Prediction of the flyability of proteotypic peptides
Prediction of the flyability of proteotypic peptides.
## Default S3 method: proteotypic(fasta, apex_model, min_aa=4 , max_aa=20, ...)
fasta |
a amino acid FASTA file. |
apex_model |
an |
min_aa |
the minimum number of amino acids for proteotypic peptides. |
max_aa |
the maximum number of amino acids for proteotypic peptides. |
... |
future extensions. |
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.
A data.frame containing peptide sequences and associated APEX scores.
George Rosenberger gr2578@cumc.columbia.edu
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).
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.