Quantification
Namespace: QConQuantifier
Nested types and modules
| Type | Description |
| QuantifiedPeptide | |
| averagePSM |
Functions and values
| Function or value | Description |
average(...)
Signature: reader:(type) -> rtIndex:(type) -> qConQuantifierParams:QConQuantifierParams -> psms:seq<(type)> -> averagePSM
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Given a list of psms mapping to the same ion species this function estimates an average psm. For this various estimators of central tendency are computed e.g the mean of the precursorMz, the mean ScanTime as well as an precursor intensity weighted scan time mean. This psm average reduces the risk of picking a wrong XIC peak. |
createAveragePSM(...)
Signature: meanPrecMz:float -> meanScanTime:float -> weightedAvgScanTime:float -> meanScore:float -> xXic:float [] -> yXic:float [] -> averagePSM
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createQuantifiedPeptide(...)
Signature: stringSequence:string -> globalMod:int -> scanTime:float -> avgSequestScore:float -> charge:int -> experimentalMass:float -> n14MZ:float -> n14Quant:float -> n15MZ:float -> n15Quant:float -> n15Minus1MZ:float -> n15Minus1Quant:float -> QuantifiedPeptide
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initGetIsotopicVariant(qConCatPeps)
Signature: qConCatPeps:seq<QConcatPeptide> -> string -> int -> QConcatPeptide
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Returns a function that given an isotopic variant of a qConcat peptide returns the respective labled/unlabeled version. |
quantifyBy(...)
Signature: reader:(type) -> rtIndex:(type) -> qConQuantifierParams:QConQuantifierParams -> targetMz:float -> targetScanTime:float -> (type) * float [] * float [] * float []
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Performs XIC extraction at a given targetMz and scan Time. Offsets are defined in qConQuantifierParams. Subsequently, peak detection is performed and a levenberg marquardt routine (FSharp.Stats) is employed to fit a gaussian, or in case tailed peak is observed, an exponentially modified gaussian to the selected peak. |
quantifyPSMs(...)
Signature: plotDirectory:string -> reader:(type) -> rtIndex:(type) -> qConQuantifierParams:QConQuantifierParams -> getIsotopicVariant:(string -> int -> QConcatPeptide) -> psms:(type) list -> QuantifiedPeptide list
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Quantifies every Ion identified by at least one psm. Given a collection of PSMs this function first performs an aggregation, grouping all psms mapping to the same ion species. Afterwards the average PSM is computed. Based uppon this, XIC extraction and quantification is performed. Additionally, a paired quantification is performed. This means that if a light variant (e.g a N14 labeled peptide) was identified, the XIC corresponding to the heavy variant is extracted and quantified. This does not only enlarge the fraction of quantified peptides it also alows to control for the quality of the quantification if an ion is quantified from both perspectives (in case of both, Heavy-To-Light and Light-To-Heavy inference). Besides the monoisotopic peak this function also quantifies the N15Minus1 peak this allows to calculate the labeling efficiency. |
