aLFQ (version 1.0)

import: import of mass spectrometry proteomics data analysis software reports.

Description

import of mass spectrometry proteomics data analysis software reports.

Usage

## S3 method for class 'default':
import(ms_filenames, ms_filetype, concentration_filename=NA, fasta = NA,
targeted_fdr=0.01, spectral_prob=0.95, target_column="ADJNSAF", mergeruns=FALSE,
sumruns=FALSE, replace_run_id=FALSE, filtertop=TRUE, removedecoys=TRUE, ...)

Arguments

ms_filenames

the paths and filenames of files to import in a character or array class.

ms_filetype

one of "skyline", "openswath", "mprophet", "openmslfq", "abacus_peptide" or "abacus_protein" filetypes. Multiple files of the same type can be supplied in a vector.

concentration_filename

the filename of a csv with concentrations (in any unit). Needs to have the columns "peptide_id" (or "protein_id") and "concentration".

fasta

(abacus_peptide only:) the path and filename to an amino acid fasta file containing the proteins of interest with identical identifier.

targeted_fdr

(openswath and mprophet only:) the FDR cutoff for OpenSWATH and mProphet reports.

spectral_prob

(abacus_peptide and abacus_protein only:) the spectral probability cutoff for Abacus reports.

target_column

(abacus_protein only:) target score: one of "NUMSPECSTOT","TOTNSAF","NUMSPECSUNIQ", "UNIQNSAF","NUMSPECSADJ" or "ADJNSAF".

mergeruns

whether different MS runs should be merged.

sumruns

whether different MS runs should be summed.

replace_run_id

whether the run_id of the MS data should be replaced by the filename.

filtertop

whether different MS runs should be merged.

removedecoys

(openswath and mprophet only:) whether only the top peakgroup should be considered.

...

future extensions.

Value

• A standard aLFQ import data frame, either on transition, peptide (precursor) or protein level.

Details

The import function provides unified access to the results of various standard proteomic quantification applications like OpenMS (Sturm et al., 2008; Weisser et al., 2013), Abacus (Fermin et al., 2011), Skyline (MacLean et al., 2010) and mProphet (Reiter et al., 2011). This enables generic application of all further steps using the same data structure and enables extension to support other data formats. If multiple runs, i.e. replicates, are supplied, the mean values can be used to summarize the experimental data. In addition to the input from the analysis software, an input table with the anchor peptides or proteins and sample specific absolute abundance, or an estimate of the total protein concentration in the sample is required. The endpoint of this step is a unified input data structure.

References

Sturm, M. et al. OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics 9, 163 (2008).

Weisser, H. et al. An automated pipeline for high-throughput label-free quantitative proteomics. J. Proteome Res. 130208071745007 (2013). doi:10.1021/pr300992u

Fermin, D., Basrur, V., Yocum, A. K. & Nesvizhskii, A. I. Abacus: A computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. PROTEOMICS 11, 1340-1345 (2011).

MacLean, B. et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966-968 (2010).

Reiter, L. et al. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Meth 8, 430-435 (2011).

See Also

ProteinInference, AbsoluteQuantification, ALF, APEX, apexFeatures, proteotypic

Examples

import(ms_filenames = system.file("extdata","example_abacus_peptide.txt",package="aLFQ"),
ms_filetype = "abacus_peptide", concentration_filename =
system.file("extdata","example_concentration_peptide.csv",
package="aLFQ"), fasta = system.file("extdata","example.fasta",package="aLFQ"), spectral_prob=0.95)

import(ms_filenames = system.file("extdata","example_abacus_protein.txt",package="aLFQ"),
ms_filetype = "abacus_protein", concentration_filename =
system.file("extdata","example_concentration_protein.csv",
package="aLFQ"), spectral_prob=0.95, target_column="ADJNSAF")

import(ms_filenames = system.file("extdata","example_mprophet.txt",package="aLFQ"),
ms_filetype = "mprophet",
concentration_filename = system.file("extdata","example_concentration_peptide.csv",package="aLFQ"),
targeted_fdr=0.01)

import(ms_filenames = system.file("extdata","example_openmslfq.csv",package="aLFQ"),
ms_filetype = "openmslfq", targeted_fdr=0.01)

import(ms_filenames = system.file("extdata","example_openswath.txt",package="aLFQ"),
ms_filetype = "openswath", targeted_fdr=1)

import(ms_filenames = system.file("extdata","example_skyline.csv",package="aLFQ"),
ms_filetype = "skyline",
concentration_filename = system.file("extdata","example_concentration_protein.csv",package="aLFQ"))