z1.type, z2.type)
ms2mz <- c(c1, c2, z1, z2)
}
results_list[[sequence_number]] <- data.frame(ms1seq,
ms1z1, ms1z2, ms1z3, ms2seq, ms2type, ms2mz)
}
}
return(as.data.frame(do.call("rbind", results_list)))
}
ManuelPerisDiaz/CysMpro documentation built on Oct. 18, 2020, 6:44 a.m.
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MSMS2<-function (sequence, fragments = "by", IAA = TRUE, N15 = FALSE,
custom = list(),Metal,Nmetal,Adduct
)
{
results_list <- vector("list")
for (sequence_number in 1:length(sequence)) {
peptide_vector <- strsplit(sequence[sequence_number],
split = "")[[1]]
peptide_length <- length(peptide_vector)
if (peptide_length < 2)
stop("sequence must contain two or more residues")
C <- 12
H <- 1.0078250321
O <- 15.9949146221
S <- 31.97207069
N <- ifelse(N15 == TRUE, 15.0001088984, 14.0030740052)
proton <- 1.007276466
Zn=63.928047
Cd=113.903358
Hg=201.970596
Cu=62.929600
Pb=207.976593
NH4=18.033823
Na=23
K=39
NH3=17
H20=18
#Nmetalseq<-seq(0,Nmetal)
if (Metal== "Zn"){
element<-Zn*Nmetal
}
if (Metal=="Cd"){
element<-Cd* Nmetal}
if (Metal=="Hg"){
element<-Hg* Nmetal}
if (Metal=="Cu"){
element<-Cu* Nmetal}
if (Metal=="Pb"){
element<-Pb* Nmetal}
if(length(Metal)==0){
element<-0
}
if(Nmetal==0){
element<-0
}
electron <- 0.00054857990943
residueMass <- function(residue) {
if (residue == "A")
mass = C * 3 + H * 5 + N + O
if (residue == "R")
mass = C * 6 + H * 12 + N * 4 + O
if (residue == "N")
mass = C * 4 + H * 6 + N * 2 + O * 2
if (residue == "D")
mass = C * 4 + H * 5 + N + O * 3
if (residue == "E")
mass = C * 5 + H * 7 + N + O * 3
if (residue == "Q")
mass = C * 5 + H * 8 + N * 2 + O * 2
if (residue == "G")
mass = C * 2 + H * 3 + N + O
if (residue == "H")
mass = C * 6 + H * 7 + N * 3 + O
if (residue == "I")
mass = C * 6 + H * 11 + N + O
if (residue == "L")
mass = C * 6 + H * 11 + N + O
if (residue == "K")
mass = C * 6 + H * 12 + N * 2 + O
if (residue == "M")
mass = C * 5 + H * 9 + N + O + S
if (residue == "F")
mass = C * 9 + H * 9 + N + O
if (residue == "P")
mass = C * 5 + H * 7 + N + O
if (residue == "S")
mass = C * 3 + H * 5 + N + O * 2
if (residue == "T")
mass = C * 4 + H * 7 + N + O * 2
if (residue == "W")
mass = C * 11 + H * 10 + N * 2 + O
if (residue == "Y")
mass = C * 9 + H * 9 + N + O * 2
if (residue == "V")
mass = C * 5 + H * 9 + N + O
if (residue == "C" )
mass = C * 3 + H * 5 + N + O + S
if (residue == "X" & IAA == TRUE)
mass <- ifelse(N15 == FALSE, C * 5 + H * 8 +
N * 2 + O * 2 + S, C * 5 + H * 8 + N + 14.0030740052 +
O * 2 + S)
if (length(custom) != 0)
for (i in 1:length(custom$code)) if (residue ==
custom$code[i])
mass = custom$mass[i]
return(mass)
}
masses <- sapply(peptide_vector, residueMass)
pm <- sum(masses,element)
if (is.null(Adduct)){
p1 <- round(pm + H * 2 + O + proton, digits = 3)
p2 <- round((pm + H * 2 + O + (2 * proton))/2, digits = 3)
p3 <- round((pm + H * 2 + O + (3 * proton))/3, digits = 3)
p4 <- round((pm + H * 2 + O + (4 * proton))/4, digits = 3)
p5 <- round((pm + H * 2 + O + (5 * proton))/5, digits = 3)
p6 <- round((pm + H * 2 + O + (6 * proton))/6, digits = 3)
if (fragments == "by") {
b1 <- vector(mode = "numeric", length = 0)
b2 <- vector(mode = "numeric", length = 0)
b3 <- vector(mode = "numeric", length = 0)
b4 <- vector(mode = "numeric", length = 0)
b5 <- vector(mode = "numeric", length = 0)
bs <- vector(mode = "character", length = 0)
bi <- vector(mode = "integer", length = 0)
y1 <- vector(mode = "numeric", length = 0)
y2 <- vector(mode = "numeric", length = 0)
y3 <- vector(mode = "numeric", length = 0)
y4 <- vector(mode = "numeric", length = 0)
y5 <- vector(mode = "numeric", length = 0)
ys <- vector(mode = "character", length = 0)
yi <- vector(mode = "integer", length = 0)
for (i in 1:(peptide_length - 1)) {
mass <- sum(masses[1:i], element)
b1[i] <- round(mass + proton, digits = 3)
b2[i] <- round((b1[i] + proton)/2, digits = 3)
b3[i] <- round((b1[i] + proton)/3, digits = 3)
b4[i] <- round((b1[i] + proton)/4, digits = 3)
b5[i] <- round((b1[i] + proton)/5, digits = 3)
bs[i] <- paste(peptide_vector[1:i], collapse = "")
bi[i] <- i
}
for (j in 2:peptide_length) {
mass <- sum(masses[j:peptide_length],element)
y1[j - 1] <- round(mass + H * 2 + O + proton,
digits = 3)
y2[j - 1] <- round((y1[j - 1] + proton)/2, digits = 3)
y3[j - 1] <- round((y1[j - 1] + proton)/3, digits = 3)
y4[j - 1] <- round((y1[j - 1] + proton)/4, digits = 3)
y5[j - 1] <- round((y1[j - 1] + proton)/5, digits = 3)
ys[j - 1] <- paste(peptide_vector[j:peptide_length],
collapse = "")
yi[j - 1] <- peptide_length - j + 1
}
ms1seq <- rep(sequence[sequence_number], times = ((5 *
(length(bi))) + (5 * (length(yi)))))
ms1z1 <- rep(p1, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z2 <- rep(p2, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z3 <- rep(p3, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z4 <- rep(p4, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z5 <- rep(p5, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms1z6 <- rep(p6, times = ((5 * (length(bi))) + (5 *
(length(yi)))))
ms2seq <- c(rep(bs, times = 5), rep(ys, times = 5))
b1.type <- paste("[b", bi, "]1+", sep = "")
b2.type <- paste("[b", bi, "]2+", sep = "")
b3.type <- paste("[b", bi, "]3+", sep = "")
b4.type <- paste("[b", bi, "]4+", sep = "")
b5.type <- paste("[b", bi, "]5+", sep = "")
y1.type <- paste("[y", yi, "]1+", sep = "")
y2.type <- paste("[y", yi, "]2+", sep = "")
y3.type <- paste("[y", yi, "]3+", sep = "")
y4.type <- paste("[y", yi, "]4+", sep = "")
y5.type <- paste("[y", yi, "]5+", sep = "")
ms2type <- c(b1.type, b2.type,b3.type,b4.type,b5.type, y1.type, y2.type,y3.type,y4.type,y5.type)
ms2mz <- c(b1, b2,b3,b4,b5, y1, y2,y3,y4,y5)
}
####
if (fragments == "cz") {
c1 <- vector(mode = "numeric", length = 0)
c2 <- vector(mode = "numeric", length = 0)
cs <- vector(mode = "character", length = 0)
ci <- vector(mode = "integer", length = 0)
z1 <- vector(mode = "numeric", length = 0)
z2 <- vector(mode = "numeric", length = 0)
zs <- vector(mode = "character", length = 0)
zi <- vector(mode = "integer", length = 0)
for (i in 1:(peptide_length - 1)) {
mass <- sum(masses[1:i],element)
c1[i] <- round(mass + 3 * H + N + proton, digits = 3)
c2[i] <- round((c1[i] + proton)/2, digits = 3)
cs[i] <- paste(peptide_vector[1:i], collapse = "")
ci[i] <- i
}
for (j in 2:peptide_length) {
mass <- sum(masses[j:peptide_length],element)
z1[j - 1] <- round(mass + O - N, digits = 3)
z2[j - 1] <- round((z1[j - 1] + proton)/2, digits = 3)
zs[j - 1] <- paste(peptide_vector[j:peptide_length],
collapse = "")
zi[j - 1] <- peptide_length - j + 1
}
ms1seq <- rep(sequence[sequence_number], times = ((2 *
(length(ci))) + (2 * (length(zi)))))
ms1z1 <- rep(p1, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms1z2 <- rep(p2, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms1z3 <- rep(p3, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms2seq <- c(rep(cs, times = 2), rep(zs, times = 2))
c1.type <- paste("[c", ci, "]1+", sep = "")
c2.type <- paste("[c", ci, "]2+", sep = "")
z1.type <- paste("[z", zi, "]1+", sep = "")
z2.type <- paste("[z", zi, "]2+", sep = "")
ms2type <- c(c1.type, c2.type, z1.type, z2.type)
ms2mz <- c(c1, c2, z1, z2)
}
results_list[[sequence_number]] <- data.frame(ms1seq,
ms1z1, ms1z2, ms1z3,ms1z4,ms1z5,ms1z6, ms2seq, ms2type, ms2mz,Nmetal)
}else{
proton<-18.033823
p1 <- round(pm + H * 2 + O + proton, digits = 3)
p2 <- round((pm + H * 2 + O + (2 * proton))/2, digits = 3)
p3 <- round((pm + H * 2 + O + (3 * proton))/3, digits = 3)
if (fragments == "by") {
b1 <- vector(mode = "numeric", length = 0)
b2 <- vector(mode = "numeric", length = 0)
bs <- vector(mode = "character", length = 0)
bi <- vector(mode = "integer", length = 0)
y1 <- vector(mode = "numeric", length = 0)
y2 <- vector(mode = "numeric", length = 0)
ys <- vector(mode = "character", length = 0)
yi <- vector(mode = "integer", length = 0)
for (i in 1:(peptide_length - 1)) {
mass <- sum(masses[1:i], element)
b1[i] <- round(mass + proton, digits = 3)
b2[i] <- round((b1[i] + proton)/2, digits = 3)
bs[i] <- paste(peptide_vector[1:i], collapse = "")
bi[i] <- i
}
for (j in 2:peptide_length) {
mass <- sum(masses[j:peptide_length],element)
y1[j - 1] <- round(mass + H * 2 + O + proton,
digits = 3)
y2[j - 1] <- round((y1[j - 1] + proton)/2, digits = 3)
ys[j - 1] <- paste(peptide_vector[j:peptide_length],
collapse = "")
yi[j - 1] <- peptide_length - j + 1
}
ms1seq <- rep(sequence[sequence_number], times = ((2 *
(length(bi))) + (2 * (length(yi)))))
ms1z1 <- rep(p1, times = ((2 * (length(bi))) + (2 *
(length(yi)))))
ms1z2 <- rep(p2, times = ((2 * (length(bi))) + (2 *
(length(yi)))))
ms1z3 <- rep(p3, times = ((2 * (length(bi))) + (2 *
(length(yi)))))
ms2seq <- c(rep(bs, times = 2), rep(ys, times = 2))
b1.type <- paste("[b", bi, "]1+", sep = "")
b2.type <- paste("[b", bi, "]2+", sep = "")
y1.type <- paste("[y", yi, "]1+", sep = "")
y2.type <- paste("[y", yi, "]2+", sep = "")
ms2type <- c(b1.type, b2.type, y1.type, y2.type)
ms2mz <- c(b1, b2, y1, y2)
}
if (fragments == "cz") {
c1 <- vector(mode = "numeric", length = 0)
c2 <- vector(mode = "numeric", length = 0)
cs <- vector(mode = "character", length = 0)
ci <- vector(mode = "integer", length = 0)
z1 <- vector(mode = "numeric", length = 0)
z2 <- vector(mode = "numeric", length = 0)
zs <- vector(mode = "character", length = 0)
zi <- vector(mode = "integer", length = 0)
for (i in 1:(peptide_length - 1)) {
mass <- sum(masses[1:i],element)
c1[i] <- round(mass + 3 * H + N + proton, digits = 3)
c2[i] <- round((c1[i] + proton)/2, digits = 3)
cs[i] <- paste(peptide_vector[1:i], collapse = "")
ci[i] <- i
}
for (j in 2:peptide_length) {
mass <- sum(masses[j:peptide_length],element)
z1[j - 1] <- round(mass + O - N, digits = 3)
z2[j - 1] <- round((z1[j - 1] + proton)/2, digits = 3)
zs[j - 1] <- paste(peptide_vector[j:peptide_length],
collapse = "")
zi[j - 1] <- peptide_length - j + 1
}
ms1seq <- rep(sequence[sequence_number], times = ((2 *
(length(ci))) + (2 * (length(zi)))))
ms1z1 <- rep(p1, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms1z2 <- rep(p2, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms1z3 <- rep(p3, times = ((2 * (length(ci))) + (2 *
(length(zi)))))
ms2seq <- c(rep(cs, times = 2), rep(zs, times = 2))
c1.type <- paste("[c", ci, "]1+", sep = "")
c2.type <- paste("[c", ci, "]2+", sep = "")
z1.type <- paste("[z", zi, "]1+", sep = "")
z2.type <- paste("[z", zi, "]2+", sep = "")
ms2type <- c(c1.type, c2.type, z1.type, z2.type)
ms2mz <- c(c1, c2, z1, z2)
}
results_list[[sequence_number]] <- data.frame(ms1seq,
ms1z1, ms1z2, ms1z3, ms2seq, ms2type, ms2mz)
}
}
return(as.data.frame(do.call("rbind", results_list)))
}
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