diff --git a/DESCRIPTION b/DESCRIPTION
index 32b8f59..8ac8f5a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: mzion
 Type: Package
 Title: Database Searches of Proteomic Mass-spectrometrirc Data
-Version: 1.2.6.1
+Version: 1.2.6.2
 Authors@R: 
     person(given = "Qiang",
            family = "Zhang",
diff --git a/R/mgfs.R b/R/mgfs.R
index bda8eda..7283333 100644
--- a/R/mgfs.R
+++ b/R/mgfs.R
@@ -97,7 +97,7 @@ load_mgfs <- function (out_path, mgf_path, min_mass = 200L, max_mass = 4500L,
   
   delete_files(
     out_path, 
-    ignores = c("\\.[Rr]$", "\\.(mgf|MGF)$", "\\.xlsx$", 
+    ignores = c("\\.[Rr]$", "\\.(mgf|MGF)$", "\\.mzML$", "\\.xlsx$", 
                 "\\.xls$", "\\.csv$", "\\.txt$", "\\.tsv$", 
                 "^mgf$", "^mgfs$", "Calls", 
                 # in case of reprocessing after proteoQ
@@ -1339,8 +1339,8 @@ readmzML <- function (filepath = NULL, filelist = NULL,
   # parallel here
   files <- file.path(filepath, filelist)
   sizes <- max(unlist(lapply(files, file.size)))/1024^3
-  # n_cores <- min(detect_cores(16L), floor((max_ram <- 32)/(sizes * 8)), len)
-  n_cores <- min(detect_cores(32L), floor((find_free_mem()/1024)/(sizes * 8)), len)
+  # n_cores <- min(detect_cores(32L), floor((find_free_mem()/1024)/(sizes * 8)), len)
+  n_cores <- min(detect_cores(32L), floor((find_free_mem()/1024)/(sizes * 8)) + 1L, len)
   n_cores <- max(1L, n_cores)
   
   if (n_cores == 1L) {
diff --git a/R/ms2_gen.R b/R/ms2_gen.R
index 6192be1..e6ec1a3 100644
--- a/R/ms2_gen.R
+++ b/R/ms2_gen.R
@@ -109,9 +109,9 @@ gen_ms2ions_base <- function (aa_seq = NULL, ms1_mass = NULL,
   aas <- .Internal(strsplit(aa_seq, "", fixed = TRUE, perl = FALSE, useBytes = FALSE))
   aas <- .Internal(unlist(aas, recursive = FALSE, use.names = FALSE))
   aam <- aa_masses[aas]
-  
   naa <- length(aas)
-  nm <- .Internal(paste0(list(rep("0", naa)), collapse = "", recycle0 = FALSE))
+  
+  nm <- .Internal(paste0(list(rep_len("0", naa)), collapse = "", recycle0 = FALSE))
   af <- ms2ions_by_type(aam, ntmass, ctmass, type_ms2ions, digits)
   
   av <- list(calc_rev_ms2(af, aas))
@@ -190,6 +190,21 @@ gen_ms2ions_a0_vnl0_fnl1 <- function (aa_seq, ms1_mass = NULL,
                                       maxn_vmods_sitescombi_per_pep = 64L, 
                                       digits = 4L) 
 {
+  if (maxn_fnl_per_seq < 2L)
+    return(
+      gen_ms2ions_base(aa_seq = aa_seq, ms1_mass = ms1_mass, 
+                       aa_masses = aa_masses, ms1vmods = NULL, ms2vmods = NULL, 
+                       ntmod = NULL, ctmod = NULL, 
+                       ntmass = ntmass, ctmass = ctmass, 
+                       amods = NULL, vmods_nl = NULL, fmods_nl = NULL, 
+                       mod_indexes = mod_indexes, 
+                       type_ms2ions = type_ms2ions, 
+                       maxn_vmods_per_pep = maxn_vmods_per_pep, 
+                       maxn_sites_per_vmod = maxn_sites_per_vmod, 
+                       maxn_vmods_sitescombi_per_pep = 
+                         maxn_vmods_sitescombi_per_pep, 
+                       digits = digits))
+
   # (1, 2) "amods- tmod+ vnl- fnl-", "amods- tmod- vnl- fnl-" 
   # (no pep_seq dispatching by Anywhere fmod residues -> possible no matched sites)
   
@@ -233,8 +248,7 @@ gen_ms2ions_a0_vnl0_fnl1 <- function (aa_seq, ms1_mass = NULL,
   
   # ---
   fmods_combi <- aas[idxes]
-  # names(fmods_combi) <- idxes
-  
+
   if (length(fmods_combi) == 1L) {
     fnls <- fmods_nl[[fmods_combi]]
     len <- length(fnls)
@@ -490,8 +504,9 @@ gen_ms2ions_a1_vnl0_fnl0 <- function (aa_seq, ms1_mass = NULL, aa_masses = NULL,
                                 aa_masses = aa_masses, 
                                 ntmod = ntmod, ctmod = ctmod, 
                                 ms1_mass = ms1_mass)
+  ms2vmods <- ms2vmods[idxes]
   
-  if (!length(ms2vmods <- ms2vmods[idxes])) 
+  if (!length(ms2vmods)) 
     return(NULL)
   
   # most likely a list-one
@@ -499,27 +514,22 @@ gen_ms2ions_a1_vnl0_fnl0 <- function (aa_seq, ms1_mass = NULL, aa_masses = NULL,
   ms2vmods <- ms2vmods[[1]]
 
   if (attr(ms2vmods, "single")) {
-    vmods_combi <- 
-      find_vmodposU(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
-    
-    M <- attr(vmods_combi, "mods", exact = TRUE)
+    P <- find_vmodposU(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
+    M <- attr(P, "mods", exact = TRUE)
     
     af <- calc_ms2ions_a1_vnl0_fnl0(
-      M = M, vmods_combi = vmods_combi, aam = aam, aa_masses = aa_masses, 
+      M = M, P = P, aam = aam, aa_masses = aa_masses, 
       ntmass = ntmass, ctmass = ctmass, type_ms2ions = type_ms2ions, 
       mod_indexes = mod_indexes, digits = digits)
   }
   else {
-    vmods_combi <- 
-      find_vmodposM(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
-    
-    M <- attr(vmods_combi, "mods", exact = TRUE)
+    P <- find_vmodposM(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
+    M <- attr(P, "mods", exact = TRUE)
 
     af <- lapply(split_matrix(M, by = "row"), calc_ms2ions_a1_vnl0_fnl0, 
-                 vmods_combi = vmods_combi, aam = aam, aa_masses = aa_masses, 
+                 P = P, aam = aam, aa_masses = aa_masses, 
                  ntmass = ntmass, ctmass = ctmass, type_ms2ions = type_ms2ions, 
                  mod_indexes = mod_indexes, digits = digits)
-    
     af <- .Internal(unlist(af, recursive = FALSE, use.names = TRUE))
   }
 
@@ -532,23 +542,23 @@ gen_ms2ions_a1_vnl0_fnl0 <- function (aa_seq, ms1_mass = NULL, aa_masses = NULL,
 #' Helper for the calculation of MS2 ion series.
 #' 
 #' @param M A modification matrix or vector.
-#' @param vmods_combi Lists of variable modifications.
+#' @param P A matrix of position permutations.
 #' @param mod_indexes Modification indexes.
 #' @inheritParams ms2ions_by_type
 #' @inheritParams add_var_masses
-calc_ms2ions_a1_vnl0_fnl0 <- function (M, vmods_combi, aam, aa_masses, 
-                                       ntmass, ctmass, type_ms2ions = "by", 
-                                       mod_indexes, digits = 4L) 
+calc_ms2ions_a1_vnl0_fnl0 <- function (M, P, aam, aa_masses, ntmass, ctmass, 
+                                       type_ms2ions = "by", mod_indexes, 
+                                       digits = 4L) 
 {
   ds  <- aa_masses[M]
-  nvm <- nrow(vmods_combi)
+  nvm <- nrow(P)
   out <- vector("list", nvm)
   
   naa <- length(aam)
   hex0 <- rep_len("0", naa)
 
   for (i in 1:nvm) {
-    vi <- vmods_combi[i, ]
+    vi <- P[i, ]
     aam_i <- aam
     aam_i[vi] <- aam_i[vi] + ds
     out[[i]] <- ms2ions_by_type(aam_i, ntmass, ctmass, type_ms2ions, digits)
@@ -767,10 +777,29 @@ gen_ms2ions_a1_vnl0_fnl1 <- function (aa_seq = NULL, ms1_mass = NULL,
                                       maxn_vnl_per_seq = 3L, 
                                       digits = 4L) 
 {
+  if (maxn_fnl_per_seq < 2L)
+    return(
+      gen_ms2ions_a1_vnl0_fnl0(aa_seq = aa_seq, ms1_mass = ms1_mass, 
+                               aa_masses = aa_masses, 
+                               ms1vmods = ms1vmods, ms2vmods = ms2vmods, 
+                               ntmod = ntmod, ctmod = ctmod, 
+                               ntmass = ntmass, ctmass = ctmass, 
+                               amods = amods, mod_indexes = mod_indexes, 
+                               type_ms2ions = type_ms2ions, 
+                               maxn_vmods_per_pep = maxn_vmods_per_pep, 
+                               maxn_sites_per_vmod = maxn_sites_per_vmod, 
+                               maxn_vmods_sitescombi_per_pep = 
+                                 maxn_vmods_sitescombi_per_pep, 
+                               digits = digits))
+
   # (7, 8) "amods+ tmod- vnl- fnl-", "amods+ tmod+ vnl- fnl-"
   # (no pep_seq dispatching by fmod residues -> possible no matched sites)
   sites <- names(fmods_nl)
-  pattern <- .Internal(paste(list(sites), sep = " ", collapse = "|", recycle0 = FALSE))
+  # pattern <- .Internal(paste(list(sites), sep = " ", collapse = "|", recycle0 = FALSE))
+  pattern <- if (length(sites) > 1L)
+    .Internal(paste0(list(sites), collapse = "|", recycle0 = FALSE))
+  else
+    sites
   
   if (!grepl(pattern, aa_seq)) 
     return(
@@ -800,8 +829,9 @@ gen_ms2ions_a1_vnl0_fnl1 <- function (aa_seq = NULL, ms1_mass = NULL,
                                 aa_masses = aa_masses, 
                                 ntmod = ntmod, ctmod = ctmod, 
                                 ms1_mass = ms1_mass)
+  ms2vmods <- ms2vmods[idxes]
   
-  if (!length(ms2vmods <- ms2vmods[idxes])) 
+  if (!length(ms2vmods)) 
     return(NULL)
   
   fnl_idxes <- .Internal(which(aas %fin% names(fmods_nl)))
@@ -826,25 +856,21 @@ gen_ms2ions_a1_vnl0_fnl1 <- function (aa_seq = NULL, ms1_mass = NULL,
   ms2vmods <- ms2vmods[[1]]
 
   if (attr(ms2vmods, "single")) {
-    vmods_combi <- 
-      find_vmodposU(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
-    
-    M <- attr(vmods_combi, "mods", exact = TRUE)
+    P <- find_vmodposU(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
+    M <- attr(P, "mods", exact = TRUE)
     
     af <- calc_ms2ions_a1_vnl0_fnl1(
-      M = M, vmods_combi = vmods_combi, fnl_combi = fnl_combi, 
+      M = M, P = P, fnl_combi = fnl_combi, 
       fnl_idxes = fnl_idxes, aam = aam, aa_masses = aa_masses, ntmass = ntmass, 
       ctmass = ctmass, type_ms2ions = type_ms2ions, mod_indexes = mod_indexes, 
       digits = digits)
   }
   else {
-    vmods_combi <- 
-      find_vmodposM(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
-    
-    M <- attr(vmods_combi, "mods", exact = TRUE)
+    P <- find_vmodposM(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
+    M <- attr(P, "mods", exact = TRUE)
 
     af <- lapply(split_matrix(M, by = "row"), calc_ms2ions_a1_vnl0_fnl1, 
-                 vmods_combi = vmods_combi, fnl_combi = fnl_combi, 
+                 P = P, fnl_combi = fnl_combi, 
                  fnl_idxes = fnl_idxes, aam = aam, aa_masses = aa_masses, 
                  ntmass = ntmass, ctmass = ctmass, type_ms2ions = type_ms2ions, 
                  mod_indexes = mod_indexes, digits = digits)
@@ -866,13 +892,13 @@ gen_ms2ions_a1_vnl0_fnl1 <- function (aa_seq = NULL, ms1_mass = NULL,
 #' @param mod_indexes Modification indexes.
 #' @inheritParams calc_ms2ions_a1_vnl0_fnl0
 #' @inheritParams hms1_a0_vnl0_fnl1
-calc_ms2ions_a1_vnl0_fnl1 <- function (M, vmods_combi, fnl_combi, fnl_idxes, 
+calc_ms2ions_a1_vnl0_fnl1 <- function (M, P, fnl_combi, fnl_idxes, 
                                        aam, aa_masses, ntmass, ctmass, 
                                        type_ms2ions = "by", mod_indexes, 
                                        digits = 4L) 
 {
   ds  <- aa_masses[M]
-  nvm <- nrow(vmods_combi)
+  nvm <- nrow(P)
   nnl <- length(fnl_combi)
   len <- nvm * nnl
   out <- vector("list", len)
@@ -882,7 +908,7 @@ calc_ms2ions_a1_vnl0_fnl1 <- function (M, vmods_combi, fnl_combi, fnl_idxes,
   hex0 <- rep_len("0", naa)
   
   for (i in 1:nvm) {
-    vi <- vmods_combi[i, ]
+    vi <- P[i, ]
     aam_i <- aam
     aam_i[vi] <- aam_i[vi] + ds
     
@@ -1129,10 +1155,23 @@ gen_ms2ions_a1_vnl1_fnl0 <- function (aa_seq = NULL, ms1_mass = NULL,
                                       
                                       # dummy
                                       maxn_fnl_per_seq = 3L, 
-                                      
                                       maxn_vnl_per_seq = 3L, 
                                       digits = 4L) 
 {
+  if (maxn_vnl_per_seq < 2L)
+    return(gen_ms2ions_a1_vnl0_fnl0(aa_seq = aa_seq, ms1_mass = ms1_mass, 
+                                    aa_masses = aa_masses, 
+                                    ms1vmods = ms1vmods, ms2vmods = ms2vmods, 
+                                    ntmod = ntmod, ctmod = ctmod, 
+                                    ntmass = ntmass, ctmass = ctmass, 
+                                    amods = amods, mod_indexes = mod_indexes, 
+                                    type_ms2ions = type_ms2ions, 
+                                    maxn_vmods_per_pep = maxn_vmods_per_pep, 
+                                    maxn_sites_per_vmod = maxn_sites_per_vmod, 
+                                    maxn_vmods_sitescombi_per_pep = 
+                                      maxn_vmods_sitescombi_per_pep, 
+                                    digits = digits))
+
   aas <- .Internal(strsplit(aa_seq, "", fixed = TRUE, perl = FALSE, useBytes = FALSE))
   aas <- .Internal(unlist(aas, recursive = FALSE, use.names = FALSE))
   aam <- aa_masses[aas]
@@ -1145,8 +1184,9 @@ gen_ms2ions_a1_vnl1_fnl0 <- function (aa_seq = NULL, ms1_mass = NULL,
                                 aa_masses = aa_masses, 
                                 ntmod = ntmod, ctmod = ctmod, 
                                 ms1_mass = ms1_mass)
-
-  if (!length(ms2vmods <- ms2vmods[idxes])) 
+  ms2vmods <- ms2vmods[idxes]
+  
+  if (!length(ms2vmods)) 
     return(NULL)
   
   # most likely a list-one
@@ -1154,57 +1194,101 @@ gen_ms2ions_a1_vnl1_fnl0 <- function (aa_seq = NULL, ms1_mass = NULL,
   ms2vmods <- ms2vmods[[1]]
 
   if (attr(ms2vmods, "single")) {
-    vmods_combi <- 
-      find_vmodposU(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
-    
-    M <- attr(vmods_combi, "mods", exact = TRUE)
-    vnl_combi <- expand_grid_rows(vmods_nl[ms2vmods], nmax = maxn_vnl_per_seq)
+    P  <- find_vmodposU(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
+    M  <- attr(P, "mods", exact = TRUE)
+    nP <- nrow(P)
     
-    af <- calc_ms2ions_a1_vnl1_fnl0(
-      vnl_combi = vnl_combi, 
-      M = M, 
-      vmods_combi = vmods_combi, 
-      aam = aam, 
-      aa_masses = aa_masses, 
-      ntmass = ntmass, 
-      ctmass = ctmass, 
-      type_ms2ions = type_ms2ions, 
-      mod_indexes = mod_indexes, 
-      maxn_vmods_sitescombi_per_pep = 
-        maxn_vmods_sitescombi_per_pep, 
-      digits = digits)
+    if (nP >= maxn_vmods_sitescombi_per_pep)
+      af <- calc_ms2ions_a1_vnl0_fnl0(
+        M = M, P = P, aam = aam, aa_masses = aa_masses, 
+        ntmass = ntmass, ctmass = ctmass, type_ms2ions = type_ms2ions, 
+        mod_indexes = mod_indexes, digits = digits)
+    else {
+      nnl <- min(maxn_vmods_sitescombi_per_pep %/% nP, maxn_vnl_per_seq)
+      
+      if (nnl <= 1L)
+        af <- calc_ms2ions_a1_vnl0_fnl0(
+          M = M, P = P, aam = aam, aa_masses = aa_masses, 
+          ntmass = ntmass, ctmass = ctmass, type_ms2ions = type_ms2ions, 
+          mod_indexes = mod_indexes, digits = digits)
+      else
+        af <- calc_ms2ions_a1_vnl1_fnl0(
+          N = expand_grid_rows(vmods_nl[ms2vmods], nmax = nnl), 
+          M = M, 
+          P = P, 
+          aam = aam, 
+          aa_masses = aa_masses, 
+          ntmass = ntmass, 
+          ctmass = ctmass, 
+          type_ms2ions = type_ms2ions, 
+          mod_indexes = mod_indexes, 
+          digits = digits)
+    }
   }
   else {
-    vmods_combi <- 
-      find_vmodposM(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
-    
-    M <- attr(vmods_combi, "mods", exact = TRUE)
-    M <- split_matrix(M, by = "row")
-    
-    vnl_combi <- 
-      lapply(M, function (x) expand_grid_rows(vmods_nl[x], nmax = maxn_vnl_per_seq))
+    P  <- find_vmodposM(M = ms2vmods, aas = aas, nmax = maxn_vmods_sitescombi_per_pep)
+    M  <- attr(P, "mods", exact = TRUE)
+    nP <- nrow(P)
+    nM <- nrow(M)
+    n1 <- nP * nM
 
-    # garanteed from matchMS: maxn_vmods_sitescombi_per_pep >= 2L
-    maxnvmods <- max(maxn_vmods_sitescombi_per_pep %/% length(M), 2L)
-    
-    af <- mapply(
-      calc_ms2ions_a1_vnl1_fnl0, 
-      vnl_combi, M, 
-      MoreArgs = list(
-        vmods_combi = vmods_combi, 
-        aam = aam, 
-        aa_masses = aa_masses, 
-        ntmass = ntmass, 
-        ctmass = ctmass, 
-        type_ms2ions = type_ms2ions, 
-        mod_indexes = mod_indexes, 
-        maxn_vmods_sitescombi_per_pep = maxnvmods, 
-        digits = digits
-      ), 
-      SIMPLIFY = FALSE, 
-      USE.NAMES = FALSE)
-    
-    af <- .Internal(unlist(af, recursive = FALSE, use.names = TRUE))
+    if (n1 > maxn_vmods_sitescombi_per_pep) {
+      l <- maxn_vmods_sitescombi_per_pep %/% nP
+      M <- M[1:l, ] # l >= 1L
+
+      if (l == 1L) {
+        af <- calc_ms2ions_a1_vnl0_fnl0(
+          M = M, P = P, aam = aam, aa_masses = aa_masses, 
+          ntmass = ntmass, ctmass = ctmass, type_ms2ions = type_ms2ions, 
+          mod_indexes = mod_indexes, digits = digits)
+      }
+      else {
+        M  <- split_matrix(M, by = "row")
+        af <- lapply(M, calc_ms2ions_a1_vnl0_fnl0, 
+                     P = P, aam = aam, aa_masses = aa_masses, 
+                     ntmass = ntmass, ctmass = ctmass, type_ms2ions = type_ms2ions, 
+                     mod_indexes = mod_indexes, digits = digits)
+        af <- .Internal(unlist(af, recursive = FALSE, use.names = TRUE))
+      }
+    }
+    else {
+      M <- split_matrix(M, by = "row")
+      l <- maxn_vmods_sitescombi_per_pep  %/% n1
+      
+      if (l == 1L) {
+        af <- lapply(M, calc_ms2ions_a1_vnl0_fnl0, 
+                     P = P, aam = aam, aa_masses = aa_masses, 
+                     ntmass = ntmass, ctmass = ctmass, type_ms2ions = type_ms2ions, 
+                     mod_indexes = mod_indexes, digits = digits)
+        af <- .Internal(unlist(af, recursive = FALSE, use.names = TRUE))
+      }
+      else {
+        n2 <- n1 * prod(lengths(vmods_nl))
+        
+        N <- if (n2 > maxn_vmods_sitescombi_per_pep)
+          lapply(M, function (x) expand_grid_rows(vmods_nl[x], nmax = 2L))
+        else
+          lapply(M, function (x) expand_grid_rows(vmods_nl[x], nmax = maxn_vnl_per_seq))
+        
+        af <- mapply(
+          calc_ms2ions_a1_vnl1_fnl0, 
+          N, M, 
+          MoreArgs = list(
+            P = P, 
+            aam = aam, 
+            aa_masses = aa_masses, 
+            ntmass = ntmass, 
+            ctmass = ctmass, 
+            type_ms2ions = type_ms2ions, 
+            mod_indexes = mod_indexes, 
+            digits = digits
+          ), 
+          SIMPLIFY = FALSE, 
+          USE.NAMES = FALSE)
+        
+        af <- .Internal(unlist(af, recursive = FALSE, use.names = TRUE))
+      }
+    }
   }
 
   # hexcodes of the reversed entries are not yet reversed; 
@@ -1217,47 +1301,40 @@ gen_ms2ions_a1_vnl1_fnl0 <- function (aa_seq = NULL, ms1_mass = NULL,
 
 
 #' Calculates MS2 ions.
-#' 
-#' @param M A modification matrix or vector.
-#' @param vmods_combi Lists of variable modifications.
-#' @param vnl_combi Lists of combinations of neutral losses for corresponding
-#'   \code{vmods_combi}. Each list contains a table where each column
-#'   corresponds to a set of neutral loss. The first column corresponds to the
-#'   combination without NLs.
+#'
+#' @param M A vector of modifications.
+#' @param P A matrix of positions.
+#' @param N Lists of combinations of neutral losses for corresponding \code{P}.
+#'   Each list contains a table where each column corresponds to a set of
+#'   neutral loss. The first column corresponds to the combination without NLs.
 #' @param mod_indexes Modification indexes.
 #' @inheritParams ms2ions_by_type
 #' @inheritParams add_var_masses
 #' @inheritParams matchMS
-calc_ms2ions_a1_vnl1_fnl0 <- function (vnl_combi, M, vmods_combi, aam, aa_masses, 
+calc_ms2ions_a1_vnl1_fnl0 <- function (N, M, P, aam, aa_masses, 
                                        ntmass, ctmass, 
                                        type_ms2ions = "by", mod_indexes, 
-                                       maxn_vmods_sitescombi_per_pep = 64L, 
                                        digits = 4L) 
 {
-  naa <- length(aam)
+  naa  <- length(aam)
   hex0 <- rep_len("0", naa)
   
   ds  <- aa_masses[M]
-  nnl <- length(vnl_combi)
-  nvm <- nrow(vmods_combi)
-  
-  mod <- maxn_vmods_sitescombi_per_pep %/% nnl
-  maxn_vmods_sitescombi_per_pep <- mod * nnl
-  len <- min(nvm * nnl, maxn_vmods_sitescombi_per_pep)
+  nnl <- length(N)
+  nvm <- nrow(P)
+  len <- nvm * nnl
   out <- vector("list", len)
   
-  ite <- min(mod, nvm)
   r   <- 1L
 
-  for (i in 1:ite) {
-    vi <- vmods_combi[i, ]
+  for (i in 1:nvm) {
+    vi <- P[i, ]
     aam_i <- aam
     aam_i[vi] <- aam_i[vi] + ds
     
     for (j in 1:nnl) {
       aam_j <- aam_i
-      delta_nl <- .Internal(unlist(vnl_combi[[j]], recursive = FALSE, 
-                                   use.names = FALSE))
+      delta_nl <- .Internal(unlist(N[[j]], recursive = FALSE, use.names = FALSE))
       aam_j[vi] <- aam_j[vi] - delta_nl
       out[[r]] <- ms2ions_by_type(aam_j, ntmass, ctmass, type_ms2ions, digits)
       r <- r + 1L
diff --git a/R/ms2frames.R b/R/ms2frames.R
index cf18c9e..6150625 100644
--- a/R/ms2frames.R
+++ b/R/ms2frames.R
@@ -166,8 +166,8 @@ pair_mgftheo <- function (mgf_path, n_modules, .path_bin, by_modules = TRUE,
 hms2match <- function (aa_masses_all, funs_ms2, ms1vmods_all, ms2vmods_all, 
                        mod_indexes, mgf_path, out_path, 
                        type_ms2ions = "by", maxn_vmods_per_pep = 5L, 
-                       maxn_sites_per_vmod = 3L, maxn_fnl_per_seq = 64L, 
-                       maxn_vnl_per_seq = 64L, 
+                       maxn_sites_per_vmod = 3L, maxn_fnl_per_seq = 3L, 
+                       maxn_vnl_per_seq = 3L, 
                        maxn_vmods_sitescombi_per_pep = 64L, 
                        minn_ms2 = 6L, ppm_ms1 = 10L, ppm_ms2 = 10L, 
                        min_ms2mass = 115L, index_mgf_ms2 = FALSE, 
@@ -272,8 +272,8 @@ hms2match <- function (aa_masses_all, funs_ms2, ms1vmods_all, ms2vmods_all,
 ms2match_all <- function (mgth, aa_masses_all, funs_ms2, ms1vmods_all, 
                           ms2vmods_all, mod_indexes, mgf_path, out_path, 
                           type_ms2ions = "by", maxn_vmods_per_pep = 5L, 
-                          maxn_sites_per_vmod = 3L, maxn_fnl_per_seq = 64L, 
-                          maxn_vnl_per_seq = 64L, 
+                          maxn_sites_per_vmod = 3L, maxn_fnl_per_seq = 3L, 
+                          maxn_vnl_per_seq = 3L, 
                           maxn_vmods_sitescombi_per_pep = 64L, 
                           minn_ms2 = 6L, ppm_ms1 = 10L, ppm_ms2 = 10L, 
                           min_ms2mass = 115L, index_mgf_ms2 = FALSE, 
@@ -367,8 +367,8 @@ mframes_adv <- function (mgf_frames = NULL, theopeps = NULL,
                          aa_masses_all, funs_ms2, ms1vmods_all, ms2vmods_all, 
                          mod_indexes = NULL, 
                          type_ms2ions = "by", maxn_vmods_per_pep = 5L, 
-                         maxn_sites_per_vmod = 3L, maxn_fnl_per_seq = 64L, 
-                         maxn_vnl_per_seq = 64L, 
+                         maxn_sites_per_vmod = 3L, maxn_fnl_per_seq = 3L, 
+                         maxn_vnl_per_seq = 3L, 
                          maxn_vmods_sitescombi_per_pep = 64L, 
                          minn_ms2 = 6L, ppm_ms1 = 10L, ppm_ms2 = 10L, 
                          min_ms2mass = 115L, index_mgf_ms2 = FALSE, 
@@ -1403,7 +1403,7 @@ ms2match_one <- function (pep_mod_group, aa_masses, FUN,
                           ms1vmods, ms2vmods, cl, 
                           mod_indexes, mgf_path, out_path, type_ms2ions = "by", 
                           maxn_vmods_per_pep = 5L, maxn_sites_per_vmod = 3L, 
-                          maxn_fnl_per_seq = 8L, maxn_vnl_per_seq = 8L, 
+                          maxn_fnl_per_seq = 3L, maxn_vnl_per_seq = 3L, 
                           maxn_vmods_sitescombi_per_pep = 64L, 
                           minn_ms2 = 6L, ppm_ms1 = 10L, ppm_ms2 = 10L, 
                           min_ms2mass = 115L, index_mgf_ms2 = FALSE, 
@@ -1543,7 +1543,7 @@ frames_adv <- function (mgf_frames = NULL, theopeps = NULL,
                         pep_mod_group = NULL, mod_indexes = NULL, 
                         type_ms2ions = "by", 
                         maxn_vmods_per_pep = 5L, maxn_sites_per_vmod = 3L, 
-                        maxn_fnl_per_seq = 8L, maxn_vnl_per_seq = 8L, 
+                        maxn_fnl_per_seq = 3L, maxn_vnl_per_seq = 3L, 
                         maxn_vmods_sitescombi_per_pep = 64L, 
                         minn_ms2 = 6L, ppm_ms1 = 10L, ppm_ms2 = 10L, 
                         min_ms2mass = 115L, index_mgf_ms2 = FALSE, 
diff --git a/R/msmsmatches.R b/R/msmsmatches.R
index 6fb458b..cc78fbb 100644
--- a/R/msmsmatches.R
+++ b/R/msmsmatches.R
@@ -139,9 +139,13 @@
 #'   considered, the value of \code{maxn_sites_per_vmod} needs to be four or
 #'   greater.
 #' @param maxn_fnl_per_seq A non-negative integer; the maximum number of
-#'   permutative neutral losses per peptide sequence for fixed modifications.
+#'   permutative neutral losses per peptide sequence for fixed modifications. To
+#'   bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+#'   or \code{0}.
 #' @param maxn_vnl_per_seq A non-negative integer; the maximum number of
 #'   permutative neutral losses per peptide sequence for variable modifications.
+#'   To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+#'   1} or \code{0}.
 #' @param maxn_vmods_sitescombi_per_pep A non-negative integer; the maximum
 #'   number of combinatorial variable modifications per peptide sequence (per
 #'   module). The combinations include the ways of neutral losses and
@@ -868,7 +872,7 @@ matchMS <- function (out_path = "~/mzion/outs",
   stopifnot(min_len >= 1L, max_len >= min_len, max_miss <= 10L, minn_ms2 >= 2L, 
             min_mass >= 1L, max_mass >= min_mass, 
             min_ms2mass >= 1L, max_ms2mass > min_ms2mass, 
-            maxn_fnl_per_seq >= 2L, maxn_vnl_per_seq >= 2L, 
+            # maxn_fnl_per_seq >= 2L, maxn_vnl_per_seq >= 2L, 
             maxn_vmods_sitescombi_per_pep >= 2L, 
             n_13c >= 0L, noenzyme_maxn >= 0L, 
             maxn_vmods_per_pep >= maxn_sites_per_vmod, max_n_prots > 1000L, 
diff --git a/R/vmod_ms2_labels.R b/R/vmod_ms2_labels.R
index 2a4d128..5910bd2 100644
--- a/R/vmod_ms2_labels.R
+++ b/R/vmod_ms2_labels.R
@@ -3,13 +3,8 @@
 #' One-to-one correspondence between Names and Sites. Finds the positions of
 #' residues (sites) from a given amino acid sequence (aas).
 #'
-#' @param M A matrix of labels of modification names with permutation. Each
-#'   permutation in a row. The corresponding matrix of site permutations in the
-#'   attribute of \code{resids}.
-#'
-#'   Note that M is a matrix other than lists of vectors, which allows the
-#'   application of one copy of attributes to all rows.
-#' @param nmax The maximum number of combinations.
+#' @param M A vector of modifications. 
+#' @param nmax The maximum number of combinations being allowed.
 #' @param aas \code{aa_seq} split in a sequence of LETTERS.
 #' @examples
 #' \donttest{
@@ -46,14 +41,14 @@
 #' }
 find_vmodposU <- function (M, aas, nmax = 64L) 
 {
-  rs <- attr(M, "resids")
+  rs <- attr(M, "resids", exact = TRUE)
   nr <- length(rs)
-  ps <- attr(M, "ps")
+  ps <- attr(M, "ps", exact = TRUE)
   ss <- names(ps)
 
   if (nmax == 1L) {
     ns <- length(ss)
-    combi <- character(nr)
+    P  <- character(nr)
     ends <- cumsum(ps)
     r1 <- 1L
 
@@ -61,44 +56,44 @@ find_vmodposU <- function (M, aas, nmax = 64L)
       si <- ss[[i]]
       pi <- ps[[i]]
       ei <- ends[[i]]
-      combi[r1:ei] <- .Internal(which(aas == si))[1:pi]
+      P[r1:ei] <- .Internal(which(aas == si))[1:pi]
       r1 <- pi + 1L
     }
     
     # one-row matrix
-    combi <- .Internal(matrix(combi, nrow = 1L, ncol = 1L, byrow = FALSE, 
+    P <- .Internal(matrix(P, nrow = 1L, ncol = 1L, byrow = FALSE, 
                               dimnames = NULL, FALSE, TRUE))
     # remove attributes
-    attr(combi, "mods") <- M[1:nr]
-    
-    return(combi)
+    attr(P, "mods") <- M[1:nr]
+    return(P)
   }
   
   if (nr == 1L) {
-    combi <- .Internal(which(aas == ss))
-    combi <- .Internal(matrix(combi, nrow = 1L, ncol = 1L, byrow = FALSE, 
-                              dimnames = NULL, TRUE, FALSE))
+    P <- .Internal(which(aas == ss))
+    P <- .Internal(matrix(P, nrow = 1L, ncol = 1L, byrow = FALSE, 
+                          dimnames = NULL, TRUE, FALSE))
+    attr(P, "mods") <- M[1:nr]
+    return(P)
   }
-  else {
-    ns <- length(ss)
-    X  <- vector("list", ns)
-    
-    for (i in 1:ns) {
-      si <- .Internal(which(aas == names(ps)[i]))
-      ni <- ps[[i]]
-      
-      X[[i]] <- if (ni == 1L) 
-        matrix(si) 
-      else 
-        arrangements::combinations(si, ni, nitem = nmax, layout = "row")
-    }
+  
+  ns <- length(ss)
+  X  <- vector("list", ns)
+  
+  for (i in 1:ns) {
+    si <- .Internal(which(aas == names(ps)[i]))
+    ni <- ps[[i]]
     
-    combi <- expand_gr(X, nmax = nmax)
+    X[[i]] <- if (ni == 1L) 
+      matrix(si) 
+    else 
+      arrangements::combinations(si, ni, nitem = nmax, layout = "row")
   }
   
-  attr(combi, "mods") <- M[1:nr]
+  P <- expand_gr(X, nmax = nmax)
   
-  combi
+  attr(P, "mods") <- M[1:nr]
+  
+  P
 }
 
 
@@ -113,6 +108,19 @@ find_vmodposU <- function (M, aas, nmax = 64L)
 #' \donttest{
 #' library(mzion)
 #' 
+#' Vec <- c("Carbamidomethyl (M)", "Carbamyl (M)")
+#' vec <- c("M", "M")
+#' aas <- unlist(strsplit("HQGVMNVGMGQKMNS", ""))
+#' ps <- c(2)
+#' names(ps) <- c("M")
+#' attr(Vec, "ps") <- ps
+#' attr(Vec, "resids") <- vec
+#' rs <- unique(vec)
+#' inds <- lapply(rs, function (x) which(vec == x))
+#' attr(Vec, "inds") <- inds
+#' mzion:::find_vmodposM(Vec, aas)
+#' mzion:::find_vmodposM(Vec, aas, nmax = 1L)
+#' 
 #' Vec <- c("Carbamidomethyl (M)", "Deamidated (N)", "Carbamyl (M)")
 #' vec <- c("M", "N", "M")
 #' aas <- unlist(strsplit("HQGVMNVGMGQKMNS", ""))
@@ -152,29 +160,58 @@ find_vmodposU <- function (M, aas, nmax = 64L)
 #' attr(Vec, "inds") <- inds
 #' mzion:::find_vmodposM(Vec, aas)
 #' mzion:::find_vmodposM(Vec, aas, nmax = 1L)
+#' mzion:::find_vmodposM(Vec, aas, nmax = 16L)
+#' mzion:::find_vmodposM(Vec, aas, nmax = 8L)
+#' lapply(1:32, function (x) mzion:::find_vmodposM(Vec, aas, nmax = x))
 #' }
 find_vmodposM <- function (M, aas, nmax = 64L) 
 {
   rs <- attr(M, "resids", exact = TRUE)
   ps <- attr(M, "ps", exact = TRUE)
-  inds <- attr(M, "inds", exact = TRUE)
-  
+  ds <- attr(M, "inds", exact = TRUE)
   np <- length(ps)
   A <- P <- vector("list", np)
-  
+  nmax2 <- nmax
+
   for (i in 1:np) {
     ri <- names(ps)[i]
     si <- .Internal(which(aas == ri))
     ni <- ps[[i]]
-    P[[i]] <- arrangements::combinations(si, ni, nitem = nmax, layout = "row")
 
-    pi <- inds[[i]]
-    ai <- unique(arrangements::permutations(M[pi], nitem = nmax, layout = "list"))
-    A[[i]] <- do.call(rbind, ai)
+    nP <- nrow(P[[i]] <- arrangements::combinations(si, ni, nitem = nmax, layout = "row"))
+    nmax2 <- nmax2 %/% nP
+    
+    if (nmax2 <= 1L) {
+      A[[i]] <- .Internal(matrix(M[ds[[i]]], nrow = 1L, ncol = 1L, byrow = FALSE, 
+                                 dimnames = NULL, FALSE, TRUE))
+      A <- A[1:i]
+      P <- P[1:i]
+      # np <- i
+      break
+    }
+    else {
+      Mi <- M[ds[[i]]]
+      
+      nA <- if (length(Mi) == 1L) # Deamidated (N)
+        nrow(A[[i]] <- .Internal(matrix(Mi, nrow = 1L, ncol = 1L, byrow = FALSE, 
+                                              dimnames = NULL, TRUE, FALSE)))
+      else # Carbamidomethyl (M), Carbamyl (M)
+        nrow(A[[i]] <- unique(arrangements::permutations(Mi, nitem = nmax, layout = "row")))
+
+      nmax2 <- nmax2 %/% nA
+    }
+  }
+  
+  if (np == 1L) {
+    combP <- P[[1]]
+    combA <- A[[1]]
+  }
+  else {
+    combP <- expand_gr(P, nmax = nmax)
+    # combA <- expand_gr(A, nmax = max(nmax %/% nrow(combP), 1L))
+    combA <- expand_gr(A, nmax = nmax)
   }
   
-  combP <- expand_gr(P, nmax = nmax)
-  combA <- expand_gr(A, nmax = nmax)
   attr(combP, "mods") <- combA
 
   combP
diff --git a/man/calc_ms2ions.Rd b/man/calc_ms2ions.Rd
index 3240976..bb1f650 100644
--- a/man/calc_ms2ions.Rd
+++ b/man/calc_ms2ions.Rd
@@ -45,10 +45,14 @@ variable modifications per site in a per peptide sequence.}
 combinatorial variable modifications per peptide sequence.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{digits}{Integer; the number of decimal places to be used.}
 }
diff --git a/man/calc_ms2ions_a1_vnl0_fnl0.Rd b/man/calc_ms2ions_a1_vnl0_fnl0.Rd
index 89e9b07..2e43f7c 100644
--- a/man/calc_ms2ions_a1_vnl0_fnl0.Rd
+++ b/man/calc_ms2ions_a1_vnl0_fnl0.Rd
@@ -6,7 +6,7 @@
 \usage{
 calc_ms2ions_a1_vnl0_fnl0(
   M,
-  vmods_combi,
+  P,
   aam,
   aa_masses,
   ntmass,
@@ -19,7 +19,7 @@ calc_ms2ions_a1_vnl0_fnl0(
 \arguments{
 \item{M}{A modification matrix or vector.}
 
-\item{vmods_combi}{Lists of variable modifications.}
+\item{P}{A matrix of position permutations.}
 
 \item{aam}{A sequence of amino-acid residues with \emph{masses}. Residues
 are in names and masses in values (note that argument \code{aas}
diff --git a/man/calc_ms2ions_a1_vnl0_fnl1.Rd b/man/calc_ms2ions_a1_vnl0_fnl1.Rd
index c7d18c9..ed5ff3a 100644
--- a/man/calc_ms2ions_a1_vnl0_fnl1.Rd
+++ b/man/calc_ms2ions_a1_vnl0_fnl1.Rd
@@ -6,7 +6,7 @@
 \usage{
 calc_ms2ions_a1_vnl0_fnl1(
   M,
-  vmods_combi,
+  P,
   fnl_combi,
   fnl_idxes,
   aam,
@@ -21,7 +21,7 @@ calc_ms2ions_a1_vnl0_fnl1(
 \arguments{
 \item{M}{A modification matrix or vector.}
 
-\item{vmods_combi}{Lists of variable modifications.}
+\item{P}{A matrix of position permutations.}
 
 \item{fnl_combi}{A data.frame of combinations of neutral losses for fixed
 modifications. Each row corresponds to a set of neutral loss. The first row
diff --git a/man/calc_ms2ions_a1_vnl1_fnl0.Rd b/man/calc_ms2ions_a1_vnl1_fnl0.Rd
index b113b87..ec152f5 100644
--- a/man/calc_ms2ions_a1_vnl1_fnl0.Rd
+++ b/man/calc_ms2ions_a1_vnl1_fnl0.Rd
@@ -5,28 +5,26 @@
 \title{Calculates MS2 ions.}
 \usage{
 calc_ms2ions_a1_vnl1_fnl0(
-  vnl_combi,
+  N,
   M,
-  vmods_combi,
+  P,
   aam,
   aa_masses,
   ntmass,
   ctmass,
   type_ms2ions = "by",
   mod_indexes,
-  maxn_vmods_sitescombi_per_pep = 64L,
   digits = 4L
 )
 }
 \arguments{
-\item{vnl_combi}{Lists of combinations of neutral losses for corresponding
-\code{vmods_combi}. Each list contains a table where each column
-corresponds to a set of neutral loss. The first column corresponds to the
-combination without NLs.}
+\item{N}{Lists of combinations of neutral losses for corresponding \code{P}.
+Each list contains a table where each column corresponds to a set of
+neutral loss. The first column corresponds to the combination without NLs.}
 
-\item{M}{A modification matrix or vector.}
+\item{M}{A vector of modifications.}
 
-\item{vmods_combi}{Lists of variable modifications.}
+\item{P}{A matrix of positions.}
 
 \item{aam}{A sequence of amino-acid residues with \emph{masses}. Residues
 are in names and masses in values (note that argument \code{aas}
@@ -46,15 +44,6 @@ and y-ions.}
 
 \item{mod_indexes}{Modification indexes.}
 
-\item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
-number of combinatorial variable modifications per peptide sequence (per
-module). The combinations include the ways of neutral losses and
-modification labels. For instance, at \code{maxn_vnl_per_seq = 2}, the ways
-of allowed position permutation will be 32. Similarly, at
-\code{maxn_vnl_per_seq = 2} and, for example, the permutation of labels
-\code{Acetyl (K)} and \code{TMT (K)} (let's say three ways), the ways of
-position permutation will be limited to \code{64/2/3}.}
-
 \item{digits}{A non-negative integer; the number of decimal places to be
 used. The default is 4.}
 }
diff --git a/man/calc_ms2ionseries.Rd b/man/calc_ms2ionseries.Rd
index c8b1c38..f8bd962 100644
--- a/man/calc_ms2ionseries.Rd
+++ b/man/calc_ms2ionseries.Rd
@@ -48,10 +48,14 @@ variable modifications per site in a per peptide sequence.}
 combinatorial variable modifications per peptide sequence.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{digits}{Integer; the number of decimal places to be used.}
 }
diff --git a/man/calib_mgf.Rd b/man/calib_mgf.Rd
index 455627f..c77757f 100644
--- a/man/calib_mgf.Rd
+++ b/man/calib_mgf.Rd
@@ -80,10 +80,14 @@ default is 5.}
   greater.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
 number of combinatorial variable modifications per peptide sequence (per
diff --git a/man/find_vmodposM.Rd b/man/find_vmodposM.Rd
index 0c2f2dd..acbdce9 100644
--- a/man/find_vmodposM.Rd
+++ b/man/find_vmodposM.Rd
@@ -20,6 +20,19 @@ Multiple Names to the same Site.
 \donttest{
 library(mzion)
 
+Vec <- c("Carbamidomethyl (M)", "Carbamyl (M)")
+vec <- c("M", "M")
+aas <- unlist(strsplit("HQGVMNVGMGQKMNS", ""))
+ps <- c(2)
+names(ps) <- c("M")
+attr(Vec, "ps") <- ps
+attr(Vec, "resids") <- vec
+rs <- unique(vec)
+inds <- lapply(rs, function (x) which(vec == x))
+attr(Vec, "inds") <- inds
+mzion:::find_vmodposM(Vec, aas)
+mzion:::find_vmodposM(Vec, aas, nmax = 1L)
+
 Vec <- c("Carbamidomethyl (M)", "Deamidated (N)", "Carbamyl (M)")
 vec <- c("M", "N", "M")
 aas <- unlist(strsplit("HQGVMNVGMGQKMNS", ""))
@@ -59,5 +72,8 @@ inds <- lapply(rs, function (x) which(vec == x))
 attr(Vec, "inds") <- inds
 mzion:::find_vmodposM(Vec, aas)
 mzion:::find_vmodposM(Vec, aas, nmax = 1L)
+mzion:::find_vmodposM(Vec, aas, nmax = 16L)
+mzion:::find_vmodposM(Vec, aas, nmax = 8L)
+lapply(1:32, function (x) mzion:::find_vmodposM(Vec, aas, nmax = x))
 }
 }
diff --git a/man/find_vmodposU.Rd b/man/find_vmodposU.Rd
index 5c9c310..e06436f 100644
--- a/man/find_vmodposU.Rd
+++ b/man/find_vmodposU.Rd
@@ -7,16 +7,11 @@
 find_vmodposU(M, aas, nmax = 64L)
 }
 \arguments{
-\item{M}{A matrix of labels of modification names with permutation. Each
-  permutation in a row. The corresponding matrix of site permutations in the
-  attribute of \code{resids}.
-
-  Note that M is a matrix other than lists of vectors, which allows the
-  application of one copy of attributes to all rows.}
+\item{M}{A vector of modifications.}
 
 \item{aas}{\code{aa_seq} split in a sequence of LETTERS.}
 
-\item{nmax}{The maximum number of combinations.}
+\item{nmax}{The maximum number of combinations being allowed.}
 }
 \description{
 One-to-one correspondence between Names and Sites. Finds the positions of
diff --git a/man/frames_adv.Rd b/man/frames_adv.Rd
index dcd788f..5dabdf1 100644
--- a/man/frames_adv.Rd
+++ b/man/frames_adv.Rd
@@ -22,8 +22,8 @@ frames_adv(
   type_ms2ions = "by",
   maxn_vmods_per_pep = 5L,
   maxn_sites_per_vmod = 3L,
-  maxn_fnl_per_seq = 8L,
-  maxn_vnl_per_seq = 8L,
+  maxn_fnl_per_seq = 3L,
+  maxn_vnl_per_seq = 3L,
   maxn_vmods_sitescombi_per_pep = 64L,
   minn_ms2 = 6L,
   ppm_ms1 = 10L,
@@ -90,10 +90,14 @@ default is 5.}
   greater.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
 number of combinatorial variable modifications per peptide sequence (per
diff --git a/man/gen_ms2ions_base.Rd b/man/gen_ms2ions_base.Rd
index 10ff31c..d0c6b17 100644
--- a/man/gen_ms2ions_base.Rd
+++ b/man/gen_ms2ions_base.Rd
@@ -176,10 +176,14 @@ default is 5.}
   greater.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
 number of combinatorial variable modifications per peptide sequence (per
diff --git a/man/hms2match.Rd b/man/hms2match.Rd
index 7abf11a..7f346cf 100644
--- a/man/hms2match.Rd
+++ b/man/hms2match.Rd
@@ -15,8 +15,8 @@ hms2match(
   type_ms2ions = "by",
   maxn_vmods_per_pep = 5L,
   maxn_sites_per_vmod = 3L,
-  maxn_fnl_per_seq = 64L,
-  maxn_vnl_per_seq = 64L,
+  maxn_fnl_per_seq = 3L,
+  maxn_vnl_per_seq = 3L,
   maxn_vmods_sitescombi_per_pep = 64L,
   minn_ms2 = 6L,
   ppm_ms1 = 10L,
@@ -75,10 +75,14 @@ default is 5.}
   greater.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
 number of combinatorial variable modifications per peptide sequence (per
diff --git a/man/matchMS.Rd b/man/matchMS.Rd
index 1acbd76..924f48c 100644
--- a/man/matchMS.Rd
+++ b/man/matchMS.Rd
@@ -228,10 +228,14 @@ default is 5.}
   greater.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
 number of combinatorial variable modifications per peptide sequence (per
diff --git a/man/mframes_adv.Rd b/man/mframes_adv.Rd
index f1c47d7..5b62ad4 100644
--- a/man/mframes_adv.Rd
+++ b/man/mframes_adv.Rd
@@ -15,8 +15,8 @@ mframes_adv(
   type_ms2ions = "by",
   maxn_vmods_per_pep = 5L,
   maxn_sites_per_vmod = 3L,
-  maxn_fnl_per_seq = 64L,
-  maxn_vnl_per_seq = 64L,
+  maxn_fnl_per_seq = 3L,
+  maxn_vnl_per_seq = 3L,
   maxn_vmods_sitescombi_per_pep = 64L,
   minn_ms2 = 6L,
   ppm_ms1 = 10L,
@@ -70,10 +70,14 @@ default is 5.}
   greater.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
 number of combinatorial variable modifications per peptide sequence (per
diff --git a/man/ms2match.Rd b/man/ms2match.Rd
index 580c1c2..e37ca85 100644
--- a/man/ms2match.Rd
+++ b/man/ms2match.Rd
@@ -82,10 +82,14 @@ default is 5.}
   greater.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
 number of combinatorial variable modifications per peptide sequence (per
diff --git a/man/ms2match_all.Rd b/man/ms2match_all.Rd
index 289fed0..3334938 100644
--- a/man/ms2match_all.Rd
+++ b/man/ms2match_all.Rd
@@ -16,8 +16,8 @@ ms2match_all(
   type_ms2ions = "by",
   maxn_vmods_per_pep = 5L,
   maxn_sites_per_vmod = 3L,
-  maxn_fnl_per_seq = 64L,
-  maxn_vnl_per_seq = 64L,
+  maxn_fnl_per_seq = 3L,
+  maxn_vnl_per_seq = 3L,
   maxn_vmods_sitescombi_per_pep = 64L,
   minn_ms2 = 6L,
   ppm_ms1 = 10L,
@@ -77,10 +77,14 @@ default is 5.}
   greater.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
 number of combinatorial variable modifications per peptide sequence (per
diff --git a/man/ms2match_one.Rd b/man/ms2match_one.Rd
index d3ab4a3..e12efa7 100644
--- a/man/ms2match_one.Rd
+++ b/man/ms2match_one.Rd
@@ -17,8 +17,8 @@ ms2match_one(
   type_ms2ions = "by",
   maxn_vmods_per_pep = 5L,
   maxn_sites_per_vmod = 3L,
-  maxn_fnl_per_seq = 8L,
-  maxn_vnl_per_seq = 8L,
+  maxn_fnl_per_seq = 3L,
+  maxn_vnl_per_seq = 3L,
   maxn_vmods_sitescombi_per_pep = 64L,
   minn_ms2 = 6L,
   ppm_ms1 = 10L,
@@ -80,10 +80,14 @@ default is 5.}
   greater.}
 
 \item{maxn_fnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for fixed modifications.}
+permutative neutral losses per peptide sequence for fixed modifications. To
+bypass the combinatorial of neutral losses, set \code{maxn_fnl_per_seq = 1}
+or \code{0}.}
 
 \item{maxn_vnl_per_seq}{A non-negative integer; the maximum number of
-permutative neutral losses per peptide sequence for variable modifications.}
+permutative neutral losses per peptide sequence for variable modifications.
+To bypass the combinatorial of neutral losses, set \code{maxn_vnl_per_seq =
+1} or \code{0}.}
 
 \item{maxn_vmods_sitescombi_per_pep}{A non-negative integer; the maximum
 number of combinatorial variable modifications per peptide sequence (per