R/anno.R

In enviGCMS: GC/LC-MS Data Analysis for Environmental Science

#' Align two peaks vectors by mass to charge ratio and/or retention time
#' @param mz1 the mass to charge of reference peaks
#' @param mz2 the mass to charge of peaks to be aligned
#' @param ppm mass accuracy, default 10
#' @param deltart retention time shift table, default 10 seconds
#' @param rt1 retention time of reference peaks
#' @param rt2 retention time of peaks to be aligned
#' @return data frame with aligned peaks table
#' @examples
#' mz1 <- c(221.1171, 227.1390, 229.1546, 233.1497, 271.0790 )
#' mz2 <- c(282.279, 281.113, 227.139, 227.139, 302.207)
#' rt1 <- c(590.8710, 251.3820, 102.9230, 85.8850, 313.8240)
#' rt2 <- c(787.08, 160.02, 251.76, 251.76, 220.26)
#' getalign(mz1,mz2,rt1,rt2)
#' @export
getalign <-
        function(mz1,
                 mz2,
                 rt1 = NULL,
                 rt2 = NULL,
                 ppm = 10,
                 deltart = 10) {
                mza <-
                        data.table::as.data.table(cbind.data.frame(
                                mzmin = mz1 * (1 - ppm * 10e-6),
                                mzmax = mz1 * (1 + ppm * 10e-6)
                        ))
                mzb <-
                        data.table::as.data.table(cbind.data.frame(
                                mzmin = mz2 * (1 - ppm * 10e-6),
                                mzmax = mz2 * (1 + ppm * 10e-6)
                        ))
                colnames(mza) <- colnames(mzb) <- c("min", "max")
                data.table::setkey(mzb, min, max)
                overlapms <- data.table::foverlaps(mza, mzb, which = TRUE)

                overlapms$mz1 <- mz1[overlapms$xid]
                overlapms$mz2 <-
                        mz2[order(mz2, decreasing = FALSE)][overlapms$yid]
                if (!is.null(rt1) & !is.null(rt2)) {
                        overlapms$rt1 <- rt1[overlapms$xid]
                        overlapms$rt2 <-
                                rt2[order(mz2, decreasing = FALSE)][overlapms$yid]
                        drt <- abs(overlapms$rt1 - overlapms$rt2)
                        overlapms <- overlapms[drt < deltart, -c(2)]
                        re <-
                                data.frame(overlapms[!duplicated(overlapms) &
                                                             stats::complete.cases(overlapms), ])

                        if (nrow(re) > 0) {
                                return(re)
                        } else{
                                message('No result could be found.')
                        }

                } else{
                        message('No retention time information!')
                        over <- overlapms[, -2]
                        over2 <-
                                over[stats::complete.cases(over) & !duplicated(over), ]
                        re <- data.frame(over2)
                        if (nrow(re) > 0) {
                                return(re)
                        } else{
                                message('No result could be found.')
                        }
                }
        }
#' Align mass to charge ratio and/or retention time to remove redundancy
#' @param mz the mass to charge of reference peaks
#' @param rt retention time of reference peaks
#' @param ppm mass accuracy, default 10
#' @param deltart retention time shift table, default 10 seconds
#' @return index for
#' @examples
#' mz <- c(221.1171, 221.1170, 229.1546, 233.1497, 271.0790 )
#' rt <- c(590.8710, 587.3820, 102.9230, 85.8850, 313.8240)
#' getalign2(mz,rt)
#' @export
getalign2 <- function(mz,
                      rt,
                      ppm = 5,
                      deltart = 5) {
        mzr <-
                data.table::as.data.table(cbind.data.frame(
                        mzmin = mz * (1 - ppm * 10e-6),
                        mzmax = mz * (1 + ppm * 10e-6)
                ))
        colnames(mzr) <- c("min", "max")
        data.table::setkey(mzr, min, max)
        overlapms <- data.table::foverlaps(mzr, mzr, which = TRUE)
        overlapms$mz1 <- mz[overlapms$xid]
        overlapms$rt1 <- rt[overlapms$xid]
        overlapms$mz2 <- mz[overlapms$yid]
        overlapms$rt2 <- rt[overlapms$yid]
        drt <- abs(overlapms$rt1 - overlapms$rt2)
        overlapms <- overlapms[drt < deltart, ]

        overlap1 <- overlapms[overlapms$xid == overlapms$yid, ]
        overlap2 <- overlapms[overlapms$xid != overlapms$yid, ]
        overlap3 <- overlap1[!overlap1$xid %in% overlap2$xid, ]
        x <-
                igraph::graph_from_data_frame(overlap2, directed = FALSE)
        y <-
                names(igraph::components(x)$membership[!duplicated(igraph::components(x)$membership)])
        idx <- c(overlap3$xid, as.numeric(y))
        idxx <- idx[order(idx, decreasing = FALSE)]
        if (length(idxx) > 0) {
                return(idxx)
        } else{
                message('No result could be found.')
        }
}
#' Get the overlap peaks by mass and retention time range
#' @param list1 list with data as peaks list, mz, rt, mzrange, rtrange and group information to be overlapped
#' @param list2 list with data as peaks list, mz, rt, mzrange, rtrange and group information to overlap
#' @return logical index for list 1's peaks
#' @export
#' @seealso \code{\link{getmzrt}}, \code{\link{getimputation}}, \code{\link{getmr}},\code{\link{getdoe}}
getoverlappeak <- function(list1, list2) {
        mz1 <- data.table::as.data.table(list1$mzrange)
        rt1 <- data.table::as.data.table(list1$rtrange)
        mz2 <- data.table::as.data.table(list2$mzrange)
        rt2 <- data.table::as.data.table(list2$rtrange)
        colnames(mz1) <-
                colnames(mz2) <-
                colnames(rt1) <- colnames(rt2) <- c('min', 'max')
        data.table::setkey(mz2, min, max)
        data.table::setkey(rt2, min, max)
        overlapms <-
                data.table::foverlaps(mz1, mz2, which = TRUE, mult = 'first')
        overlaprt <-
                data.table::foverlaps(rt1, rt2, which = TRUE, mult = 'first')
        index <- (!is.na(overlapms)) & (!is.na(overlaprt))
        if (length(index) > 0) {
                return(index)
        } else{
                message('No result could be found.')
        }
}

#' Annotation of MS1 data by compounds database by predefined paired mass distance
#' @param pmd adducts formula or paired mass distance for ions
#' @param mz unknown mass to charge ratios vector
#' @param ppm mass accuracy
#' @param db compounds database as dataframe. Two required columns are name and monoisotopic molecular weight with column names of name and mass
#' @return list or data frame
#' @export
getms1anno <- function(pmd, mz, ppm = 10, db = NULL) {
        # hr <- get(hr)
        if (is.character(pmd)) {
                pmds <- unlist(Map(enviGCMS::getmass, pmd))
        } else{
                pmds <- pmd
        }

        if (length(pmd) > 1) {
                pmdmt <- outer(db$mass, pmds, '+')
                rownames(pmdmt) <- db$name
                li <- list()
                for (i in seq_along(pmd)) {
                        re <- enviGCMS::getalign(pmdmt[, i], mz, ppm = ppm)
                        re2 <- db[re$xid, ]
                        re3 <- cbind.data.frame(re[, -1], re2)
                        colnames(re3)[1] <- pmd[i]
                        li[[i]] <- re3
                }
                return(li)
        } else{
                pmdmt <- outer(db$mass, pmds, '+')
                rownames(pmdmt) <- db$name
                re <- enviGCMS::getalign(pmdmt, mz, ppm = ppm)
                re2 <- db[re$xid, ]
                re3 <- cbind.data.frame(re[, -1], re2)
                colnames(re3)[1] <- pmd
                return(re3)
        }
}

#' Perform MS/MS dot product annotation for mgf file
#' @param file mgf file generated from MS/MS data
#' @param db database could be list object from `getMSP`
#' @param ppm mass accuracy, default 10
#' @param prems precursor mass range, default 1.1 to include M+H or M-H
#' @param binstep bin step for consin similarity
#' @param consinc consin similarity cutoff for annotation. Default 0.6.
#' @return list with MSMS annotation results
#' @export
dotpanno <- function(file,
                     db = NULL,
                     ppm = 10,
                     prems = 1.1,
                     binstep = 1,
                     consinc = 0.6) {
        namemgf <- basename(file)
        sample <- MSnbase::readMgfData(file)
        prec <- MSnbase::precursorMz(sample)
        mz <- MSnbase::mz(sample)
        ins <- MSnbase::intensity(sample)
        idx <- unlist(ins) / max(unlist(ins)) > 0
        if (sum(idx) > 0) {
                mz <- unlist(mz)[idx]
                ins <- unlist(ins)[idx]
                ins <- ins / max(ins) * 100
                mz2bin <-
                        cut(
                                mz,
                                breaks = seq(min(mz), max(mz) + binstep, binstep),
                                include.lowest = TRUE
                        )
                mz2bint <- stats::aggregate(ins, list(mz2bin), sum)
                colnames(mz2bint) <- c('factor', 'ins')
                if (inherits(db, 'list')) {
                        range <- cbind(db$mz - prems, db$mz + prems)
                        idxmz <-
                                enviGCMS::getalign(range, matrix(
                                        c(
                                                prec - ppm / prec * 1e-06,
                                                prec + ppm / prec * 1e-06
                                        ),
                                        nrow = 1
                                ))
                        idxmz <- idxmz[, 1]
                        if (sum(idxmz) > 0) {
                                name <- db$name[idxmz]
                                mz2 <- db$mz[idxmz]
                                msmsraw <- db$msmsraw[idxmz]

                                ms2bindb <- function(x) {
                                        ms2mz <-
                                                cut(
                                                        x[, 1],
                                                        breaks = seq(
                                                                min(x[, 1]),
                                                                max(x[, 1]) + binstep,
                                                                binstep
                                                        ),
                                                        include.lowest = TRUE
                                                )
                                        ms2ins <-
                                                stats::aggregate(x[, 2], list(ms2mz), sum)
                                        colnames(ms2ins) <-
                                                c('factor', 'insdb')

                                        db <- merge(mz2bint, ms2ins)
                                        cosscore <-
                                                crossprod(db$ins, db$insdb) / sqrt(crossprod(db$ins) * crossprod(db$insdb))
                                        return(cosscore)
                                }
                                ms2bin <-
                                        vapply(msmsraw, ms2bindb, 1)

                                t <-
                                        list(
                                                name = name[ms2bin > consinc & !is.na(ms2bin > consinc)],
                                                mz = mz2[ms2bin > consinc &
                                                                 !is.na(ms2bin > consinc)],
                                                msmsraw = msmsraw[ms2bin >
                                                                          consinc &
                                                                          !is.na(ms2bin > consinc)],
                                                coss = ms2bin[ms2bin >
                                                                      consinc &
                                                                      !is.na(ms2bin > consinc)],
                                                dmz = mz,
                                                dprc = prec,
                                                dins = ins,
                                                file = namemgf
                                        )
                        } else{
                                return(NULL)
                        }
                } else{
                        return(NULL)
                }
        } else{
                return(NULL)
        }
}

#' Perform MS/MS X rank annotation for mgf file
#' @param file mgf file generated from MS/MS data
#' @param db database could be list object from `getms2pmd`
#' @param ppm mass accuracy, default 10
#' @param prems precursor mass range, default 1.1 to include M+H or M-H
#' @param intc intensity cutoff for peaks. Default 0.1
#' @param quantile X rank quantiles cutoff for annotation. Default 0.75.
#' @return list with MSMS annotation results
#' @export
xrankanno <- function(file,
                      db = NULL,
                      ppm = 10,
                      prems = 1.1,
                      intc = 0.1,
                      quantile = 0.75) {
        # the score table is copied from MatchWeiz package https://github.com/AharoniLab/MatchWeiz
        xrankm <- data.frame(
                V2 = c(
                        5.1141927,
                        4.6402166,
                        4.0347778,
                        3.2659687,
                        2.8868788,
                        2.5778594,
                        2.4243286,
                        2.3812965,
                        2.3287661,
                        2.2854422,
                        2.1004184,
                        1.8994774,
                        1.5654162,
                        0.8235242,
                        0.4100572,
                        0.7430581,
                        1.0656059,
                        1.0032377,
                        0.8241324,
                        0.7564311,
                        0.917284,
                        1.0002008,
                        1.0621707,
                        1.1566258,
                        1.1392231,
                        0.9148275,
                        1.1658015,
                        1.3023251,
                        1.3606814,
                        1.3072061,
                        -1.0277345
                ),
                V3 = c(
                        4.4662252,
                        4.2625276,
                        4.0266953,
                        3.7418072,
                        3.3847624,
                        3.1361971,
                        2.9080739,
                        2.713817,
                        2.4905474,
                        2.304285,
                        2.049122,
                        1.8832838,
                        1.868606,
                        1.9907963,
                        2.1194155,
                        1.9654197,
                        1.5399935,
                        0.9886019,
                        0.5569938,
                        0.8646485,
                        1.2852703,
                        1.2970452,
                        1.1906578,
                        1.0054851,
                        0.4643638,
                        0.3149796,
                        0.6530265,
                        0.9365217,
                        1.276735,
                        1.6331704,
                        -0.8794154
                ),
                V4 = c(
                        3.6795088,
                        3.7669894,
                        3.7782841,
                        3.7152657,
                        3.5313373,
                        3.2815733,
                        3.0549055,
                        2.8764497,
                        2.6851887,
                        2.4204358,
                        2.2089195,
                        2.0982346,
                        1.9607808,
                        1.7542598,
                        1.3818804,
                        1.198171,
                        1.246158,
                        1.2886556,
                        1.2656819,
                        1.2415007,
                        1.1999841,
                        1.0194242,
                        0.9042444,
                        0.8420256,
                        0.7771686,
                        0.4544566,
                        0.5260332,
                        0.6261827,
                        0.7254316,
                        0.8462921,
                        -0.7569588
                ),
                V5 = c(
                        3.2839027,
                        3.5150629,
                        3.6093468,
                        3.6011231,
                        3.4368337,
                        3.2726368,
                        3.1239369,
                        2.9851635,
                        2.8044835,
                        2.4863963,
                        2.2902994,
                        2.2353244,
                        2.2524986,
                        2.2618101,
                        2.0346991,
                        1.7207373,
                        1.3948365,
                        0.7286686,
                        0.1800626,
                        0.551818,
                        0.9307692,
                        1.2736242,
                        1.3806847,
                        1.2709348,
                        1.0789728,
                        1.0715978,
                        1.3090899,
                        1.3045615,
                        1.1549414,
                        0.5900862,
                        -0.654933
                ),
                V6 = c(
                        2.5984291,
                        3.0046244,
                        3.203698,
                        3.2877079,
                        3.2571621,
                        3.1834096,
                        3.085427,
                        2.9219801,
                        2.6760367,
                        2.4617591,
                        2.3534256,
                        2.2377258,
                        2.0590923,
                        1.9655526,
                        1.9060469,
                        1.9008196,
                        1.7993952,
                        1.6434069,
                        1.71971,
                        1.64201,
                        1.4450944,
                        1.2230123,
                        1.0367481,
                        1.1504708,
                        1.1010623,
                        0.9585488,
                        0.8015804,
                        0.7383734,
                        0.6980518,
                        0.7457697,-0.5689874
                ),
                V7 = c(
                        2.2602371,
                        2.7464055,
                        3.0054499,
                        3.1477893,
                        3.2077435,
                        3.165352,
                        3.0703202,
                        2.9495569,
                        2.8437625,
                        2.7068907,
                        2.3780462,
                        2.0283327,
                        1.9713898,
                        2.0096547,
                        1.9692381,
                        1.7104057,
                        1.3232825,
                        1.2789279,
                        1.3324883,
                        1.3299554,
                        1.3211272,
                        1.2046809,
                        1.1817414,
                        0.8955127,
                        0.7820397,
                        1.0082414,
                        0.8953015,
                        0.8201049,
                        0.7231856,
                        0.6023505,
                        -0.4953545
                ),
                V8 = c(
                        1.780844,
                        2.4251461,
                        2.7362897,
                        2.9017494,
                        2.9748077,
                        2.9993037,
                        2.9341194,
                        2.8141705,
                        2.6106826,
                        2.437433,
                        2.3719587,
                        2.2569385,
                        2.0227376,
                        1.7871484,
                        1.7484059,
                        1.7687429,
                        1.6906459,
                        1.3787828,
                        1.1912703,
                        1.1235638,
                        0.8294797,
                        0.40528,
                        0.2093585,
                        0.4069855,
                        0.6013594,
                        0.6819047,
                        0.7574698,
                        0.7689249,
                        0.7047324,
                        0.5285583,
                        -0.4316488
                ),
                V9 = c(
                        1.3428288,
                        2.1247415,
                        2.4586731,
                        2.6210534,
                        2.6626053,
                        2.6148896,
                        2.55033,
                        2.4725361,
                        2.387539,
                        2.2699826,
                        2.0674599,
                        1.8867581,
                        1.8696961,
                        1.9600889,
                        1.9703743,
                        1.9428283,
                        1.9346449,
                        1.9797194,
                        1.866236,
                        1.5232692,
                        1.3395643,
                        1.3270395,
                        1.2546527,
                        1.2453368,
                        0.9798871,
                        0.8051503,
                        0.8642886,
                        0.7171807,
                        0.3767922,-0.6804648,
                        -0.376095
                ),
                V10 = c(
                        1.9469214,
                        2.0541428,
                        2.2259246,
                        2.4281479,
                        2.6737424,
                        2.8176345,
                        2.7858621,
                        2.6781424,
                        2.6216533,
                        2.6928871,
                        2.6242811,
                        2.2949485,
                        1.8479744,
                        1.3822823,
                        1.4812091,
                        1.861727,
                        1.9892546,
                        1.9760403,
                        1.7386677,
                        1.4067558,
                        1.2361354,
                        1.0888057,
                        1.2080851,
                        1.3518449,
                        1.4029794,
                        1.3922017,
                        1.1391871,
                        0.8259857,
                        0.3274847,-0.8479935,
                        -0.3285679
                ),
                V11 = c(
                        1.032439,
                        1.868163,
                        2.227866,
                        2.420178,
                        2.49452,
                        2.452937,
                        2.511973,
                        2.608769,
                        2.682327,
                        2.715736,
                        2.574212,
                        2.300455,
                        2.043854,
                        1.940104,
                        2.079843,
                        2.059508,
                        1.800115,
                        1.632611,
                        1.504172,
                        1.570284,
                        1.713437,
                        1.810089,
                        1.908065,
                        1.709064,
                        1.385227,
                        1.284118,
                        1.257085,
                        1.261826,
                        1.320244,
                        1.418463,
                        -0.288381
                ),
                V12 = c(
                        1.7018212,
                        1.6708563,
                        1.7280936,
                        1.8510958,
                        2.0413064,
                        2.219501,
                        2.300718,
                        2.410956,
                        2.5309432,
                        2.642857,
                        2.6473313,
                        2.533732,
                        2.3803898,
                        2.1034979,
                        1.8401677,
                        1.7326038,
                        1.6869479,
                        1.6361263,
                        1.422603,
                        1.2904044,
                        1.519895,
                        1.781235,
                        1.7759146,
                        1.4436766,
                        0.754851,
                        0.2016948,
                        0.8460149,
                        1.0949137,
                        1.2622762,
                        1.3558464,-0.2535718
                ),
                V13 = c(
                        1.0238163,
                        1.3920828,
                        1.6508524,
                        1.8516509,
                        2.0140125,
                        2.0816779,
                        2.1657678,
                        2.3173347,
                        2.5305612,
                        2.646542,
                        2.6022692,
                        2.4213696,
                        2.1419737,
                        1.9741682,
                        2.019168,
                        2.0968997,
                        2.1768472,
                        2.1030137,
                        1.8888521,
                        1.6483642,
                        1.5851545,
                        1.5515542,
                        1.3544017,
                        1.1527845,
                        1.012491,
                        1.2094269,
                        1.2503864,
                        1.2568069,
                        1.2503217,
                        1.2125666,
                        -0.2224962
                ),
                V14 = c(
                        0.3468005,
                        1.2964461,
                        1.684207,
                        1.8864016,
                        1.9847797,
                        1.9246173,
                        1.7570264,
                        1.5098705,
                        1.423666,
                        1.6670175,
                        1.8653912,
                        1.8688202,
                        1.9000031,
                        2.1181577,
                        2.2916102,
                        2.2332598,
                        2.0661117,
                        2.0224624,
                        2.1251125,
                        2.1607475,
                        2.0161522,
                        1.778285,
                        1.6032933,
                        1.4739095,
                        1.257173,
                        1.153034,
                        1.0964124,
                        1.0498028,
                        1.1531411,
                        1.3371823,
                        -0.1989078
                ),
                V15 = c(
                        0.0507587,
                        0.6336722,
                        0.9255884,
                        1.0862229,
                        1.1237131,
                        1.3705725,
                        1.6614447,
                        1.7259731,
                        1.7236453,
                        1.7218323,
                        1.7646869,
                        2.0101464,
                        2.2578926,
                        2.3815446,
                        2.2970573,
                        2.0461818,
                        1.8252976,
                        1.7460836,
                        1.445195,
                        0.826319,
                        0.8080851,
                        1.4811161,
                        1.8048276,
                        1.7409854,
                        1.299695,
                        0.4519152,
                        0.4793704,
                        0.466986,
                        0.5728771,
                        0.744037,
                        -0.1824328
                ),
                V16 = c(
                        -0.4738215,
                        0.4727348,
                        0.9274847,
                        1.2048411,
                        1.421322,
                        1.5537476,
                        1.5433123,
                        1.5296399,
                        1.639142,
                        1.6306439,
                        1.6520935,
                        1.9257464,
                        2.0885409,
                        2.0734827,
                        1.8262528,
                        1.5423633,
                        1.5733343,
                        1.7136354,
                        1.7929254,
                        1.8988632,
                        1.8928769,
                        1.5880022,
                        1.0706523,
                        0.6158382,
                        0.5398145,
                        0.7050322,
                        0.6450264,
                        0.795963,
                        1.0421368,
                        1.3426467,
                        -0.1659159
                ),
                V17 = c(
                        0.415412306,
                        0.669041161,
                        0.887952888,
                        1.065570319,
                        1.252917184,
                        1.437232432,
                        1.42398399,
                        1.470966126,
                        1.480313211,
                        1.446783162,
                        1.653113718,
                        1.796406092,
                        1.834872806,
                        1.819048923,
                        1.769825465,
                        1.899545685,
                        2.039529007,
                        1.9965402,
                        1.863095503,
                        1.681937696,
                        1.521084486,
                        1.360576445,
                        0.89712193,
                        0.453765169,
                        0.739650412,
                        1.171870428,
                        1.286366885,
                        1.226049366,
                        0.940129628,
                        0.006144024,
                        -0.148891361
                ),
                V18 = c(
                        0.4029431,
                        0.578631,
                        0.6844446,
                        0.7526526,
                        0.6999427,
                        0.8538586,
                        1.3808023,
                        1.7124098,
                        1.8394157,
                        1.8609021,
                        1.7973889,
                        1.7942522,
                        1.7493591,
                        1.6624452,
                        1.8384434,
                        1.9720332,
                        1.9264542,
                        1.7442466,
                        1.6220334,
                        1.7065845,
                        1.698036,
                        1.5573873,
                        1.4871053,
                        1.5647806,
                        1.616974,
                        1.4225419,
                        1.1540925,
                        1.0463909,
                        1.1018232,
                        1.3238546,
                        -0.1346162
                ),
                V19 = c(
                        -0.2086738,
                        0.104658,
                        0.4236391,
                        0.7020921,
                        0.9581844,
                        1.1563411,
                        1.4202728,
                        1.5447069,
                        1.5203407,
                        1.3263225,
                        1.4763387,
                        1.9044777,
                        2.1088163,
                        2.1955835,
                        2.1880875,
                        2.0593745,
                        1.868448,
                        1.6182065,
                        1.5225032,
                        1.4718988,
                        1.3159038,
                        1.0773942,
                        0.7954514,
                        1.2300444,
                        1.6228633,
                        1.7196485,
                        1.50843,
                        1.2931858,
                        0.9776897,
                        0.5346483,
                        -0.1219615
                ),
                V20 = c(
                        -1.17466298,
                        -0.57517985,
                        -0.09469124,
                        0.29341358,
                        0.6275681,
                        0.85657918,
                        0.97005964,
                        1.08544676,
                        1.24737813,
                        1.28432685,
                        1.34063508,
                        1.44902602,
                        1.47152529,
                        1.46396956,
                        1.4450822,
                        1.50800797,
                        1.51509685,
                        1.4236821,
                        1.36516257,
                        1.39389767,
                        1.50727537,
                        1.61656326,
                        1.72162222,
                        1.6186774,
                        1.26994512,
                        1.0449613,
                        1.18170636,
                        1.20705172,
                        1.18974513,
                        1.10240654,-0.10986603
                ),
                V21 = c(
                        -0.64155598,
                        0.05612773,
                        0.46926615,
                        0.74609668,
                        0.9417987,
                        1.10472549,
                        1.21313115,
                        1.32259961,
                        1.3824699,
                        1.16137716,
                        1.14685416,
                        1.28688178,
                        1.48932069,
                        1.65493148,
                        1.64094851,
                        1.64199637,
                        1.61422595,
                        1.52110189,
                        1.44505869,
                        1.29578841,
                        1.28058613,
                        1.4234758,
                        1.61148215,
                        1.60230881,
                        1.37761036,
                        1.07941075,
                        1.23067113,
                        1.39335228,
                        1.59333376,
                        1.81099522,-0.09853742
                ),
                V22 = c(
                        -0.25237878,
                        -0.14055822,
                        -0.04412339,
                        0.05458255,
                        0.15600038,
                        0.16282601,
                        0.32542217,
                        0.48810514,
                        0.62898278,
                        0.80684616,
                        1.19067836,
                        1.36729266,
                        1.33640048,
                        1.39873367,
                        1.60794424,
                        1.82212914,
                        1.77806477,
                        1.36875503,
                        1.19615472,
                        1.62992665,
                        1.94805433,
                        1.91215583,
                        1.48434178,
                        1.02365593,
                        1.10686547,
                        1.42563978,
                        1.62560531,
                        1.55871876,
                        1.26887519,
                        0.28447474,-0.08871415
                ),
                V23 = c(
                        -0.16115903,
                        -0.08391832,
                        -0.01647319,
                        0.02485493,
                        0.05622159,
                        0.08114541,
                        0.08074582,
                        0.286037,
                        0.8045066,
                        1.11176416,
                        1.19684153,
                        1.1567433,
                        1.16076905,
                        1.27902749,
                        1.22616615,
                        0.91111231,
                        0.60854019,
                        0.75664073,
                        1.21895461,
                        1.36165573,
                        1.11617657,
                        0.91607543,
                        0.95890797,
                        1.03957485,
                        1.16212089,
                        1.04901458,
                        0.84476625,
                        0.67451634,
                        0.47356615,
                        0.23627478,-0.08018362
                ),
                V24 = c(
                        -0.71580503,
                        -0.27217826,
                        -0.0436726,
                        0.05140871,
                        0.06902796,
                        0.04674192,
                        0.1338606,
                        0.29404185,
                        0.67017027,
                        0.97898454,
                        1.07231188,
                        1.15895578,
                        1.07801359,
                        0.91601943,
                        0.94290241,
                        0.87139595,
                        1.0393812,
                        1.35791832,
                        1.41817197,
                        1.40620617,
                        1.23069528,
                        1.12921573,
                        1.26412864,
                        1.27032549,
                        1.23857962,
                        1.20233683,
                        1.12570276,
                        1.14053571,
                        1.23413259,
                        1.3865318,-0.07274541
                ),
                V25 = c(
                        -0.80447615,
                        -0.36978346,
                        -0.1149565,
                        0.06442209,
                        0.15423803,
                        0.11491788,
                        0.24894237,
                        0.46719968,
                        0.75581492,
                        0.79729455,
                        0.56349886,
                        0.75343982,
                        1.19469527,
                        1.33759283,
                        1.18629656,
                        0.69901844,
                        0.49800694,
                        1.0295121,
                        1.21341662,
                        1.31957509,
                        1.50155538,
                        1.44061521,
                        1.50586986,
                        1.59421589,
                        1.49538858,
                        1.42624738,
                        1.29586545,
                        1.11294976,
                        0.85942509,
                        0.4968517,-0.06641275
                ),
                V26 = c(
                        -0.88028928,
                        -0.87742406,
                        -0.81625187,
                        -0.71987089,-0.56049376,
                        -0.55713467,
                        -0.351607,
                        0.1028415,
                        0.32873133,
                        0.21449839,
                        0.21092383,
                        0.43334989,
                        0.63600237,
                        0.52970601,
                        0.27485446,
                        0.66284492,
                        1.08874861,
                        1.27593303,
                        1.23844583,
                        0.9993165,
                        0.68768581,
                        0.7926368,
                        1.23239054,
                        1.44573497,
                        1.42903186,
                        1.19000917,
                        1.02234449,
                        0.80780815,
                        0.52961934,
                        0.06918921,-0.06128711
                ),
                V27 = c(
                        0.75839995,
                        -1.3518103,
                        -0.66685695,
                        -0.35336782,-0.18595038,
                        -0.2319309,
                        -0.08208004,
                        0.17125204,
                        0.24066322,
                        0.02703125,
                        -0.3487187,-0.35423592,
                        -0.1599313,
                        0.13835646,
                        0.38145214,
                        0.79939512,
                        1.1332018,
                        1.08063781,
                        0.94091869,
                        0.89119766,
                        1.00726349,
                        1.16833776,
                        1.02817672,
                        0.78434039,
                        0.5377862,
                        0.32062451,
                        0.30234168,
                        0.51861785,
                        0.87403661,
                        1.25392001,-0.05731214
                ),
                V28 = c(
                        -1.64425473,
                        -1.46995102,
                        -1.05072124,
                        -0.60697974,-0.14356611,
                        -0.04617828,
                        -0.22441688,-0.23753935,
                        0.0992326,
                        0.49057842,
                        0.54421444,
                        0.184126,
                        -0.46020092,
                        -0.58709485,
                        0.09349281,
                        0.49746967,
                        0.61976976,
                        0.5339048,
                        0.30912358,
                        0.41219825,
                        0.72645343,
                        0.87199364,
                        0.89251851,
                        0.64601449,
                        0.52924344,
                        0.7819728,
                        0.89644932,
                        0.84901067,
                        0.6284136,
                        0.03421563,-0.05443636
                ),
                V29 = c(
                        -0.91133014,
                        -0.50186916,
                        -0.36481741,
                        -0.37947046,-0.58111115,
                        -0.70460767,
                        -0.18327545,
                        0.16473325,
                        0.33814655,
                        0.49096046,
                        0.89235074,
                        1.23157558,
                        1.18777596,
                        0.97225027,
                        0.67527971,
                        0.50100392,
                        0.66630452,
                        0.77393421,
                        1.18952284,
                        1.46158781,
                        1.37466942,
                        1.1170623,
                        0.83685894,
                        0.90365669,
                        1.08840309,
                        0.98018994,
                        0.88652635,
                        0.96012355,
                        1.12100016,
                        1.34711566,-0.05258754
                ),
                V30 = c(
                        -0.20610999,
                        -0.27010751,
                        -0.33343182,
                        -0.39049313,-0.47370422,
                        -0.45503989,
                        -0.71344963,-1.15403172,
                        -0.32208072,
                        0.32604399,
                        0.41668408,
                        0.14504194,
                        -0.03456606,
                        0.35753346,
                        0.75340612,
                        0.67381566,
                        0.446751,
                        0.75319635,
                        1.1025185,
                        1.21055796,
                        1.03444437,
                        0.69610997,
                        0.58632956,
                        0.57997311,
                        0.62885149,
                        0.91179354,
                        0.89000259,
                        0.88535445,
                        0.90948994,
                        0.93495735,-0.05178215
                ),
                V31 = c(
                        -3.10534277,
                        -2.08074716,
                        -1.58449918,
                        -1.28784782,-1.0321364,
                        -0.9420936,
                        -1.38186672,-1.4291478,
                        -0.7798967,
                        -0.33427203,
                        0.09787527,
                        0.20863284,
                        0.22152833,
                        0.17018238,
                        0.11081253,
                        0.36453404,
                        0.39386712,
                        0.47080299,
                        0.55998291,
                        0.48994446,
                        0.64023255,
                        0.6359818,
                        0.45718184,
                        0.39041628,
                        0.29089896,
                        0.45555962,
                        0.67865541,
                        0.82889259,
                        0.94950862,
                        1.05494627,-0.05210723
                )
        )
        namemgf <- basename(file)
        sample <- MSnbase::readMgfData(file)
        prec <- MSnbase::precursorMz(sample)
        mz <- MSnbase::mz(sample)
        ins <- MSnbase::intensity(sample)
        idx <- unlist(ins) / max(unlist(ins)) > intc
        if (sum(idx) > 0) {
                mz <- unlist(mz)[idx]
                ins <- unlist(ins)[idx]
                ins <- ins / max(ins) * 100
                mzr <- mz[order(ins, decreasing = TRUE)]
                if (length(mzr) > 30) {
                        mzr <- mzr[1:30]
                }
                if (inherits(db, 'list')) {
                        range <- cbind(db$mz - prems, db$mz + prems)
                        idxmz <-
                                enviGCMS::getalign(range, matrix(
                                        c(
                                                prec - ppm / prec * 1e-06,
                                                prec + ppm / prec * 1e-06
                                        ),
                                        nrow = 1
                                ))
                        idxmz <- idxmz[, 1]
                        if (sum(idxmz) > 0) {
                                name <- db$name[idxmz]
                                mz2 <- db$mz[idxmz]
                                msmsraw <- db$msmsraw[idxmz]

                                ms2rank <- function(x) {
                                        mz <- x[, 1]
                                        ins <- x[, 2]
                                        idx <-
                                                (ins / max(ins)) > intc
                                        mz <- mz[idx]
                                        ins <- ins[idx]
                                        mzrdb <-
                                                mz[order(ins, decreasing = TRUE)]
                                        if (length(mzrdb) > 30) {
                                                mzrdb <- mzrdb[1:30]
                                        }
                                        score <- rep(NA, length(mzr))
                                        for (i in seq_along(mzr)) {
                                                match <- which.min(abs(mzrdb - mzr[i]) / mzr[i] * 1e06 < ppm)
                                                if (length(match) > 0) {
                                                        match <-  match[which.min(
                                                                abs(
                                                                        mzrdb - mzr[i]
                                                                ) / mzr[i] * 1e06 < ppm
                                                        )]
                                                        score[i] <-
                                                                xrankm[match, i]
                                                } else{
                                                        score[i] <- xrankm[31, i]
                                                }
                                        }
                                        # reverse score
                                        score2 <-
                                                rep(NA, length(mzrdb))
                                        for (i in seq_along(mzrdb)) {
                                                match <- which.min(
                                                        abs(mzr - mzrdb[i]) / mzrdb[i] * 1e06 < ppm
                                                )
                                                if (length(match) > 0) {
                                                        match <-  match[which.min(
                                                                abs(
                                                                        mzr - mzrdb[i]
                                                                ) / mzrdb[i] * 1e06 < ppm
                                                        )]
                                                        score2[i] <-
                                                                xrankm[match, i]
                                                } else{
                                                        score2[i] <- xrankm[31, i]
                                                }
                                        }

                                        return(mean(c(
                                                sum(score),
                                                sum(score2)
                                        )))
                                }
                                ms2xr <- vapply(msmsraw, ms2rank, 1)
                                idx <-
                                        ms2xr / max(ms2xr, na.rm = TRUE) > quantile

                                t <-
                                        list(
                                                name = name[idx & !is.na(ms2xr)],
                                                mz = mz2[idx &
                                                                 !is.na(ms2xr)],
                                                msmsraw = msmsraw[idx &
                                                                          !is.na(ms2xr)],
                                                score = ms2xr[idx &
                                                                      !is.na(ms2xr)],
                                                dmz = mz,
                                                dprc = prec,
                                                dins = ins,
                                                file = namemgf
                                        )
                        } else{
                                return(NULL)
                        }
                } else{
                        return(NULL)
                }
        } else{
                return(NULL)
        }
}

#' Show MS/MS pmd annotation result
#' @param anno list from MSMS anno function
#' @param ... other parameter for plot function
#' @return NULL
#' @export
plotanno <- function(anno, ...) {
        for (i in seq_along(anno$name)) {
                graphics::plot(anno$msmsraw[[i]],
                               type = 'h',
                               main = anno$name[[i]],
                               ...)
                graphics::points(anno$dins ~ anno$dmz,
                                 type = 'h',
                                 col = 'red')
        }
}