The TopDownSet class is a container for a whole top-down proteomics experiment.
# S4 method for TopDownSet
aggregate(x, by = x$Sample, ...)
# S4 method for TopDownSet,TopDownSet
combine(x, y)
# S4 method for TopDownSet
filterCv(object, threshold, by = object$Sample, ...)
# S4 method for TopDownSet
filterInjectionTime(
object,
maxDeviation = log2(3),
keepTopN = 2,
by = object$Sample,
...
)
# S4 method for TopDownSet
filterIntensity(object, threshold, relative = TRUE, ...)
# S4 method for TopDownSet
filterNonReplicatedFragments(object, minN = 2, by = object$Sample, ...)
# S4 method for TopDownSet
normalize(object, method = "TIC", ...)
# S4 method for TopDownSet,missing
plot(x, y, ..., verbose = interactive())
# S4 method for TopDownSet
show(object)
# S4 method for TopDownSet
summary(object, what = c("conditions", "fragments"), ...)| x, object |
|
|---|---|
| by |
|
| y |
|
| threshold |
|
| maxDeviation |
|
| keepTopN |
|
| relative |
|
| minN |
|
| method |
|
| verbose |
|
| what |
|
| ... | arguments passed to internal/other methods.
replicates (that's why the default is the
|
An TopDownSet object.
See vignette("analysis", package="topdownr")
for a detailed example how to work with
TopDownSet objects.
aggregate: Aggregate conditions/runs.
Aggregates conditions/runs (columns) in an
TopDownSet object
by a
user-given value (default is the
"Sample" column of colData
which has the same value for technical replicates).
It combines intensity values and numeric metadata of the grouped
conditions/runs (columns) by mean and returns a reduced
TopDownSet object.
combine: Combine TopDownSet objects.
combine allows to combine two or more TopDownSet objects.
Please note that it uses the default
sampleColumns to define technical replicates (see readTopDownFiles()).and
the default by argument to group ion injection times for the calculation of
the median time (see updateMedianInjectionTime()). Both could be modified
after combine by calling updateConditionNames() (with modified
sampleColumns argument) and updateMedianInjectionTime() (with modified
by argument).
filterCv: Filter by CV.
Filtering is done by coefficient of variation across technical replicates
(defined by the by argument).
All fragments below a given threshold
are removed. The threshold is the maximal allowed CV in percent
(sd/mean * 100 < threshold).
filterInjectionTime: Filter by ion injection time.
Filtering is done by maximal allowed deviation and just the technical
keepTopN replicates with the lowest deviation from the median ion
injection time are kept.
filterIntensity: Filter by intensity.
Filtering is done by removing all fragments that are below a given
(absolute/relative) intensity threshold.
filterNonReplicatedFragments: Filter by non-replicated fragments.
Filtering is done by removing all fragments that don't replicate across technical replicates.
normalize: Normalise.
Applies Total Ion Current normalisation to a TopDownSet object. The normalisation ist done per scans/conditions (column-wise normalisation).
plot: Plotting.
Plots an TopDownSet object. The function returns a list
of ggplot objects (one item per condtion).
Use pdf or another non-interactive device to plot the list of ggplot
objects (see example section).
summary: Summary statistics.
Returns a matrix
with some statistics: number of fragments,
total/min/first quartile/median/mean/third quartile/maximum of
intensity values.
rowViewsFragmentViews, information about fragments (name, type, sequence, mass, charge), see FragmentViews for details.
colDataS4Vectors::DataFrame, information about the MS2 experiments and the fragmentation conditions.
assayMatrix::dgCMatrix, intensity values of the fragments. The rows correspond to the fragments and the columns to the condition/run. It just stores values that are different from zero.
filescharacter, files that were imported.
tolerancedouble,
tolerance in ppm that were used for matching the
experimental mz values to the theoretical fragments.
redundantMatchingcharacter, matching strategies for redundant
ion/fragment matches. See redundantIonMatch and
redundantFragmentMatch in readTopDownFiles() for details.
processingcharacter, log messages.
`as(object, "MSnSet"): Coerce an TopDownSet object into an MSnbase::MSnSet object.
`as(object, "NCBSet"): Coerce an TopDownSet object into an NCBSet object.
FragmentViews for the row view interface.
Matrix::dgCMatrix for technical details about the intensity storage.
?vignette("analysis", package="topdownr")
for a full documented example of an analysis using topdownr.
Sebastian Gibb mail@sebastiangibb.de
## Example data
data(tds, package="topdownr")
tds
#> TopDownSet object (0.72 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 1949
#> Theoretical fragment types (12): a, a*, b, b*, c, ..., x*, y, y*, z, z*
#> Theoretical mass range: [72.04;16925.98]
#> - - - Condition data - - -
#> Number of conditions: 222
#> Number of scans: 351
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 1949x351 (2.12% != 0)
#> Number of matched fragments: 14518
#> Intensity range: [126.42;1454253.25]
#> - - - 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.
head(summary(tds))
#> Fragments Total Min Q1 Median
#> C1.0e+05_1.0e+06_02.50_07_00_1 48 3350602 5289.57 14243.25 31047.62
#> C1.0e+05_1.0e+06_02.50_07_00_2 46 3352669 3147.54 17875.76 29926.68
#> C1.0e+05_1.0e+06_02.50_14_00_1 46 3204442 3842.46 17372.92 29012.01
#> C1.0e+05_1.0e+06_02.50_14_00_2 48 3320782 3848.07 11656.87 32890.28
#> C1.0e+05_1.0e+06_02.50_21_00 57 3590927 3787.77 12579.74 27829.12
#> C1.0e+05_1.0e+06_02.50_28_00_1 58 3291440 1843.09 10398.68 21424.32
#> Mean Q3 Max
#> C1.0e+05_1.0e+06_02.50_07_00_1 1719.139 59497.87 607970.2
#> C1.0e+05_1.0e+06_02.50_07_00_2 1720.199 73423.75 641441.3
#> C1.0e+05_1.0e+06_02.50_14_00_1 1644.147 68124.07 669750.9
#> C1.0e+05_1.0e+06_02.50_14_00_2 1703.839 54575.39 601565.8
#> C1.0e+05_1.0e+06_02.50_21_00 1842.446 51986.04 607209.7
#> C1.0e+05_1.0e+06_02.50_28_00_1 1688.784 48499.72 589361.6
# Accessing slots
rowViews(tds)
#> FragmentViews on a 153-letter sequence:
#> GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPE...SKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
#> Mass:
#> 16964.964625
#> Modifications:
#> Carbamidomethyl
#> Acetyl
#> Met-loss
#> Views:
#> start end width mass name type z
#> [1] 1 1 1 72.04 a1 a 1 [G]
#> [2] 1 1 1 100.04 b1 b 1 [G]
#> [3] 1 1 1 101.02 z1 z 1 [G]
#> [4] 1 1 1 102.03 zpH1 z 1 [G]
#> [5] 1 1 1 117.07 c1 c 1 [G]
#> ... ... ... ... ... ... ... ... ...
#> [1945] 2 153 152 16893.90 x152* x* 1 [LSDGEWQQVLNVWG...NDIAAKYKELGFQG]
#> [1946] 1 152 152 16908.95 b152 b 1 [GLSDGEWQQVLNVW...RNDIAAKYKELGFQ]
#> [1947] 1 152 152 16908.95 c152* c* 1 [GLSDGEWQQVLNVW...RNDIAAKYKELGFQ]
#> [1948] 2 153 152 16910.93 x152 x 1 [LSDGEWQQVLNVWG...NDIAAKYKELGFQG]
#> [1949] 1 152 152 16925.98 c152 c 1 [GLSDGEWQQVLNVW...RNDIAAKYKELGFQ]
colData(tds)
#> DataFrame with 351 rows and 59 columns
#> File Scan SpectrumIndex
#> <Rle> <integer> <integer>
#> C1.0e+05_1.0e+06_02.50_07_00_1 myo_1211_ETDReagentT.. 33 23
#> C1.0e+05_1.0e+06_02.50_07_00_2 myo_1211_ETDReagentT.. 34 24
#> C1.0e+05_1.0e+06_02.50_14_00_1 myo_1211_ETDReagentT.. 36 26
#> C1.0e+05_1.0e+06_02.50_14_00_2 myo_1211_ETDReagentT.. 37 27
#> C1.0e+05_1.0e+06_02.50_21_00 myo_1211_ETDReagentT.. 40 30
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 myo_1211_ETDReagentT.. 265 249
#> C1.0e+06_0.0e+00_00.00_00_28_1 myo_1211_ETDReagentT.. 268 252
#> C1.0e+06_0.0e+00_00.00_00_28_2 myo_1211_ETDReagentT.. 269 253
#> C1.0e+06_0.0e+00_00.00_00_35_1 myo_1211_ETDReagentT.. 271 255
#> C1.0e+06_0.0e+00_00.00_00_35_2 myo_1211_ETDReagentT.. 272 256
#> PeaksCount TotIonCurrent RetentionTime
#> <integer> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 135 13727530 371.466
#> C1.0e+05_1.0e+06_02.50_07_00_2 133 14978619 389.412
#> C1.0e+05_1.0e+06_02.50_14_00_1 124 15124274 425.397
#> C1.0e+05_1.0e+06_02.50_14_00_2 144 14001930 443.256
#> C1.0e+05_1.0e+06_02.50_21_00 148 14008273 497.289
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 471 3388050 4764.55
#> C1.0e+06_0.0e+00_00.00_00_28_1 233 2060326 4814.02
#> C1.0e+06_0.0e+00_00.00_00_28_2 172 1970904 4830.14
#> C1.0e+06_0.0e+00_00.00_00_35_1 166 2918202 4863.09
#> C1.0e+06_0.0e+00_00.00_00_35_2 231 2861092 4878.68
#> BasePeakMz BasePeakIntensity.SpectraInformation
#> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 16943 4631841
#> C1.0e+05_1.0e+06_02.50_07_00_2 16943 5103187
#> C1.0e+05_1.0e+06_02.50_14_00_1 16943 5346571
#> C1.0e+05_1.0e+06_02.50_14_00_2 16943 4668278
#> C1.0e+05_1.0e+06_02.50_21_00 16943 4605146
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 231.123 56502.7
#> C1.0e+06_0.0e+00_00.00_00_28_1 231.123 96439.5
#> C1.0e+06_0.0e+00_00.00_00_28_2 231.123 104296.8
#> C1.0e+06_0.0e+00_00.00_00_35_1 231.123 261401.5
#> C1.0e+06_0.0e+00_00.00_00_35_2 231.123 238047.0
#> 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_07_00_2 762.390 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_14_00_2 762.391 17146.1 1211.7
#> C1.0e+05_1.0e+06_02.50_21_00 762.391 17146.1 1211.7
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 200.139 5970.087 1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_1 200.139 1460.807 1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_2 200.139 1351.744 1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_1 200.139 959.491 1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_2 200.139 1138.667 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_07_00_2 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_14_00_2 controllerType=0 con.. 14
#> C1.0e+05_1.0e+06_02.50_21_00 controllerType=0 con.. 16
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 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_28_2 controllerType=0 con.. 160
#> C1.0e+06_0.0e+00_00.00_00_35_1 controllerType=0 con.. 162
#> C1.0e+06_0.0e+00_00.00_00_35_2 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_07_00_2 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_14_00_2 FTMS + p NSI sa Full..
#> C1.0e+05_1.0e+06_02.50_21_00 FTMS + p NSI sa Full..
#> ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 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_28_2 FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_35_1 FTMS + p NSI Full ms..
#> C1.0e+06_0.0e+00_00.00_00_35_2 FTMS + p NSI Full ms..
#> SupplementalActivation RtMin Tic
#> <Rle> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 TRUE 6.19109 159451792
#> C1.0e+05_1.0e+06_02.50_07_00_2 TRUE 6.49019 171593248
#> C1.0e+05_1.0e+06_02.50_14_00_1 TRUE 7.08995 178472720
#> C1.0e+05_1.0e+06_02.50_14_00_2 TRUE 7.38760 159089344
#> C1.0e+05_1.0e+06_02.50_21_00 TRUE 8.28815 159144752
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 FALSE 79.4093 6983628
#> C1.0e+06_0.0e+00_00.00_00_28_1 FALSE 80.2337 4512664
#> C1.0e+06_0.0e+00_00.00_00_28_2 FALSE 80.5023 4734344
#> C1.0e+06_0.0e+00_00.00_00_35_1 FALSE 81.0515 6846192
#> C1.0e+06_0.0e+00_00.00_00_35_2 FALSE 81.3113 6351402
#> BasePeakPosition
#> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 1304.93
#> C1.0e+05_1.0e+06_02.50_07_00_2 1304.93
#> C1.0e+05_1.0e+06_02.50_14_00_1 1304.93
#> C1.0e+05_1.0e+06_02.50_14_00_2 1304.93
#> C1.0e+05_1.0e+06_02.50_21_00 1304.93
#> ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 231.123
#> C1.0e+06_0.0e+00_00.00_00_28_1 231.123
#> C1.0e+06_0.0e+00_00.00_00_28_2 159.091
#> C1.0e+06_0.0e+00_00.00_00_35_1 231.123
#> C1.0e+06_0.0e+00_00.00_00_35_2 231.123
#> BasePeakIntensity.HeaderInformation
#> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 3762917
#> C1.0e+05_1.0e+06_02.50_07_00_2 3784709
#> C1.0e+05_1.0e+06_02.50_14_00_1 3987072
#> C1.0e+05_1.0e+06_02.50_14_00_2 3722252
#> C1.0e+05_1.0e+06_02.50_21_00 3627429
#> ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 50586.9
#> C1.0e+06_0.0e+00_00.00_00_28_1 86218.9
#> C1.0e+06_0.0e+00_00.00_00_28_2 113096.1
#> C1.0e+06_0.0e+00_00.00_00_35_1 232769.3
#> C1.0e+06_0.0e+00_00.00_00_35_2 212045.9
#> IonInjectionTimeMs ElapsedScanTimeSec HcdEnergy
#> <numeric> <numeric> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 5.594 17.883 NA
#> C1.0e+05_1.0e+06_02.50_07_00_2 3.844 17.817 NA
#> C1.0e+05_1.0e+06_02.50_14_00_1 3.345 17.796 NA
#> C1.0e+05_1.0e+06_02.50_14_00_2 5.548 17.885 NA
#> C1.0e+05_1.0e+06_02.50_21_00 5.622 17.887 NA
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 33.946 15.801 21
#> C1.0e+06_0.0e+00_00.00_00_28_1 40.343 16.056 28
#> C1.0e+06_0.0e+00_00.00_00_28_2 26.210 15.493 28
#> C1.0e+06_0.0e+00_00.00_00_35_1 27.029 15.523 35
#> C1.0e+06_0.0e+00_00.00_00_35_2 41.227 16.093 35
#> ConversionParameterB ConversionParameterC
#> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 211703103.257927 -146989183.520749
#> C1.0e+05_1.0e+06_02.50_07_00_2 211703103.257927 -146989183.520749
#> C1.0e+05_1.0e+06_02.50_14_00_1 211703102.662952 -146989182.69859
#> C1.0e+05_1.0e+06_02.50_14_00_2 211703102.662952 -146989182.69859
#> C1.0e+05_1.0e+06_02.50_21_00 211703102.056363 -146989181.8545
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 211702381.311807 -146988181.00019
#> C1.0e+06_0.0e+00_00.00_00_28_1 211702380.623441 -146988180.050792
#> C1.0e+06_0.0e+00_00.00_00_28_2 211702380.623441 -146988180.050792
#> C1.0e+06_0.0e+00_00.00_00_35_1 211702379.937029 -146988179.095817
#> C1.0e+06_0.0e+00_00.00_00_35_2 211702379.937029 -146988179.095817
#> TemperatureCompPpm SpaceChargeCompPpm RawOvFtt
#> <Rle> <Rle> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 -14.44 -0.18 889335
#> C1.0e+05_1.0e+06_02.50_07_00_2 -14.44 -0.18 667089
#> C1.0e+05_1.0e+06_02.50_14_00_1 -14.44 -0.18 603503
#> C1.0e+05_1.0e+06_02.50_14_00_2 -14.44 -0.18 889291
#> C1.0e+05_1.0e+06_02.50_21_00 -14.44 -0.18 897244
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 -14.56 -1.76 247569
#> C1.0e+06_0.0e+00_00.00_00_28_1 -14.56 -1.76 187648
#> C1.0e+06_0.0e+00_00.00_00_28_2 -14.56 -1.76 130142
#> C1.0e+06_0.0e+00_00.00_00_35_1 -14.56 -1.76 191043
#> C1.0e+06_0.0e+00_00.00_00_35_2 -14.56 -1.76 268899
#> InjectionT0 NrCentroids SelectedMass1
#> <numeric> <integer> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 0 3513 1211.7
#> C1.0e+05_1.0e+06_02.50_07_00_2 0 3053 1211.7
#> C1.0e+05_1.0e+06_02.50_14_00_1 0 3114 1211.7
#> C1.0e+05_1.0e+06_02.50_14_00_2 0 3743 1211.7
#> C1.0e+05_1.0e+06_02.50_21_00 0 3629 1211.7
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 -0.054 4686 1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_1 0.021 2640 1211.72
#> C1.0e+06_0.0e+00_00.00_00_28_2 0.045 2052 1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_1 0.034 2123 1211.72
#> C1.0e+06_0.0e+00_00.00_00_35_2 0.036 2608 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_07_00_2 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_14_00_2 ETD 2.5 0 CID
#> C1.0e+05_1.0e+06_02.50_21_00 ETD 2.5 0 CID
#> ... ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 HCD 21 NA NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 HCD 28 NA NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 HCD 28 NA NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 HCD 35 NA NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 HCD 35 NA NA
#> Energy2 EtdActivation CidActivation
#> <Rle> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 7 2.5 7
#> C1.0e+05_1.0e+06_02.50_07_00_2 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_14_00_2 14 2.5 14
#> C1.0e+05_1.0e+06_02.50_21_00 21 2.5 21
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 NA NA NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 NA NA NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 NA NA NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 NA NA NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 NA NA NA
#> HcdActivation Activation StartTime EndTime
#> <Rle> <Rle> <numeric> <numeric>
#> C1.0e+05_1.0e+06_02.50_07_00_1 NA ETcid 6.01 6.5
#> C1.0e+05_1.0e+06_02.50_07_00_2 NA ETcid 6.01 6.5
#> C1.0e+05_1.0e+06_02.50_14_00_1 NA ETcid 7.01 7.5
#> C1.0e+05_1.0e+06_02.50_14_00_2 NA ETcid 7.01 7.5
#> C1.0e+05_1.0e+06_02.50_21_00 NA ETcid 8.01 8.5
#> ... ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 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_28_2 28 HCD 80.01 80.5
#> C1.0e+06_0.0e+00_00.00_00_35_1 35 HCD 81.01 81.5
#> C1.0e+06_0.0e+00_00.00_00_35_2 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 NA NA
#> C1.0e+05_1.0e+06_02.50_07_00_2 ETD NA NA
#> C1.0e+05_1.0e+06_02.50_14_00_1 ETD NA NA
#> C1.0e+05_1.0e+06_02.50_14_00_2 ETD NA NA
#> C1.0e+05_1.0e+06_02.50_21_00 ETD NA NA
#> ... ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 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_28_2 HCD 25 False 5
#> C1.0e+06_0.0e+00_00.00_00_35_1 HCD 25 False 5
#> C1.0e+06_0.0e+00_00.00_00_35_2 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_07_00_2 FALSE
#> C1.0e+05_1.0e+06_02.50_14_00_1 FALSE
#> C1.0e+05_1.0e+06_02.50_14_00_2 FALSE
#> C1.0e+05_1.0e+06_02.50_21_00 FALSE
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 FALSE
#> C1.0e+06_0.0e+00_00.00_00_28_1 FALSE
#> C1.0e+06_0.0e+00_00.00_00_28_2 FALSE
#> C1.0e+06_0.0e+00_00.00_00_35_1 FALSE
#> C1.0e+06_0.0e+00_00.00_00_35_2 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_07_00_2 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_14_00_2 False 2.5
#> C1.0e+05_1.0e+06_02.50_21_00 False 2.5
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 NA
#> EtdReagentTarget EtdSupplementalActivation
#> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 1000000 True
#> C1.0e+05_1.0e+06_02.50_07_00_2 1000000 True
#> C1.0e+05_1.0e+06_02.50_14_00_1 1000000 True
#> C1.0e+05_1.0e+06_02.50_14_00_2 1000000 True
#> C1.0e+05_1.0e+06_02.50_21_00 1000000 True
#> ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 NA
#> SupplementalActivationCe AgcTarget Activationq
#> <Rle> <Rle> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 7 100000 NA
#> C1.0e+05_1.0e+06_02.50_07_00_2 7 100000 NA
#> C1.0e+05_1.0e+06_02.50_14_00_1 14 100000 NA
#> C1.0e+05_1.0e+06_02.50_14_00_2 14 100000 NA
#> C1.0e+05_1.0e+06_02.50_21_00 21 100000 NA
#> ... ... ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 NA 1000000 NA
#> C1.0e+06_0.0e+00_00.00_00_28_1 NA 1000000 NA
#> C1.0e+06_0.0e+00_00.00_00_28_2 NA 1000000 NA
#> C1.0e+06_0.0e+00_00.00_00_35_1 NA 1000000 NA
#> C1.0e+06_0.0e+00_00.00_00_35_2 NA 1000000 NA
#> TargetedMassList Mz Charge Sample
#> <character> <Rle> <Rle> <integer>
#> 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_07_00_2 (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_14_00_2 (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+06_0.0e+00_00.00_00_21_2 (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_28_2 (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
#> C1.0e+06_0.0e+00_00.00_00_35_2 (mz=1211.7162 z=1 na.. 1211.7 14 222
#> MedianIonInjectionTimeMs
#> <Rle>
#> C1.0e+05_1.0e+06_02.50_07_00_1 4.837
#> C1.0e+05_1.0e+06_02.50_07_00_2 4.837
#> C1.0e+05_1.0e+06_02.50_14_00_1 4.837
#> C1.0e+05_1.0e+06_02.50_14_00_2 4.837
#> C1.0e+05_1.0e+06_02.50_21_00 4.837
#> ... ...
#> C1.0e+06_0.0e+00_00.00_00_21_2 43.14
#> C1.0e+06_0.0e+00_00.00_00_28_1 43.14
#> C1.0e+06_0.0e+00_00.00_00_28_2 43.14
#> C1.0e+06_0.0e+00_00.00_00_35_1 43.14
#> C1.0e+06_0.0e+00_00.00_00_35_2 43.14
head(assayData(tds))
#> 6 x 351 sparse Matrix of class "dgCMatrix"
#> [[ suppressing 351 column names ‘C1.0e+05_1.0e+06_02.50_07_00_1’, ‘C1.0e+05_1.0e+06_02.50_07_00_2’, ‘C1.0e+05_1.0e+06_02.50_14_00_1’ ... ]]
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#>
#> a1 . . . . . . . . . . . . . . . . . .
#> b1 . . . . . . . . . . . . . . . . . .
#> z1 . . . . . . . . . . . . . . . . . .
#> zpH1 . . . . . . . . . . . . . . . . . .
#> c1 . . . . . . . . . . . . . . . . . .
#> y1 . . . . . . . . . . . . . . . . . .
# Accessing colData
tds$Mz
#> numeric-Rle of length 351 with 1 run
#> Lengths: 351
#> Values : 1211.7
tds$FilterString
#> NULL
# Subsetting
# First 100 fragments
tds[1:100]
#> TopDownSet object (0.31 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 100
#> Theoretical fragment types (12): a, a*, b, b*, c, ..., x*, y, y*, z, z*
#> Theoretical mass range: [72.04;1142.51]
#> - - - Condition data - - -
#> Number of conditions: 222
#> Number of scans: 351
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 100x351 (3.30% != 0)
#> Number of matched fragments: 1157
#> Intensity range: [280.27;214724.06]
#> - - - 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 21:29:47] Subsetted 14518 fragments [1949;351] to 1157 fragments [100;351].
# All c fragments
tds["c"]
#> TopDownSet object (0.31 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 152
#> Theoretical fragment types (1): c
#> Theoretical mass range: [117.07;16925.98]
#> - - - Condition data - - -
#> Number of conditions: 222
#> Number of scans: 351
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 152x351 (0.63% != 0)
#> Number of matched fragments: 338
#> Intensity range: [432.91;664294.75]
#> - - - 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 21:29:47] Subsetted 14518 fragments [1949;351] to 338 fragments [152;351].
# Just c 152
tds["c152"]
#> TopDownSet object (0.28 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 1
#> Theoretical fragment types (1): c
#> Theoretical mass range: [16925.98;16925.98]
#> - - - Condition data - - -
#> Number of conditions: 222
#> Number of scans: 351
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 1x351 (33.90% != 0)
#> Number of matched fragments: 119
#> Intensity range: [979.57;664294.75]
#> - - - 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 21:29:47] Subsetted 14518 fragments [1949;351] to 119 fragments [1;351].
# Condition 1 to 10
tds[, 1:10]
#> TopDownSet object (0.35 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> Mass : 16964.96
#> Modifications (3): Carbamidomethyl, Acetyl, Met-loss
#> - - - Fragment data - - -
#> Number of theoretical fragments: 1949
#> Theoretical fragment types (12): a, a*, b, b*, c, ..., x*, y, y*, z, z*
#> Theoretical mass range: [72.04;16925.98]
#> - - - Condition data - - -
#> Number of conditions: 6
#> Number of scans: 10
#> Condition variables (59): File, Scan, ..., Sample, MedianIonInjectionTimeMs
#> - - - Intensity data - - -
#> Size of array: 1949x10 (2.69% != 0)
#> Number of matched fragments: 524
#> Intensity range: [1843.09;669750.88]
#> - - - 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 21:29:47] Subsetted 14518 fragments [1949;351] to 524 fragments [1949;10].
# Filtering
# Filter all intensities that don't have at least 10 % of the highest
# intensity per fragment.
tds <- filterIntensity(tds, threshold=0.1)
# Filter all conditions with a CV above 30 % (across technical replicates)
tds <- filterCv(tds, threshold=30)
# Filter all conditions with a large deviation in injection time
tds <- filterInjectionTime(tds, maxDeviation=log2(3), keepTopN=2)
# Filter all conditions where fragments don't replicate
tds <- filterNonReplicatedFragments(tds)
# Normalise by TIC
tds <- normalize(tds)
# Aggregate technical replicates
tds <- aggregate(tds)
head(summary(tds))
#> Fragments Total Min Q1 Median Mean
#> 1 29 0.2091889 0.0004274603 0.001837281 0.003152185 1.073314e-04
#> 2 27 0.1605411 0.0006430969 0.001462947 0.003288017 8.237099e-05
#> 3 0 0.0000000 0.0000000000 0.000000000 0.000000000 0.000000e+00
#> 4 33 0.2035319 0.0005233145 0.001117384 0.002902880 1.044289e-04
#> 5 31 0.1803964 0.0008580174 0.002069399 0.003176679 9.255844e-05
#> 6 0 0.0000000 0.0000000000 0.000000000 0.000000000 0.000000e+00
#> Q3 Max
#> 1 0.006113229 0.04228552
#> 2 0.005059019 0.04293340
#> 3 0.000000000 0.00000000
#> 4 0.004815610 0.04323451
#> 5 0.004992268 0.04246845
#> 6 0.000000000 0.00000000
# Coercion
as(tds, "NCBSet")
#> NCBSet object (0.26 Mb)
#> - - - Protein data - - -
#> Amino acid sequence (153): GLSDGEWQQVLNVWGKVEADIAGHGQ...GAMTKALELFRNDIAAKYKELGFQG
#> - - - Fragment data - - -
#> Number of N-terminal fragments: 62
#> Number of C-terminal fragments: 1987
#> Number of N- and C-terminal fragments: 4
#> - - - Condition data - - -
#> Number of conditions: 220
#> Number of scans: 220
#> Condition variables (60): File, Scan, ..., MedianIonInjectionTimeMs, AssignedIntensity
#> - - - Assay data - - -
#> Size of array: 152x220 (6.14% != 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 21:29:47] 3579 intensity values < 0.1 (relative) filtered; 10939 fragments [1949;351].
#> [2021-07-27 21:29:47] 750 fragments with CV > 30% filtered; 10189 fragments [1949;351].
#> [2021-07-27 21:29:48] Subsetted 10189 fragments [1949;351] to 10158 fragments [1949;345].
#> [2021-07-27 21:29:48] 6 scans filtered with injection time deviation >= 1.58496250072116 or rank >= 3; 10158 fragments [1949;345].
#> [2021-07-27 21:29:48] 5604 intensity values of fragments replicated < 2 times filtered; 4554 fragments [1949;345].
#> [2021-07-27 21:29:48] Intensity values normalized to TIC.
#> [2021-07-27 21:29:48] Aggregated 4554 fragments [1949;345] to 2277 fragments [1949;220].
#> [2021-07-27 21:29:48] Coerced TopDownSet into an NCBSet object; 2053 fragments [152;220].
if (require("MSnbase")) {
as(tds, "MSnSet")
}
#> Loading required package: MSnbase
#> Loading required package: Biobase
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: mzR
#> Loading required package: Rcpp
#>
#> This is MSnbase version 2.19.1
#> Visit https://lgatto.github.io/MSnbase/ to get started.
#>
#> Attaching package: ‘MSnbase’
#> The following object is masked from ‘package:base’:
#>
#> trimws
#> MSnSet (storageMode: lockedEnvironment)
#> assayData: 1949 features, 220 samples
#> element names: exprs
#> protocolData: none
#> phenoData
#> sampleNames: C1.0e+05_1.0e+06_02.50_07_00_1
#> C1.0e+05_1.0e+06_02.50_14_00_1 ... C1.0e+06_0.0e+00_00.00_00_35_1
#> (220 total)
#> varLabels: File Scan ... MedianIonInjectionTimeMs (59 total)
#> varMetadata: labelDescription
#> featureData
#> featureNames: a1 b1 ... c152 (1949 total)
#> fvarLabels: fragment start ... z (8 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:
#> - - - 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 21:29:47] 3579 intensity values < 0.1 (relative) filtered; 10939 fragments [1949;351].
#> [2021-07-27 21:29:47] 750 fragments with CV > 30% filtered; 10189 fragments [1949;351].
#> [2021-07-27 21:29:48] Subsetted 10189 fragments [1949;351] to 10158 fragments [1949;345].
#> [2021-07-27 21:29:48] 6 scans filtered with injection time deviation >= 1.58496250072116 or rank >= 3; 10158 fragments [1949;345].
#> [2021-07-27 21:29:48] 5604 intensity values of fragments replicated < 2 times filtered; 4554 fragments [1949;345].
#> [2021-07-27 21:29:48] Intensity values normalized to TIC.
#> [2021-07-27 21:29:48] Aggregated 4554 fragments [1949;345] to 2277 fragments [1949;220].
#> MSnbase version: 2.19.1
if (FALSE) {
# plot a single condition
# pseudo-code (replace topdownset with your object)
plot(topdownset[,1])
# plot the whole object
pdf("topdown-spectra.pdf", paper="a4r", width=12)
# pseudo-code (replace topdownset with your object)
plot(topdownset)
dev.off()
}