apLCMS protocols

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chevron_left Metabolite identification Peak detection Metabolite quantification Chromatogram alignment chevron_right
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apLCMS specifications


Unique identifier OMICS_02637
Name apLCMS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


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Publications for apLCMS

apLCMS in pipelines

PMCID: 5863097
PMID: 29425024
DOI: 10.1021/acs.analchem.7b04073

[…] using reverse-phase c18 liquid chromatography (ultimate 3000, dionex, sunnyvale, ca) and fourier transform mass spectrometry (q-exactive, thermo scientific, waltham, ma). data was extracted using aplcms with modifications by xmsanalyzer. see si for details. the metabolomics data set is available upon request to the corresponding authors., statistical analysis, network/pathway analysis, […]

PMCID: 4669660
PMID: 26702339
DOI: 10.1016/j.csbj.2015.10.005

[…] frequency of ions that are trapped and oscillate in a chamber. the computational aspects of metabolomics are also in rapid progress, including open source feature extraction tools (xcms , openms , aplcms , xmsanalyzer ), databases of metabolites (human metabolome database , , metlin , pubchem , chebi ), and data analysis tools (xcms online , metaboanalyst , mummichog ). it should be noted […]

PMCID: 4302260
PMID: 25468946
DOI: 10.2337/dc14-2033

[…] pooled plasma samples were included in each batch (n = 23) for quality control. peak extraction, data alignment, and feature quantification were performed using the adaptive processing software (aplcms) (,), a computer package designed for high-resolution metabolomics data analysis. feature and sample quality assessment was performed based on coefficient of variation (cv) and pearson […]

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apLCMS in publications

PMCID: 5559093
PMID: 28813452
DOI: 10.1371/journal.pone.0182819

[…] resolution mass spectrometry, the 10-minute gradient used in this study cannot resolve structural isomers and isobaric species []. peak detection, noise removal, and alignment was performed using aplcms v6.0.1[] and xcms v1.44[] with xmsanalyzer v2.0.4[], yielding a data table with accurate mass (m/z), retention time and intensity for each m/z feature across all samples. an m/z feature […]

PMCID: 5448325
PMID: 28580307
DOI: 10.22074/cellj.2017.4412

[…] decreases the need for physical separation of metabolites prior to detection. detection from 50 to 1000 m/z of ions at 20000 resolution over a 35-minute lc run with data extraction using aplcms provides a minimum of 3000 reproducible features, many with sufficient mass accuracy to allow prediction of elemental composition (). an m/z feature is defined by m/z, ion intensity, […]

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] align compounds of samples from different experiments, a hard task for metabolomics datasets that is not approached by most other tools. adaptive processing of high-resolution lc-ms data (aplcms) [] is an r package for high mass accuracy lc-ms, which tries to be user friendly by providing a file-based operation and a wrapper function for a single command line batch process of lc-ms […]

PMCID: 5436150
PMID: 28487968
DOI: 10.3892/mmr.2017.6530

[…] identification of metabolites. this system was used to detect the m/z of ions from 50 to 1,000, with 20,000 resolution (arbitrary units) over 30 min, and lc operated with data extraction using the aplcms software version 5.9.6 (http://clinicalmetabolomics.org/welcome/default/software) (), which provided a minimum of 3,000 reproducible features; a number of which displayed sufficient mass […]

PMCID: 5098236
PMID: 27819279
DOI: 10.1038/srep36490

[…] xcalibur file converter software (thermo fisher, san diego, ca) was used to convert the raw data to cdf files for further data processing in r project. an adaptive processing software package (aplcms, http://www.sph.emory.edu/aplcms) designed for lc-ftms data was used for peak extraction. this software obtained m/z feature tables through 5 major processing steps: (1) noise filter, (2) peak […]

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apLCMS institution(s)
Department of Biostatistics and Bioinformatics, Rollins School of Public Health and Department of Medicine, School of Medicine, Emory University, Atlanta, GA, USA
apLCMS funding source(s)
Supported by NIH grants P20 HL113451, P01 AI096187, U19 AI090023 and U19 AI057266.

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