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Other Useful

Shiying Xiao1^1, Charles Watt1^1, Jennifer C. Liddle2^2, Jeremy L. Balsbaugh2^2, Timothy E. Moore3^3

1^1Department of Statistics, UConn
2^2Proteomics and Metabolomics Facility, UConn
3^3Statistical Consulting Services, UConn

2026-01-27

Source: vignettes/other.Rmd
other.Rmd

Preliminary 

## load R package
library(msDiaLogue)
## preprocessing
fileName <- "../inst/extdata/Toy_Spectronaut_Data.csv"
dataSet <- preprocessing(fileName,
                         filterNaN = TRUE, filterUnique = 2,
                         replaceBlank = TRUE, saveRm = TRUE)
## transformation
dataTran <- transform(dataSet, logFold = 2)
## normalization
dataNorm <- normalize(dataTran, normalizeType = "quant")
## filtering
dataImput_pre <- filterNA(dataNorm, minProp = 0.51, by = "cond", saveRm = TRUE)
## imputation
dataImput <- impute.min_local(dataImput_pre, reportImputing = FALSE)

pullProteinPath

The function pullProteinPath() allows you to see the quantitative values associated with specific proteins at each step of processing, using either the exact match argument listname =, or the text match argument regexName =, or both.

This can be useful for questions such as,

  • “Which of the values for my favorite protein were actually measured, vs. imputed?”
  • “Why didn’t my favorite protein make it to the final list? At what step was it filtered out?”.

It can also be used to check whether the fold-change observed for a specific protein is an artifact from one of the processing steps.

Check <- pullProteinPath(
  listName = c("LYSC_CHICK", "BGAL_ECOLI"),
  regexName = c("BOVIN"),
  by = "PG.ProteinNames",
  dataSetList = list(Initial = dataSet,
                     Transformed = dataTran,
                     Normalized = dataNorm,
                     Imputed = dataImput))
PG.ProteinNames PG.Genes PG.ProteinAccession PG.ProteinAccessions PG.ProteinDescriptions PG.ProteinName R.Condition R.Replicate Initial Transformed Normalized Imputed
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 100pmol 1 111209.703 16.76292 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 100pmol 2 111659.883 16.76875 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 100pmol 3 105982.914 16.69347 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 100pmol 4 104442.562 16.67235 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 200pmol 1 109245.289 16.73721 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 200pmol 2 113357.508 16.79052 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 200pmol 3 114321.836 16.80274 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 200pmol 4 116439.820 16.82923 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 50pmol 1 117803.492 16.84602 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 50pmol 2 110086.680 16.74828 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 50pmol 3 105640.203 16.68880 16.75777 16.75777
ALBU_BOVIN ALB CON__P02769 CON__P02769 Bovine serum albumin ALBU_BOVIN 50pmol 4 110446.000 16.75298 16.75777 16.75777
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 100pmol 1 23840.031 14.54110 14.44005 14.44005
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 100pmol 2 23963.307 14.54854 14.44005 14.44005
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 100pmol 3 22957.350 14.48667 14.42169 14.42169
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 100pmol 4 22311.297 14.44549 14.20112 14.20112
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 200pmol 1 41234.672 15.33157 14.77650 14.77650
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 200pmol 2 42899.434 15.38867 14.70670 14.70670
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 200pmol 3 42904.945 15.38886 14.77650 14.77650
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 200pmol 4 43279.844 15.40141 14.70670 14.70670
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 50pmol 1 14728.673 13.84634 14.38206 14.38206
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 50pmol 2 14736.710 13.84713 14.10465 14.10465
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 50pmol 3 14160.203 13.78955 14.38206 14.38206
BGAL_ECOLI lacZ P00722 P00722 Beta-galactosidase BGAL_ECOLI 50pmol 4 14758.731 13.84928 14.10465 14.10465
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 100pmol 1 10737.953 13.39043 12.96499 12.96499
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 100pmol 2 10655.384 13.37929 13.62766 13.62766
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 100pmol 3 10663.714 13.38042 12.81909 12.81909
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 100pmol 4 10843.115 13.40449 12.96499 12.96499
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 200pmol 1 19524.863 14.25302 13.10393 13.10393
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 200pmol 2 20072.297 14.29292 12.49496 12.49496
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 200pmol 3 20787.127 14.34340 14.00189 14.00189
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 200pmol 4 19924.240 14.28224 13.38772 13.38772
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 50pmol 1 6758.298 12.72244 12.49496 12.49496
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 50pmol 2 6721.135 12.71449 12.30540 12.30540
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 50pmol 3 6172.877 12.59173 13.38772 13.38772
CYC_BOVIN CYCS CON__P62894 CON__P62894 Cytochrome c CYC_BOVIN 50pmol 4 6028.398 12.55756 12.30540 12.30540
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 100pmol 1 13798.590 13.75223 13.62766 13.62766
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 100pmol 2 13880.411 13.76076 13.97388 13.97388
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 100pmol 3 13723.719 13.74438 13.55168 13.55168
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 100pmol 4 13944.603 13.76742 13.62766 13.62766
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 200pmol 1 24344.188 14.57129 14.22236 14.22236
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 200pmol 2 24742.227 14.59469 13.88102 13.88102
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 200pmol 3 24803.633 14.59826 14.22236 14.22236
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 200pmol 4 26381.047 14.68721 14.13067 14.13067
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 50pmol 1 7169.955 12.80775 13.38772 13.38772
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 50pmol 2 7797.536 12.92880 13.25790 13.25790
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 50pmol 3 7432.793 12.85969 13.88102 13.88102
LYSC_CHICK LYZ P00698 P00698 Lysozyme C LYSC_CHICK 50pmol 4 7543.633 12.88104 13.25790 13.25790
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 100pmol 1 15097.670 13.88204 13.97388 13.97388
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 100pmol 2 15840.281 13.95131 14.20112 14.20112
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 100pmol 3 15022.215 13.87481 13.94448 13.94448
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 100pmol 4 15160.493 13.88803 13.97388 13.97388
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 200pmol 1 21577.973 14.39727 14.00189 14.00189
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 200pmol 2 22968.959 14.48740 13.38772 13.38772
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 200pmol 3 20720.127 14.33875 13.70002 13.70002
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 200pmol 4 22153.398 14.43524 13.88102 13.88102
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 50pmol 1 12183.812 13.57268 13.88102 13.88102
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 50pmol 2 12521.783 13.61215 13.84672 13.84672
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 50pmol 3 11926.220 13.54185 14.13067 14.13067
TRFE_BOVIN TF CON__Q0IIK2 CON__Q0IIK2 Serotransferrin (UP merge to Q29443) TRFE_BOVIN 50pmol 4 12021.495 13.55333 13.84672 13.84672

trimFASTA

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