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Given a folder of .mzXML input files and subsequent processing, .csv peak tables with picked peaks are written to an output folder
● Data Source:
CranContrib
● Keywords:
● Alias: enviPickbatch
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A wrapper combining data upload, partitioning, EIC clustering and EIC peak detection from readMSdata, mzagglom, mzclust and mzpick.
● Data Source:
CranContrib
● Keywords:
● Alias: enviPickwrap
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Peak picking for centroided and baseline-corrected high-resolution LC-MS data.mzXML. Built on a three-step approach of (1) data partitioning, (2) unsupervised clustering of extracted ion chromatograms (EIC) and (3) shape-independent peak detection wihtin individual EICs. Interactive plot access to all results and the underlying raw measurements. Browser UI for non-R users. Batch processing.
● Data Source:
CranContrib
● Keywords: package
● Alias: enviPick, enviPick-package
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Divisive recursive partition of LC-HRMS measurements. Preparatory step for mzclust and mzpick; altenative to mzagglom. Requires an MSlist initilialized by readMSdata as input.
● Data Source:
CranContrib
● Keywords:
● Alias: mzpart
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Given an MSlist object containing peak picking results from mzpick, export a peak table.csv.
● Data Source:
CranContrib
● Keywords:
● Alias: writePeaklist
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Initiates an MSlist object and reads LC-HRMS measurement data from .mzXML files.
● Data Source:
CranContrib
● Keywords:
● Alias: readMSdata
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plotMSlist
(Package: enviPick) :
Interactive raw data and result viewer
View your centroided LC-HRMS data and partitioning / clustering / peak-picking results. Monitor what peak-picking produces and if it fails; get a grip on optimal parameter settings from comparison with underlying raw data.
● Data Source:
CranContrib
● Keywords:
● Alias: plotMSlist
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Agglomerative partitioning of LC-HRMS measurements. Preparatory step for mzclust and mzpick. Requires an MSlist initilialized by readMSdata as input.
● Data Source:
CranContrib
● Keywords:
● Alias: mzagglom
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mzpick
(Package: enviPick) :
EIC peak picking
Peak-picking within individual EIC cluster formed by mzclust without assuming a certain peak shape. Includes a baseline subtraction step.
● Data Source:
CranContrib
● Keywords:
● Alias: mzpick
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Based on the measurement partitions generated by mzagglom, extracted ion chromatograms (EICs) are assigned by a clustering procedure. Preparatory step for mzpick.
● Data Source:
CranContrib
● Keywords:
● Alias: mzclust
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providing 
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