AlignmentBasedQuantification

QuantBasedAlignment predicts where a peptide ion identified in another run should elute in this run. AlignmentBasedQuantification goes to that place. For every peptide ion in the .align file it extracts an ion chromatogram from the .mzlite file around the predicted scan time, and, with PerformLocalWarp set, moves the scan time estimate by dynamic time warping of the extracted chromatogram against the chromatogram the ion had in the source run. Baseline correction, peak detection, peak fitting and the labeled counterpart work as in PSMBasedQuantification. The result is a .quant file that holds the quantifications of this run's own identifications together with the transferred ones.

Inputs and outputs

Each of the four input flags takes exactly one path. When -i is an existing file, the tool processes that single run and expects single files for -ii through -iv as well. When -i and -ii are directories, the tool searches -i for *.mzlite, -ii for *.align, -iii for *.alignmetric and -iv for *.quant and processes every run it can pair. Without -mf the four file lists are paired by position. With -mf they are paired by file name without extension, and a run that lacks one of the four files is skipped with a note in the log.

The tool writes <run>.quant into the output directory, a tab separated table with the rows of the input .quant file followed by one row per transferred peptide ion. The column QuantificationSource tells them apart (PSM or Alignment). AlignmentScore and AlignmentQValue hold NaN until AlignmentBasedQuantStatistics fills them. The file is also read by AddDeducedPeptides and JoinQuantPepIonsWithProteins. Next to it the tool writes <run>.alignquantMetrics, a table of the alignment metrics in quantification format. With -dc the chromatograms and the m/z correction go as HTML charts into <run>_plots. Delete an existing <run>.quant or <run>.alignquantMetrics in the output directory before a rerun, the tool appends to them. Logs go to AlignmentBasedQuantification_log.txt and one <run>_log.txt per run.

Parameters

XicExtraction is the same record PSMBasedQuantification uses.

The default file is AlignmentBasedQuantificationParams.json.

Writing a parameter file

open ProteomIQon
open ProteomIQon.Domain
open FSharp.Stats.Signal

let waveletParams : WaveletParameters =
    {
        Borderpadding          = None
        BorderPadMethod        = Padding.BorderPaddingMethod.Random
        InternalPaddingMethod  = Padding.InternalPaddingMethod.LinearInterpolation
        HugeGapPaddingMethod   = Padding.HugeGapPaddingMethod.Zero
        HugeGapPaddingDistance = 100.
        MinPeakDistance        = None
        MinPeakLength          = Some 0.1
        MaxPeakLength          = 1.5
        NoiseQuantile          = 0.01
        MinSNR                 = 0.01
    }

let alignmentBasedQuantificationParams : Dto.AlignmentBasedQuantificationParams =
    {
        PerformLabeledQuantification = true
        PerformLocalWarp             = true
        XicExtraction =
            {
                ScanTimeWindow = 2.
                MzWindow_Da    = Window.Estimate
                XicProcessing  = XicProcessing.Wavelet waveletParams
                TopKPSMs       = None
            }
        BaseLineCorrection = Some { MaxIterations = 10; Lambda = 6; P = 0.05 }
    }

// Replace the temp folder with your project folder.
let outputPath =
    System.IO.Path.Combine(System.IO.Path.GetTempPath(), "AlignmentBasedQuantificationParams.json")

Json.serializeAndWrite outputPath alignmentBasedQuantificationParams

Running the tool

Install the tool with dotnet tool install --global ProteomIQon.AlignmentBasedQuantification. The four run specific inputs share the run name, so the same base name appears four times.

proteomiqon-alignmentbasedquantification -i path/to/run.mzlite -ii path/to/run.align -iii path/to/run.alignmetric -iv path/to/run.quant -d path/to/peptides.db -o path/to/output -p path/to/AlignmentBasedQuantificationParams.json

Process every run in a set of directories, paired by position, three at a time.

proteomiqon-alignmentbasedquantification -i path/to/mzlite -ii path/to/align -iii path/to/alignmetric -iv path/to/quant -d path/to/peptides.db -o path/to/output -p path/to/AlignmentBasedQuantificationParams.json -c 3

The same, paired by file name.

proteomiqon-alignmentbasedquantification -i path/to/mzlite -ii path/to/align -iii path/to/alignmetric -iv path/to/quant -d path/to/peptides.db -o path/to/output -p path/to/AlignmentBasedQuantificationParams.json -c 3 -mf

Print the description of every argument.

proteomiqon-alignmentbasedquantification --help