aLFQ (version 1.2)

AbsoluteQuantification: Absolute label-free quantification of mass spectrometry proteomics experiments

Description

Absolute label-free quantification of mass spectrometry proteomics experiments.

Usage

## S3 method for class 'default':
AbsoluteQuantification(data, peptide_method = "top", peptide_topx = 1,
  peptide_strictness = "loose", peptide_summary = "mean", transition_topx = 3,
  transition_strictness = "loose", transition_summary = "sum", fasta = NA,
  model = NA, total_protein_concentration = 1, combine_precursors = FALSE,
  consensus_proteins = TRUE, consensus_peptides = TRUE, consensus_transitions = TRUE, ...)
## S3 method for class 'AbsoluteQuantification':
cval(object, cval_method = "mc", mcx = 1000, ...)
## S3 method for class 'AbsoluteQuantification':
print(x, ...)
## S3 method for class 'AbsoluteQuantification':
plot(x, ...)
## S3 method for class 'AbsoluteQuantification':
hist(x, ...)
## S3 method for class 'AbsoluteQuantification':
pivot(x, ...)
## S3 method for class 'AbsoluteQuantification':
export(x, file, ...)

Arguments

data

a mandatory data frame containing the columns "run_id", "protein_id", "protein_intensity", and "concentration" for quantification on the protein level. For quantification on the peptide lev

peptide_method

one of "top", "all", "iBAQ", "APEX" or "NSAF" peptide to protein intensity estimation methods.

peptide_topx

a positive integer value of the top x peptides to consider for "top" methods.

peptide_strictness

whether peptide_topx should only consider proteins with the minimal peptide number ("strict") or all ("loose").

peptide_summary

how to summarize the peptide intensities for the "top" methods: "mean", "median", "sum".

transition_topx

a positive integer value of the top x transitions to consider for transition to peptide intensity estimation methods.

transition_strictness

whether transition_topx should only consider peptides with the minimal transition number ("strict") or all ("loose").

transition_summary

how to summarize the transition intensities: "mean", "median", "sum".

fasta

the path and filename to an amino acid fasta file containing the proteins of interest, which is used for the "iBAQ", "APEX" and "NSAF" peptide to protein intensity estimation methods.

model

the name of the "APEX" model to use

total_protein_concentration

the total protein concentration in the sample in any unit. This will be used for the normalized protein and concentration columns.

combine_precursors

whether to sum all precursors of the same peptide.

object

an AbsoluteQuantification object.

cval_method

a method for doing crossvalidation: "boot" (bootstrapping), "mc" (monte carlo cross-validation), "loo" (leaving-one-out).

consensus_proteins

if multiple runs are provided, select identical proteins among all runs.

consensus_peptides

if multiple runs are provided, select identical peptides among all runs.

consensus_transitions

if multiple runs are provided, select identical transitions among all runs.

mcx

a positive integer value of the number of folds for cross-validation.

file

the location of the output csv file.

x

an AbsoluteQuantification object.

...

future extensions.

Value

• An object of class AbsoluteQuantification.

Details

If absolute quantity estimation based on anchor peptides or proteins is demanded, the calibration peptide or protein abundance must be provided. Both estimated calibration protein intensities and separately determined calibration protein concentrations are log transformed and a first order linear least-squares regression of this log-log data is calculated. The abundance of the target proteins is predicted based on this regression. The error of the regression arises from biological and technical variation as well from the protein and peptide intensity estimators. To perform model selection and to estimate the error of the predicted protein concentrations, bootstrapping and Monte Carlo cross-validation as suggested (Malmstrom et al., 2009; Ludwig et al., 2012) were implemented. For both methods, the objective function is the minimization of the mean fold-error.

If, on the other hand, the total protein concentration per cell is supplied in proteome-wide experiments, the absolute protein concentrations are estimated by normalization of the MS intensities or spectral counts to this number (Lu et al., 2006).

References

Malmstrom, J. et al. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 460, 762-765 (2009).

Ludwig, C., Claassen, M., Schmidt, A. & Aebersold, R. Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry. Molecular & Cellular Proteomics 11, M111.013987-M111.013987 (2012).

Lu, P., Vogel, C., Wang, R., Yao, X. & Marcotte, E. M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotech 25, 117-124 (2006).

See Also

import, ProteinInference, ALF, APEX, apexFeatures, proteotypic

Examples

data(UPS2MS)

UPS2_SRM<-head(UPS2_SRM,100) # Remove this line for real applications

data_AbsoluteQuantification <- predict(cval(AbsoluteQuantification(UPS2_SRM),mcx=2))
print(data_AbsoluteQuantification)
plot(data_AbsoluteQuantification)
hist(data_AbsoluteQuantification)
pivot(data_AbsoluteQuantification)