In fgcz/bfabricShiny: A Module for Bridging B-Fabric and R using REST

knitr::opts_chunk$set(fig.width=8,
                      fig.height=8,
                      echo=FALSE,
                      warning=FALSE, 
                      message=TRUE)

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Meta Data

library(knitr)
library(dplyr)
library(tidyr)
library(ggplot2)
library(bfabricShiny)

knitr::kable(rawfileQC.parameter$data.Info)

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QC

TIC versus RT

The Total Ion Chromatogram (TIC) as well as the Base Peak plot should present a quick overview about the signal distribution over the LC-MS run. It should help to descide if the proper amount of sample was loaded and give insights about the complexity of the sample.

try(QC <- bfabricShiny:::.calc.master.scan(rawfileQC.parameter$data.QC))
try(QC <- bfabricShiny:::.calc.transient(QC))

try(bfabricShiny:::.TIC.BasePeak(QC))

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Cycle Time and points over peak

The cycle time plot should help to descide if the current instrument method is suited for the LC gradient. A too long cycle time will result in to few points over the chromatographic peaks. This is especially problematic for a quantitative experiment. A estimation of the number of Ms data points over three fixed assumed peak widths (10 sec, 20 sec, 30 sec).

try(bfabricShiny:::.cycle.time(QC))

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distribution of selected m/z values

try(bfabricShiny:::.mz.dist(QC))

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Precursor mass frequency

try(bfabricShiny:::.mz.frequency(QC))

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Frequency of precursor charge states

try(bfabricShiny:::.charge.states(QC))

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Cumulative precursor charges

try(bfabricShiny:::.charge.states.quantiles(QC))

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Scan time plot

For HF instruments currently the scan to scan time difference is calculated. For Fusion data the "Elapsed Scan Time" value is plotted

try(bfabricShiny:::.scan.times(QC))

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Injection time plot

try(bfabricShiny:::.injection.times(QC))

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MS2 versus retention time

try(bfabricShiny:::.ms2.vs.RT(QC))

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MS2 cycle load

try(bfabricShiny:::.ms2.frequency(QC))

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Lock mass correction

try(bfabricShiny:::.lm.correction(QC))

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MS datapoints over chromatographic peak

try(bfabricShiny:::.ms.data.points(QC))

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Session info

This report was compiled by using bfabricShiny version r packageVersion('bfabricShiny') and r R.version.string.

References

1. New RawFileReader from Thermo Fisher Scientific planetorbitrap, 2017

2. https://github.com/cpanse/bfabricShiny

3. bfabric input resource r rawfileQC.parameter$resourceid

fgcz/bfabricShiny documentation built on Dec. 25, 2024, 2:37 a.m.