proteotypic: Prediction of the flyability of proteotypic peptides

In aLFQ: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data

Description

Prediction of the flyability of proteotypic peptides.

Usage

## Default S3 method:
proteotypic(fasta, apex_model, min_aa=4 , max_aa=20, ...)

Arguments

fasta	a amino acid FASTA file.
apex_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.

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.

Value

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

Author(s)

George Rosenberger [e-mail]

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"),
apex_model=APEX_ORBI.apex, min_aa=4 , max_aa=20)
## Not run: print(peptides)

Example output

aLFQ documentation built on Jan. 8, 2020, 5:09 p.m.