The iPQF spectra-to-protein summarisation method integrates
peptide spectra characteristics and quantitative values for protein
quantitation estimation. Spectra features, such as charge state,
sequence length, identification score and others, contain valuable
information concerning quantification accuracy. The iPQF algorithm
assigns weights to spectra according to their overall feature reliability
and computes a weighted mean to estimate protein quantities.
See also combineFeatures
for a more
general overview of feature aggregation and examples.
iPQF(
object,
groupBy,
low.support.filter = FALSE,
ratio.calc = "sum",
method.combine = FALSE,
feature.weight = c(7, 6, 4, 3, 2, 1, 5)^2
)
An instance of class MSnSet
containing
absolute ion intensities.
Vector defining spectra to protein
matching. Generally, this is a feature variable such as
fData(object)$accession
.
A logical
specifying if proteins
being supported by only 1-2 peptide spectra should be filtered
out. Default is FALSE
.
Either "none"
(don't calculate any
ratios), "sum"
(default), or a specific channel (one of
sampleNames(object)
) defining how to calculate relative
peptides intensities.
A logical
defining whether to further
use median polish to combine features.
Vector "numeric"
giving weight to the
different features. Default is the squared order of the
features redundant -unique-distance metric, charge state, ion
intensity, sequence length, identification score, modification
state, and mass based on a robustness analysis.
A matrix
with estimated protein ratios.
iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification. Fischer M, Renard BY. Bioinformatics. 2016 Apr 1;32(7):1040-7. doi:10.1093/bioinformatics/btv675. Epub 2015 Nov 20. PubMed PMID:26589272.
data(msnset2)
head(exprs(msnset2))
#> X114.ions X115.ions X116.ions X117.ions
#> 11695 7.0384398 7.6349574 7.2886949 6.7348692
#> 11696 9.4098886 10.1034528 10.0697640 9.4273709
#> 11697 4.5859834 4.6926775 4.5016924 4.2924254
#> 11698 3.7262916 3.8913142 3.7928041 3.3721019
#> 11699 1.2229379 1.4005805 1.3940034 1.2957861
#> 11700 0.8303542 0.7397313 0.7686411 0.7402981
prot <- combineFeatures(msnset2,
groupBy = fData(msnset2)$accession,
method = "iPQF")
#> The following 1 proteins are only supported by 1 or 2 peptide spectra,
#> hence, protein quantification is not reliable and can only be calculated
#> by the 'mean' in these cases, corresponding protein accessions are:
#> O95678
head(exprs(prot))
#> X114.ions X115.ions X116.ions X117.ions
#> O95678 0.2404726 0.2682764 0.2584247 0.2328263
#> P01766 0.2610278 0.2467206 0.2544715 0.2377801
#> P01776 0.2678859 0.2591250 0.2423396 0.2306495
#> P02749 0.2640340 0.2523566 0.2510357 0.2325736
#> P02763 0.2503318 0.2524583 0.2501628 0.2470472
#> P07225 0.2533961 0.2506013 0.2504353 0.2455673