The NCBSet class

Source: R/AllClasses.R, R/methods-NCBSet.R

The NCBSet class is a container for a top-down proteomics experiment similar to the TopDownSet but instead of intensity values it just stores the information if a bond is covered by a N-terminal (encoded as 1), a C-terminal (encoded as 2) and/or bidirectional fragments (encoded as 3).

# S4 method for NCBSet
bestConditions(
  object,
  n = ncol(object),
  minN = 0L,
  maximise = c("fragments", "bonds"),
  ...
)

# S4 method for NCBSet
fragmentationMap(
  object,
  nCombinations = 10,
  cumCoverage = TRUE,
  maximise = c("fragments", "bonds"),
  labels = colnames(object),
  alphaIntensity = TRUE,
  ...
)

# S4 method for NCBSet
show(object)

# S4 method for NCBSet
summary(object, what = c("conditions", "bonds"), ...)

Arguments

object

NCBSet
n

integer, max number of combinations/iterations.
minN

integer, stop if there are less than minN additional fragments
maximise

character, optimisation targeting for the highest number of "fragments" (default) or "bonds".
nCombinations

integer, number of combinations to show (0 to avoid plotting them at all).
cumCoverage

logical, if TRUE (default) cumulative coverage of combinations is shown.
labels

character, overwrite x-axis labels.
alphaIntensity

logical, if TRUE (default) the alpha level of the color is used to show the colData(object)$AssignedIntensity. If FALSE the alpha is set to 1.
what

character, specifies whether "conditions" (columns; default) or "bonds" (rows) should be summarized.
...

arguments passed to internal/other methods. added.

Value

An NCBSet object.

Methods (by generic)

  • bestConditions: Best combination of conditions.

    Finds the best combination of conditions for highest coverage of fragments or bonds. If there are two (or more conditions) that would add the same number of fragments/bonds the one with the highest assigned intensity is used. Use n to limit the number of iterations and combinations that should be returned. If minN is set at least minN fragments have to be added to the combinations. The function returns a 7-column matrix. The first column contains the index (Index) of the condition (column number). The next columns contain the newly added number of fragments or bonds (FragmentsAddedToCombination, BondsAddedToCombination), the fragments or bonds in the condition (FragmentsInCondition, BondsInCondition), and the cumulative coverage fragments or bonds (FragmentCoverage, BondCoverage).

  • fragmentationMap: Plot fragmentation map.

    Plots a fragmentation map of the Protein. Use nCombinations to add another plot with nCombinations combined conditions. If cumCoverage is TRUE (default) these combinations increase the coverage cumulatively.

  • summary: Summary statistics.

    Returns a matrix with some statistics: number of fragments, total/min/first quartile/median/mean/third quartile/maximum of intensity values.

Slots

rowViews

Biostrings::XStringViews, information about bonds (name, start, end, width, sequence), see Biostrings::XStringViews for details.

colData

S4Vectors::DataFrame, information about the MS2 experiments and the fragmentation conditions.

assay

Matrix::dgCMatrix, coverage values of the bonds. The rows correspond to the bonds and the columns to the condition/run. It just stores values that are different from zero. If a bond is covered by an N-terminal fragment its encoded with 1, by an C-terminal fragmentl with 2 and by both fragment types/bidirectional by 3 respectively.

files

character, files that were imported.

processing

character, log messages.

See also

Author

Sebastian Gibb mail@sebastiangibb.de

Examples

## Example data
data(tds, package="topdownr")

## Aggregate technical replicates
tds <- aggregate(tds)

## Coercion into an NCBSet object
ncb <- as(tds, "NCBSet")

ncb
#> NCBSet object (0.34 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG 
#> - - - Fragment data - - -
#> Number of N-terminal fragments: 438
#> Number of C-terminal fragments: 8039
#> Number of N- and C-terminal fragments: 140
#> - - - Condition data - - -
#> Number of conditions: 222 
#> Number of scans: 222 
#> Condition variables (60): File, Scan, ..., MedianIonInjectionTimeMs, AssignedIntensity
#> - - - Assay data - - -
#> Size of array: 152x222 (25.54% != 0)
#> - - - Processing information - - -
#> [2018-01-30 11:39:16] 14518 fragments [1949;351] matched (tolerance: 25 ppm, strategies ion/fragment: remove/remove).
#> [2018-01-30 11:39:16] Condition names updated based on: Mz, AgcTarget, EtdReagentTarget, EtdActivation, CidActivation, HcdActivation. Order of conditions changed. 222 conditions.
#> [2018-01-30 11:39:16] Recalculate median injection time based on: Mz, AgcTarget.
#> [2021-07-27 21:29:44] Aggregated 14518 fragments [1949;351] to 11026 fragments [1949;222].
#> [2021-07-27 21:29:45] Coerced TopDownSet into an NCBSet object; 8617 fragments [152;222]. 

head(summary(ncb))
#>                                Fragments Total Min Q1 Median      Mean Q3 Max
#> C1.0e+05_1.0e+06_02.50_07_00_1        50   100   1  2      2 0.6578947  2   3
#> C1.0e+05_1.0e+06_02.50_14_00_1        48    93   1  2      2 0.6118421  2   2
#> C1.0e+05_1.0e+06_02.50_21_00          47    94   1  2      2 0.6184211  2   3
#> C1.0e+05_1.0e+06_02.50_28_00_1        55   108   1  2      2 0.7105263  2   2
#> C1.0e+05_1.0e+06_02.50_35_00_1        51   101   1  2      2 0.6644737  2   2
#> C1.0e+05_1.0e+06_02.50_00_07          63   124   1  2      2 0.8157895  2   2

# Accessing slots
rowViews(ncb)
#> Views on a 153-letter AAString subject
#> subject: GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFT...PGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
#> views:
#>         start end width
#>     [1]     1   1     1 [G]
#>     [2]     1   2     2 [GL]
#>     [3]     1   3     3 [GLS]
#>     [4]     1   4     4 [GLSD]
#>     [5]     1   5     5 [GLSDG]
#>     ...   ... ...   ... ...
#>   [148]     1 148   148 [GLSDGEWQQVLNVWGKVEADIAGHGQ...GADAQGAMTKALELFRNDIAAKYKE]
#>   [149]     1 149   149 [GLSDGEWQQVLNVWGKVEADIAGHGQ...ADAQGAMTKALELFRNDIAAKYKEL]
#>   [150]     1 150   150 [GLSDGEWQQVLNVWGKVEADIAGHGQ...DAQGAMTKALELFRNDIAAKYKELG]
#>   [151]     1 151   151 [GLSDGEWQQVLNVWGKVEADIAGHGQ...AQGAMTKALELFRNDIAAKYKELGF]
#>   [152]     1 152   152 [GLSDGEWQQVLNVWGKVEADIAGHGQ...QGAMTKALELFRNDIAAKYKELGFQ]
colData(ncb)
#> DataFrame with 222 rows and 60 columns
#>                                                  File      Scan SpectrumIndex
#>                                                 <Rle> <integer>     <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 myo_1211_ETDReagentT..        33          23.5
#> C1.0e+05_1.0e+06_02.50_14_00_1 myo_1211_ETDReagentT..        36          26.5
#> C1.0e+05_1.0e+06_02.50_21_00   myo_1211_ETDReagentT..        40          30.0
#> C1.0e+05_1.0e+06_02.50_28_00_1 myo_1211_ETDReagentT..        43          33.5
#> C1.0e+05_1.0e+06_02.50_35_00_1 myo_1211_ETDReagentT..        46          36.5
#> ...                                               ...       ...           ...
#> C1.0e+06_0.0e+00_00.00_00_07_1 myo_1211_ETDReagentT..       257         241.5
#> C1.0e+06_0.0e+00_00.00_00_14_1 myo_1211_ETDReagentT..       260         244.5
#> C1.0e+06_0.0e+00_00.00_00_21_1 myo_1211_ETDReagentT..       264         248.5
#> C1.0e+06_0.0e+00_00.00_00_28_1 myo_1211_ETDReagentT..       268         252.5
#> C1.0e+06_0.0e+00_00.00_00_35_1 myo_1211_ETDReagentT..       271         255.5
#>                                PeaksCount TotIonCurrent RetentionTime
#>                                 <numeric>     <numeric>     <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1      134.0      14353074       380.439
#> C1.0e+05_1.0e+06_02.50_14_00_1      134.0      14563102       434.326
#> C1.0e+05_1.0e+06_02.50_21_00        148.0      14008273       497.289
#> C1.0e+05_1.0e+06_02.50_28_00_1      136.0      14285122       560.288
#> C1.0e+05_1.0e+06_02.50_35_00_1      134.5      14827734       614.126
#> ...                                   ...           ...           ...
#> C1.0e+06_0.0e+00_00.00_00_07_1       50.0        731470       4641.38
#> C1.0e+06_0.0e+00_00.00_00_14_1      368.5       5725745       4690.68
#> C1.0e+06_0.0e+00_00.00_00_21_1      520.0       3477379       4756.43
#> C1.0e+06_0.0e+00_00.00_00_28_1      202.5       2015615       4822.08
#> C1.0e+06_0.0e+00_00.00_00_35_1      198.5       2889647       4870.88
#>                                BasePeakMz BasePeakIntensity.SpectraInformation
#>                                 <numeric>                            <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1      16943                              4867514
#> C1.0e+05_1.0e+06_02.50_14_00_1      16943                              5007425
#> C1.0e+05_1.0e+06_02.50_21_00        16943                              4605146
#> C1.0e+05_1.0e+06_02.50_28_00_1      16943                              4835166
#> C1.0e+05_1.0e+06_02.50_35_00_1      16943                              5029054
#> ...                                   ...                                  ...
#> C1.0e+06_0.0e+00_00.00_00_07_1   9065.461                              31445.3
#> C1.0e+06_0.0e+00_00.00_00_14_1  16940.924                             297301.0
#> C1.0e+06_0.0e+00_00.00_00_21_1    231.123                              54766.1
#> C1.0e+06_0.0e+00_00.00_00_28_1    231.123                             100368.1
#> C1.0e+06_0.0e+00_00.00_00_35_1    231.123                             249724.3
#>                                    LowMz    HighMz PrecursorMz
#>                                <numeric> <numeric>   <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1   762.391   17146.1      1211.7
#> C1.0e+05_1.0e+06_02.50_14_00_1   762.391   17146.1      1211.7
#> C1.0e+05_1.0e+06_02.50_21_00     762.391   17146.1      1211.7
#> C1.0e+05_1.0e+06_02.50_28_00_1   762.391   17146.6      1211.7
#> C1.0e+05_1.0e+06_02.50_35_00_1   762.390   17146.1      1211.7
#> ...                                  ...       ...         ...
#> C1.0e+06_0.0e+00_00.00_00_07_1  1146.114  16941.01     1211.72
#> C1.0e+06_0.0e+00_00.00_00_14_1   244.634  16940.92     1211.72
#> C1.0e+06_0.0e+00_00.00_00_21_1   200.139   5468.80     1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_1   200.139   1406.28     1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_1   200.139   1049.08     1211.72
#>                                            SpectrumId Condition
#>                                           <character> <integer>
#> C1.0e+05_1.0e+06_02.50_07_00_1 controllerType=0 con..        12
#> C1.0e+05_1.0e+06_02.50_14_00_1 controllerType=0 con..        14
#> C1.0e+05_1.0e+06_02.50_21_00   controllerType=0 con..        16
#> C1.0e+05_1.0e+06_02.50_28_00_1 controllerType=0 con..        18
#> C1.0e+05_1.0e+06_02.50_35_00_1 controllerType=0 con..        20
#> ...                                               ...       ...
#> C1.0e+06_0.0e+00_00.00_00_07_1 controllerType=0 con..       154
#> C1.0e+06_0.0e+00_00.00_00_14_1 controllerType=0 con..       156
#> C1.0e+06_0.0e+00_00.00_00_21_1 controllerType=0 con..       158
#> C1.0e+06_0.0e+00_00.00_00_28_1 controllerType=0 con..       160
#> C1.0e+06_0.0e+00_00.00_00_35_1 controllerType=0 con..       162
#>                                FilterString.HeaderInformation
#>                                                   <character>
#> C1.0e+05_1.0e+06_02.50_07_00_1         FTMS + p NSI sa Full..
#> C1.0e+05_1.0e+06_02.50_14_00_1         FTMS + p NSI sa Full..
#> C1.0e+05_1.0e+06_02.50_21_00           FTMS + p NSI sa Full..
#> C1.0e+05_1.0e+06_02.50_28_00_1         FTMS + p NSI sa Full..
#> C1.0e+05_1.0e+06_02.50_35_00_1         FTMS + p NSI sa Full..
#> ...                                                       ...
#> C1.0e+06_0.0e+00_00.00_00_07_1         FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_14_1         FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_21_1         FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_28_1         FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_35_1         FTMS + p NSI Full ms..
#>                                SupplementalActivation     RtMin       Tic
#>                                                 <Rle> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1                   TRUE   6.34064 165522520
#> C1.0e+05_1.0e+06_02.50_14_00_1                   TRUE   7.23878 168781032
#> C1.0e+05_1.0e+06_02.50_21_00                     TRUE   8.28815 159144752
#> C1.0e+05_1.0e+06_02.50_28_00_1                   TRUE   9.33814 164578728
#> C1.0e+05_1.0e+06_02.50_35_00_1                   TRUE  10.23544 169997320
#> ...                                               ...       ...       ...
#> C1.0e+06_0.0e+00_00.00_00_07_1                  FALSE   77.3563  46251106
#> C1.0e+06_0.0e+00_00.00_00_14_1                  FALSE   78.1780  36784694
#> C1.0e+06_0.0e+00_00.00_00_21_1                  FALSE   79.2739   6848908
#> C1.0e+06_0.0e+00_00.00_00_28_1                  FALSE   80.3680   4623504
#> C1.0e+06_0.0e+00_00.00_00_35_1                  FALSE   81.1814   6598797
#>                                BasePeakPosition
#>                                       <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1          1304.93
#> C1.0e+05_1.0e+06_02.50_14_00_1          1304.93
#> C1.0e+05_1.0e+06_02.50_21_00            1304.93
#> C1.0e+05_1.0e+06_02.50_28_00_1          1304.93
#> C1.0e+05_1.0e+06_02.50_35_00_1          1304.89
#> ...                                         ...
#> C1.0e+06_0.0e+00_00.00_00_07_1         1211.746
#> C1.0e+06_0.0e+00_00.00_00_14_1         1211.755
#> C1.0e+06_0.0e+00_00.00_00_21_1          231.123
#> C1.0e+06_0.0e+00_00.00_00_28_1          195.107
#> C1.0e+06_0.0e+00_00.00_00_35_1          231.123
#>                                BasePeakIntensity.HeaderInformation
#>                                                          <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1                             3773813
#> C1.0e+05_1.0e+06_02.50_14_00_1                             3854662
#> C1.0e+05_1.0e+06_02.50_21_00                               3627429
#> C1.0e+05_1.0e+06_02.50_28_00_1                             3772335
#> C1.0e+05_1.0e+06_02.50_35_00_1                             3699570
#> ...                                                            ...
#> C1.0e+06_0.0e+00_00.00_00_07_1                          30933570.0
#> C1.0e+06_0.0e+00_00.00_00_14_1                            745855.8
#> C1.0e+06_0.0e+00_00.00_00_21_1                             49163.1
#> C1.0e+06_0.0e+00_00.00_00_28_1                             99657.5
#> C1.0e+06_0.0e+00_00.00_00_35_1                            222407.6
#>                                IonInjectionTimeMs ElapsedScanTimeSec HcdEnergy
#>                                         <numeric>          <numeric>     <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1             4.7190            17.8500       NaN
#> C1.0e+05_1.0e+06_02.50_14_00_1             4.4465            17.8405       NaN
#> C1.0e+05_1.0e+06_02.50_21_00               5.6220            17.8870       NaN
#> C1.0e+05_1.0e+06_02.50_28_00_1             4.9790            17.8605       NaN
#> C1.0e+05_1.0e+06_02.50_35_00_1             4.2125            17.8315       NaN
#> ...                                           ...                ...       ...
#> C1.0e+06_0.0e+00_00.00_00_07_1            41.5310            16.1035         7
#> C1.0e+06_0.0e+00_00.00_00_14_1            36.3915            15.8980        14
#> C1.0e+06_0.0e+00_00.00_00_21_1            38.7175            15.9905        21
#> C1.0e+06_0.0e+00_00.00_00_28_1            33.2765            15.7745        28
#> C1.0e+06_0.0e+00_00.00_00_35_1            34.1280            15.8080        35
#>                                ConversionParameterB ConversionParameterC
#>                                           <numeric>            <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1            211703103           -146989184
#> C1.0e+05_1.0e+06_02.50_14_00_1            211703103           -146989183
#> C1.0e+05_1.0e+06_02.50_21_00              211703102           -146989182
#> C1.0e+05_1.0e+06_02.50_28_00_1            211703101           -146989181
#> C1.0e+05_1.0e+06_02.50_35_00_1            211703101           -146989180
#> ...                                             ...                  ...
#> C1.0e+06_0.0e+00_00.00_00_07_1            211702383           -146988183
#> C1.0e+06_0.0e+00_00.00_00_14_1            211702382           -146988182
#> C1.0e+06_0.0e+00_00.00_00_21_1            211702381           -146988181
#> C1.0e+06_0.0e+00_00.00_00_28_1            211702381           -146988180
#> C1.0e+06_0.0e+00_00.00_00_35_1            211702380           -146988179
#>                                TemperatureCompPpm SpaceChargeCompPpm  RawOvFtt
#>                                             <Rle>              <Rle> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1             -14.44              -0.18    778212
#> C1.0e+05_1.0e+06_02.50_14_00_1             -14.44              -0.18    746397
#> C1.0e+05_1.0e+06_02.50_21_00               -14.44              -0.18    897244
#> C1.0e+05_1.0e+06_02.50_28_00_1             -14.44              -0.18    810213
#> C1.0e+05_1.0e+06_02.50_35_00_1             -14.44              -0.18    720653
#> ...                                           ...                ...       ...
#> C1.0e+06_0.0e+00_00.00_00_07_1             -14.56              -1.76   1884474
#> C1.0e+06_0.0e+00_00.00_00_14_1             -14.56              -1.76   1354524
#> C1.0e+06_0.0e+00_00.00_00_21_1             -14.56              -1.76    275211
#> C1.0e+06_0.0e+00_00.00_00_28_1             -14.56              -1.76    158895
#> C1.0e+06_0.0e+00_00.00_00_35_1             -14.56              -1.76    229971
#>                                InjectionT0 NrCentroids SelectedMass1
#>                                  <numeric>   <numeric>         <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1           0      3283.0        1211.7
#> C1.0e+05_1.0e+06_02.50_14_00_1           0      3428.5        1211.7
#> C1.0e+05_1.0e+06_02.50_21_00             0      3629.0        1211.7
#> C1.0e+05_1.0e+06_02.50_28_00_1           0      3464.5        1211.7
#> C1.0e+05_1.0e+06_02.50_35_00_1           0      3341.5        1211.7
#> ...                                    ...         ...           ...
#> C1.0e+06_0.0e+00_00.00_00_07_1       0.000      3128.0       1211.72
#> C1.0e+06_0.0e+00_00.00_00_14_1      -0.048      6190.5       1211.72
#> C1.0e+06_0.0e+00_00.00_00_21_1      -0.055      4913.0       1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_1       0.033      2346.0       1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_1       0.035      2365.5       1211.72
#>                                Activation1 Energy1 SelectedMass2 Activation2
#>                                      <Rle>   <Rle>         <Rle>       <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1         ETD     2.5             0         CID
#> C1.0e+05_1.0e+06_02.50_14_00_1         ETD     2.5             0         CID
#> C1.0e+05_1.0e+06_02.50_21_00           ETD     2.5             0         CID
#> C1.0e+05_1.0e+06_02.50_28_00_1         ETD     2.5             0         CID
#> C1.0e+05_1.0e+06_02.50_35_00_1         ETD     2.5             0         CID
#> ...                                    ...     ...           ...         ...
#> C1.0e+06_0.0e+00_00.00_00_07_1         HCD       7           NaN          NA
#> C1.0e+06_0.0e+00_00.00_00_14_1         HCD      14           NaN          NA
#> C1.0e+06_0.0e+00_00.00_00_21_1         HCD      21           NaN          NA
#> C1.0e+06_0.0e+00_00.00_00_28_1         HCD      28           NaN          NA
#> C1.0e+06_0.0e+00_00.00_00_35_1         HCD      35           NaN          NA
#>                                  Energy2 EtdActivation CidActivation
#>                                <numeric>         <Rle>     <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1         7           2.5             7
#> C1.0e+05_1.0e+06_02.50_14_00_1        14           2.5            14
#> C1.0e+05_1.0e+06_02.50_21_00          21           2.5            21
#> C1.0e+05_1.0e+06_02.50_28_00_1        28           2.5            28
#> C1.0e+05_1.0e+06_02.50_35_00_1        35           2.5            35
#> ...                                  ...           ...           ...
#> C1.0e+06_0.0e+00_00.00_00_07_1       NaN           NaN           NaN
#> C1.0e+06_0.0e+00_00.00_00_14_1       NaN           NaN           NaN
#> C1.0e+06_0.0e+00_00.00_00_21_1       NaN           NaN           NaN
#> C1.0e+06_0.0e+00_00.00_00_28_1       NaN           NaN           NaN
#> C1.0e+06_0.0e+00_00.00_00_35_1       NaN           NaN           NaN
#>                                HcdActivation Activation StartTime   EndTime
#>                                    <numeric>      <Rle> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1           NaN      ETcid      6.01       6.5
#> C1.0e+05_1.0e+06_02.50_14_00_1           NaN      ETcid      7.01       7.5
#> C1.0e+05_1.0e+06_02.50_21_00             NaN      ETcid      8.01       8.5
#> C1.0e+05_1.0e+06_02.50_28_00_1           NaN      ETcid      9.01       9.5
#> C1.0e+05_1.0e+06_02.50_35_00_1           NaN      ETcid     10.01      10.5
#> ...                                      ...        ...       ...       ...
#> C1.0e+06_0.0e+00_00.00_00_07_1             7        HCD     77.01      77.5
#> C1.0e+06_0.0e+00_00.00_00_14_1            14        HCD     78.01      78.5
#> C1.0e+06_0.0e+00_00.00_00_21_1            21        HCD     79.01      79.5
#> C1.0e+06_0.0e+00_00.00_00_28_1            28        HCD     80.01      80.5
#> C1.0e+06_0.0e+00_00.00_00_35_1            35        HCD     81.01      81.5
#>                                ActivationType    Ce SteppedCe SteppedCeValue
#>                                         <Rle> <Rle>     <Rle>          <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1            ETD   NaN                      NaN
#> C1.0e+05_1.0e+06_02.50_14_00_1            ETD   NaN                      NaN
#> C1.0e+05_1.0e+06_02.50_21_00              ETD   NaN                      NaN
#> C1.0e+05_1.0e+06_02.50_28_00_1            ETD   NaN                      NaN
#> C1.0e+05_1.0e+06_02.50_35_00_1            ETD   NaN                      NaN
#> ...                                       ...   ...       ...            ...
#> C1.0e+06_0.0e+00_00.00_00_07_1            HCD    25     False              5
#> C1.0e+06_0.0e+00_00.00_00_14_1            HCD    25     False              5
#> C1.0e+06_0.0e+00_00.00_00_21_1            HCD    25     False              5
#> C1.0e+06_0.0e+00_00.00_00_28_1            HCD    25     False              5
#> C1.0e+06_0.0e+00_00.00_00_35_1            HCD    25     False              5
#>                                MultistageActivation Ethcd
#>                                               <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1                      FALSE
#> C1.0e+05_1.0e+06_02.50_14_00_1                      FALSE
#> C1.0e+05_1.0e+06_02.50_21_00                        FALSE
#> C1.0e+05_1.0e+06_02.50_28_00_1                      FALSE
#> C1.0e+05_1.0e+06_02.50_35_00_1                      FALSE
#> ...                                             ...   ...
#> C1.0e+06_0.0e+00_00.00_00_07_1                      FALSE
#> C1.0e+06_0.0e+00_00.00_00_14_1                      FALSE
#> C1.0e+06_0.0e+00_00.00_00_21_1                      FALSE
#> C1.0e+06_0.0e+00_00.00_00_28_1                      FALSE
#> C1.0e+06_0.0e+00_00.00_00_35_1                      FALSE
#>                                UseCalibratedEtdParameters EtdReactionTime
#>                                                     <Rle>           <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1                      False             2.5
#> C1.0e+05_1.0e+06_02.50_14_00_1                      False             2.5
#> C1.0e+05_1.0e+06_02.50_21_00                        False             2.5
#> C1.0e+05_1.0e+06_02.50_28_00_1                      False             2.5
#> C1.0e+05_1.0e+06_02.50_35_00_1                      False             2.5
#> ...                                                   ...             ...
#> C1.0e+06_0.0e+00_00.00_00_07_1                                        NaN
#> C1.0e+06_0.0e+00_00.00_00_14_1                                        NaN
#> C1.0e+06_0.0e+00_00.00_00_21_1                                        NaN
#> C1.0e+06_0.0e+00_00.00_00_28_1                                        NaN
#> C1.0e+06_0.0e+00_00.00_00_35_1                                        NaN
#>                                EtdReagentTarget EtdSupplementalActivation
#>                                           <Rle>                     <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1            1e+06                      True
#> C1.0e+05_1.0e+06_02.50_14_00_1            1e+06                      True
#> C1.0e+05_1.0e+06_02.50_21_00              1e+06                      True
#> C1.0e+05_1.0e+06_02.50_28_00_1            1e+06                      True
#> C1.0e+05_1.0e+06_02.50_35_00_1            1e+06                      True
#> ...                                         ...                       ...
#> C1.0e+06_0.0e+00_00.00_00_07_1              NaN                          
#> C1.0e+06_0.0e+00_00.00_00_14_1              NaN                          
#> C1.0e+06_0.0e+00_00.00_00_21_1              NaN                          
#> C1.0e+06_0.0e+00_00.00_00_28_1              NaN                          
#> C1.0e+06_0.0e+00_00.00_00_35_1              NaN                          
#>                                SupplementalActivationCe AgcTarget Activationq
#>                                               <numeric>     <Rle>       <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1                        7     1e+05         NaN
#> C1.0e+05_1.0e+06_02.50_14_00_1                       14     1e+05         NaN
#> C1.0e+05_1.0e+06_02.50_21_00                         21     1e+05         NaN
#> C1.0e+05_1.0e+06_02.50_28_00_1                       28     1e+05         NaN
#> C1.0e+05_1.0e+06_02.50_35_00_1                       35     1e+05         NaN
#> ...                                                 ...       ...         ...
#> C1.0e+06_0.0e+00_00.00_00_07_1                      NaN     1e+06         NaN
#> C1.0e+06_0.0e+00_00.00_00_14_1                      NaN     1e+06         NaN
#> C1.0e+06_0.0e+00_00.00_00_21_1                      NaN     1e+06         NaN
#> C1.0e+06_0.0e+00_00.00_00_28_1                      NaN     1e+06         NaN
#> C1.0e+06_0.0e+00_00.00_00_35_1                      NaN     1e+06         NaN
#>                                      TargetedMassList     Mz Charge    Sample
#>                                           <character>  <Rle>  <Rle> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 (mz=1211.7012 z=1 na.. 1211.7     14         1
#> C1.0e+05_1.0e+06_02.50_14_00_1 (mz=1211.7014 z=1 na.. 1211.7     14         2
#> C1.0e+05_1.0e+06_02.50_21_00   (mz=1211.7016 z=1 na.. 1211.7     14         3
#> C1.0e+05_1.0e+06_02.50_28_00_1 (mz=1211.7018 z=1 na.. 1211.7     14         4
#> C1.0e+05_1.0e+06_02.50_35_00_1 (mz=1211.702 z=1 nam.. 1211.7     14         5
#> ...                                               ...    ...    ...       ...
#> C1.0e+06_0.0e+00_00.00_00_07_1 (mz=1211.7154 z=1 na.. 1211.7     14       218
#> C1.0e+06_0.0e+00_00.00_00_14_1 (mz=1211.7156 z=1 na.. 1211.7     14       219
#> C1.0e+06_0.0e+00_00.00_00_21_1 (mz=1211.7158 z=1 na.. 1211.7     14       220
#> C1.0e+06_0.0e+00_00.00_00_28_1 (mz=1211.716 z=1 nam.. 1211.7     14       221
#> C1.0e+06_0.0e+00_00.00_00_35_1 (mz=1211.7162 z=1 na.. 1211.7     14       222
#>                                MedianIonInjectionTimeMs AssignedIntensity
#>                                                   <Rle>         <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1                    4.837           3584559
#> C1.0e+05_1.0e+06_02.50_14_00_1                    4.837           3693918
#> C1.0e+05_1.0e+06_02.50_21_00                      4.837           3590927
#> C1.0e+05_1.0e+06_02.50_28_00_1                    4.837           3935368
#> C1.0e+05_1.0e+06_02.50_35_00_1                    4.837           3773703
#> ...                                                 ...               ...
#> C1.0e+06_0.0e+00_00.00_00_07_1                    43.14          105927.6
#> C1.0e+06_0.0e+00_00.00_00_14_1                    43.14         1786586.1
#> C1.0e+06_0.0e+00_00.00_00_21_1                    43.14          400658.5
#> C1.0e+06_0.0e+00_00.00_00_28_1                    43.14           53933.0
#> C1.0e+06_0.0e+00_00.00_00_35_1                    43.14           56438.2
head(assayData(ncb))
#> 6 x 222 sparse Matrix of class "dgCMatrix"
#>    [[ suppressing 222 column names ‘C1.0e+05_1.0e+06_02.50_07_00_1’, ‘C1.0e+05_1.0e+06_02.50_14_00_1’, ‘C1.0e+05_1.0e+06_02.50_21_00’ ... ]]
#>                                                                                
#> bond001 2 2 2 2 2 2 2 . . . 2 2 2 . 2 2 2 2 . . . . . . . . 2 . . . . . . . . .
#> bond002 . . . . . 2 2 2 . . . . . 2 . . 2 2 2 . . . . . . . 2 . . . . . . . . .
#> bond003 . . . . . 2 . . . . . . . . . . 2 . . . . . . . . . . . . . . . . . . .
#> bond004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> bond005 . . . . . 2 . . . . . . . . . . 2 . . . . . . . . . . . . . . . . . . .
#> bond006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>                                                                                
#> bond001 . 2 . . . . . . . . . . . . . . . . . . . . . . . 2 2 2 . . 2 . . . . 2
#> bond002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 . 2 . . . .
#> bond003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2 . 2 . . . 2
#> bond004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2 . 2 . . . .
#> bond005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 . . 2 . . . .
#> bond006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 . 2 . . . .
#>                                                                                
#> bond001 2 2 2 2 2 . 2 . . 2 2 . 2 . 2 2 2 . . . . . . . . . 2 2 . . . . . . . .
#> bond002 . . 2 . 2 . 2 . 1 . 2 . 2 2 2 2 2 2 . 1 2 . . . . 2 2 2 . . . 2 . . . 2
#> bond003 . 2 . . 2 . 2 1 1 . . . . . . 2 2 . . 1 . . . . . . 2 . . . . . . . . .
#> bond004 . . . . . . . . 1 . . . . . . . . . . . . . . . . . . 2 . . . . . . . .
#> bond005 . . . . 2 . . . . . . . . . . 2 . . . . . . . . . . . . . . . . . . . .
#> bond006 . . . . 2 . 2 . . . . . . . . . . 2 . . . . . . . . . . . . . . . . . .
#>                                                                                
#> bond001 . 2 . . . . . . . . . 2 . . . . . . . . . . . . . . . . 2 2 2 . . 2 . .
#> bond002 . 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 . 2 2 1
#> bond003 . 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 . 2 . . 2 1
#> bond004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2 . 2 1
#> bond005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2 . 2 .
#> bond006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 .
#>                                                                                
#> bond001 . . 2 2 2 2 . 2 2 . . . 2 2 2 2 2 2 2 2 . . . 2 . . 2 . . 2 2 2 . . . .
#> bond002 1 1 2 . . 2 . 2 2 2 . 1 2 2 2 2 2 . 2 2 2 . 1 2 2 . 2 . 2 2 2 2 . . . .
#> bond003 1 1 . . . 2 . 2 2 2 1 1 . . . . . . 2 2 2 1 1 2 . . . . . 2 . . . 1 . .
#> bond004 . . . . . . . 2 2 2 1 1 . . . . . . 2 2 2 . . . . . . . . . . . . . . .
#> bond005 . . . . . . . 2 2 . . . . . . . . . 2 2 . . . . . . . . . 2 . . . 1 . .
#> bond006 . . . . . . . . . . . . . . 2 . 2 . . . . . . . . . . . . 2 . . . . . .
#>                                                                                
#> bond001 2 . . . 2 2 . 2 . . . . . . . 2 2 . . . . . . . . . . . . . . . 2 . 2 2
#> bond002 . . 2 . 2 2 2 2 . . . . . 2 . . 2 . . . . . . . . . . . . . . . 2 . . 2
#> bond003 . . . . 2 2 . . 1 2 . . . . . . . . . 1 . . . . . . . . . . . . . . . .
#> bond004 . . . . . 2 . 1 . . . . . . . . 2 . 1 . . . . . . . . . . . . . . . . 2
#> bond005 . . . . 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> bond006 . . . . . 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>                    
#> bond001 . 2 . . . .
#> bond002 2 2 . . 1 1
#> bond003 . . . 1 1 1
#> bond004 2 . 2 1 1 1
#> bond005 . . 2 . . .
#> bond006 . . 2 . . .

# Accessing colData
ncb$Mz
#> numeric-Rle of length 222 with 1 run
#>   Lengths:    222
#>   Values : 1211.7

# Subsetting

# First 100 bonds
ncb[1:100]
#> NCBSet object (0.28 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG 
#> - - - Fragment data - - -
#> Number of N-terminal fragments: 263
#> Number of C-terminal fragments: 4191
#> Number of N- and C-terminal fragments: 120
#> - - - Condition data - - -
#> Number of conditions: 222 
#> Number of scans: 222 
#> Condition variables (60): File, Scan, ..., MedianIonInjectionTimeMs, AssignedIntensity
#> - - - Assay data - - -
#> Size of array: 100x222 (20.60% != 0)
#> - - - Processing information - - -
#> [2018-01-30 11:39:16] 14518 fragments [1949;351] matched (tolerance: 25 ppm, strategies ion/fragment: remove/remove).
#> [2018-01-30 11:39:16] Condition names updated based on: Mz, AgcTarget, EtdReagentTarget, EtdActivation, CidActivation, HcdActivation. Order of conditions changed. 222 conditions.
#> [2018-01-30 11:39:16] Recalculate median injection time based on: Mz, AgcTarget.
#> [2021-07-27 21:29:44] Aggregated 14518 fragments [1949;351] to 11026 fragments [1949;222].
#> [2021-07-27 21:29:45] Coerced TopDownSet into an NCBSet object; 8617 fragments [152;222].
#> [2021-07-27 21:29:45] Subsetted 8617 fragments [152;222] to 4574 fragments [100;222]. 

# Just bond 152
ncb["bond152"]
#> NCBSet object (0.22 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG 
#> - - - Fragment data - - -
#> Number of N-terminal fragments: 97
#> Number of C-terminal fragments: 0
#> Number of N- and C-terminal fragments: 0
#> - - - Condition data - - -
#> Number of conditions: 222 
#> Number of scans: 222 
#> Condition variables (60): File, Scan, ..., MedianIonInjectionTimeMs, AssignedIntensity
#> - - - Assay data - - -
#> Size of array: 1x222 (43.69% != 0)
#> - - - Processing information - - -
#> [2018-01-30 11:39:16] 14518 fragments [1949;351] matched (tolerance: 25 ppm, strategies ion/fragment: remove/remove).
#> [2018-01-30 11:39:16] Condition names updated based on: Mz, AgcTarget, EtdReagentTarget, EtdActivation, CidActivation, HcdActivation. Order of conditions changed. 222 conditions.
#> [2018-01-30 11:39:16] Recalculate median injection time based on: Mz, AgcTarget.
#> [2021-07-27 21:29:44] Aggregated 14518 fragments [1949;351] to 11026 fragments [1949;222].
#> [2021-07-27 21:29:45] Coerced TopDownSet into an NCBSet object; 8617 fragments [152;222].
#> [2021-07-27 21:29:45] Subsetted 8617 fragments [152;222] to 97 fragments [1;222]. 

# Condition 1 to 10
ncb[, 1:10]
#> NCBSet object (0.08 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG 
#> - - - Fragment data - - -
#> Number of N-terminal fragments: 11
#> Number of C-terminal fragments: 372
#> Number of N- and C-terminal fragments: 2
#> - - - Condition data - - -
#> Number of conditions: 10 
#> Number of scans: 10 
#> Condition variables (60): File, Scan, ..., MedianIonInjectionTimeMs, AssignedIntensity
#> - - - Assay data - - -
#> Size of array: 152x10 (25.33% != 0)
#> - - - Processing information - - -
#> [2018-01-30 11:39:16] 14518 fragments [1949;351] matched (tolerance: 25 ppm, strategies ion/fragment: remove/remove).
#> [2018-01-30 11:39:16] Condition names updated based on: Mz, AgcTarget, EtdReagentTarget, EtdActivation, CidActivation, HcdActivation. Order of conditions changed. 222 conditions.
#> [2018-01-30 11:39:16] Recalculate median injection time based on: Mz, AgcTarget.
#> [2021-07-27 21:29:44] Aggregated 14518 fragments [1949;351] to 11026 fragments [1949;222].
#> [2021-07-27 21:29:45] Coerced TopDownSet into an NCBSet object; 8617 fragments [152;222].
#> [2021-07-27 21:29:45] Subsetted 8617 fragments [152;222] to 385 fragments [152;10]. 

# Plot fragmentation map
fragmentationMap(ncb)
#> Warning: Raster pixels are placed at uneven vertical intervals and will be shifted. Consider using geom_tile() instead.