Summary of Study ST001861

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001174. The data can be accessed directly via it's Project DOI: 10.21228/M8Z98Q This work is supported by NIH grant, U2C- DK119886.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001861
Study TitleParallelized multidimensional analytic framework, PAMAF, applied to mammalian cells uncovers novel regulatory principles in EMT
Study SummaryPainting a holistic picture of disease etiology will require longitudinal systems-scale reconstruction of the multitiered architecture of eukaryotic signaling. As opposed to ‘one omic at a time’, which provides an incomplete view on disease mechanisms, here we developed an experimental and analytics framework, PAMAF, to simultaneously acquire and analyze twelve omic modalities from the same set of samples, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; peptidome; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. We applied PAMAF in a well-studied in vitro model of TGFβ-induced EMT to generate the EMT-ExMap dataset, cataloguing >61,000 expression profiles (>10,000 differential) over 12 days. PAMAF revealed that EMT is more complex than currently understood and identified numerous stage-specific mechanisms and vulnerabilities not captured in literature. Broad application of PAMAF will provide unprecedented insights into multifaceted biological processes relevant to human health and disease.
Boston University
Last NamePaul
First NameIndranil
Address71 East Concord St
Submit Date2021-06-22
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-11-11
Release Version1
Indranil Paul Indranil Paul application/zip

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Combined analysis:

Analysis ID AN003017
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Scientific EASY-nLC 1200 System
Column Thermo Easy Spray
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Units Neutral Mass


MS ID:MS002806
Analysis ID:AN003017
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Comments:For metabolite identifications we used the R package MAIT (Fernández-Albert et al., 2014), which integrates peak detection, peak annotation and statistical analysis. Briefly, XCMS (Tautenhahn et al., 2012) is used to detect and align peaks followed by annotation with CAMERA (Kuhl et al., 2012). A special function ‘Biotransformations’ is applied to refine annotations and measured ions are then putatively identified by matching mass-to-charge ratios to a reference list of calculated masses of metabolites listed in the Human Metabolome Database (HMDB,, 2019).