aLFQ (version 1.2)

proteotypic: Prediction of the flyability of proteotypic peptides

Description

Prediction of the flyability of proteotypic peptides.

Usage

## S3 method for class 'default':
proteotypic(fasta, model, min_aa=4 , max_aa=20, ...)

Arguments

fasta

a amino acid FASTA file.

model

an APEX object.

min_aa

the minimum number of amino acids for proteotypic peptides.

max_aa

the maximum number of amino acids for proteotypic peptides.

...

future extensions.

Value

• A data.frame containing peptide sequences and associated APEX scores.

Details

This function provides prediction of the "flyability" of proteotypic peptides using the APEX method (Lu et al., 2006; Vogel et al., 2008). The APEX scores are probabilities that indicate detectability of the peptide amino acid sequence in LC-MS/MS experiments.

References

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). Vogel, C. & Marcotte, E. M. Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat Protoc 3, 1444-1451 (2008).

See Also

import, ProteinInference, AbsoluteQuantification, ALF, APEX, apexFeatures

Examples

set.seed(131)

data(APEXMS)

APEX_ORBI<-head(APEX_ORBI,20) # Remove this line for real applications
APEX_ORBI.af <- apexFeatures(APEX_ORBI)
APEX_ORBI.apex <- APEX(data=APEX_ORBI.af)

peptides <- proteotypic(fasta=system.file("extdata","example.fasta",package="aLFQ"),
model=APEX_ORBI.apex, min_aa=4 , max_aa=20)
print(peptides)