Summary of Study ST001173
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000785. The data can be accessed directly via it's Project DOI: 10.21228/M86T1D This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001173 |
| Study Title | Combinatorial metabolic mixtures for encoding abstract digital data |
| Study Type | MALDI MS |
| Study Summary | We present several kilobyte-scale image datasets stored in synthetic metabolomes, which are decoded with accuracy exceeding 98-99% using multi-mass logistic regression. |
| Institute | Brown University |
| Department | Engineering |
| Laboratory | Rosenstein Lab |
| Last Name | Kennedy |
| First Name | Eamonn |
| Address | Barus & Holley room 353, 184 Hope St |
| eamonn_kennedy@brown.edu | |
| Phone | 7737507192 |
| Submit Date | 2019-04-19 |
| Publications | E. Kennedy et al. “Encoding information in synthetic metabolomes” Plos One, accepted, 2019 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | hdf5 |
| Analysis Type Detail | MALDI-MS |
| Release Date | 2019-05-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000785 |
| Project DOI: | doi: 10.21228/M86T1D |
| Project Title: | Combinatorial metabolic mixtures for encoding abstract digital data |
| Project Type: | FTICR-MS acquisition of 1536-spot MALDI plates, comprising thousands of mixtures of common metabolites |
| Project Summary: | This data comprises FT-ICR MS readouts of 1536-spot MALDI plates. Each spectra is a measure of a specific metabolic mixture from a library of 36 common metabolites. The combinatorial mixtures of metabolites are used to encode abstract digital data (images). A comprehensive list of the metabolites and specific mixture present in each spot on each plate are provided in metadata files. Data is provided in open-source .hdf5 files. |
| Institute: | Brown University |
| Department: | Engineering |
| Laboratory: | Rosenstein Lab |
| Last Name: | Kennedy |
| First Name: | Eamonn |
| Address: | Barus & Holley room 446, 184 Hope St |
| Email: | eamonn_kennedy@brown.edu |
| Phone: | 7737507192 |
| Funding Source: | DARPA |
| Publications: | E. Kennedy et al. “Encoding information in synthetic metabolomes” Plos One, accepted, 2019 |
| Contributors: | Eamonn Kennedy, Christopher E. Arcadia, Joseph Geiser Peter M. Weber, Christopher Rose, Brenda M. Rubenstein and Jacob K. Rosenstein |
Subject:
| Subject ID: | SU001239 |
| Subject Type: | Synthetic |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
Factors:
Subject type: Synthetic; Subject species: Escherichia coli (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample Type |
|---|---|---|
| SA081500 | e0114p03t02 | standard |
| SA081501 | e0112p01t01 | standard |
| SA081502 | e0117p01t01 | standard |
| Showing results 1 to 3 of 3 |
Collection:
| Collection ID: | CO001233 |
| Collection Summary: | Extensive details of the collection parameters are provided in metadata .mat files (see in raw data zip file : README.pdf). Briefly, a Solarix 7T was used to collect FTICR MS data of thousands of MALDI spots comprised of synthetic metabolite mixtures. |
| Collection Protocol ID: | NA |
| Collection Protocol Filename: | There are multiple provided, e.g. please see : raw data zip file, e0114p03t02_instrument_settings.mat |
| Sample Type: | Synthetic Mixture |
| Collection Method: | FTICR MS |
| Collection Location: | Brown University |
| Collection Frequency: | 2000 |
| Collection Duration: | shot_count: 500, 4x averaging, 1 second duration |
| Volumeoramount Collected: | 0.1 nL |
| Storage Conditions: | Room temperature |
| Collection Vials: | 1 |
| Storage Vials: | 36 |
| Collection Tube Temp: | RT |
| Additives: | Aminoacridine matrix |
Treatment:
| Treatment ID: | TR001254 |
| Treatment Summary: | Combinatorial mixtures of metabolites were deposited using a Labcyte Echo 550 on to a MALDI steel plate at 30-60 nL volumes. Aminoacridine matrix was added in the ratio 0.7:1 to 1:.7 to metabolite concentrations. The spot droplets were air dried. No further treatments were performed prior to data acquisition. |
Sample Preparation:
| Sampleprep ID: | SP001247 |
| Sampleprep Summary: | Combinatorial mixtures of metabolites were deposited using a Labcyte Echo 550 on to a MALDI steel plate at 30-60 nL volumes. Aminoacridine matrix was added in the ratio 0.7:1 to 1:.7 to metabolite concentrations. The spot droplets were air dried. No further preparations were performed prior to data acquisition. |
Combined analysis:
| Analysis ID | AN001948 |
|---|---|
| Analysis type | MS |
| Chromatography type | None (Direct infusion) |
| Chromatography system | none |
| Column | none |
| MS Type | MALDI |
| MS instrument type | FT-ICR |
| MS instrument name | Bruker Solarix FT-ICR-MS |
| Ion Mode | POSITIVE |
| Units | mM |
Chromatography:
| Chromatography ID: | CH001413 |
| Instrument Name: | none |
| Column Name: | none |
| Chromatography Type: | None (Direct infusion) |
MS:
| MS ID: | MS001804 |
| Analysis ID: | AN001948 |
| Instrument Name: | Bruker Solarix FT-ICR-MS |
| Instrument Type: | FT-ICR |
| MS Type: | MALDI |
| MS Comments: | Extensive details of the data processing are provided in the readme.pdf file, and scripts for directly reading the data in Python are also provided. |
| Ion Mode: | POSITIVE |
