Summary of Study ST002744
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 PR001509. The data can be accessed directly via it's Project DOI: 10.21228/M8N71K This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST002744 |
| Study Title | Biomolecular condensates create phospholipid-enriched microenvironments (Part 4) |
| Study Summary | Proteins and RNA are able to phase separate from the aqueous cellular environment to form sub-cellular compartments called condensates. This process results in a protein-RNA mixture that is chemically distinct from the surrounding aqueous phase. Here we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and cellular metabolites and identified metabolites enriched in the condensate phase. Here, we confirmed the presence of lipids in MED1 samples and condensates using reversed-phase LC-MS. |
| Institute | Cornell University |
| Last Name | Dumelie |
| First Name | Jason |
| Address | 1300 York Ave, LC-524, New York City, NY |
| srj2003@med.cornell.edu | |
| Phone | 6466590174 |
| Submit Date | 2023-06-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzdata.xml |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-07-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001509 |
| Project DOI: | doi: 10.21228/M8N71K |
| Project Title: | Biomolecular condensates create phospholipid-enriched microenvironments |
| Project Type: | Metabolomics of in vitro condensates |
| Project Summary: | Proteins and RNA are able to phase separate from the aqueous cellular environment to form sub-cellular compartments called condensates. This process results in a protein-RNA mixture that is chemically distinct from the surrounding aqueous phase. Here we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and cellular metabolites and identified metabolites enriched in the condensate phase. These proteins included SARS-CoV-2 nucleocapsid, as well as low complexity domains of MED1 and HNRNPA1. |
| Institute: | Cornell University |
| Department: | Department of Pharmacology |
| Laboratory: | Dr. Samie Jaffrey |
| Last Name: | Dumelie |
| First Name: | Jason |
| Address: | 1300 York Ave, LC-524, New York City, NY |
| Email: | jdumes98@gmail.com |
| Phone: | 6465690174 |
| Funding Source: | This work was supported by the National Institutes of Health grants R35NS111631 and R01CA186702 (S.R.J.); R01AR076029, R21ES032347 and R21NS118633 (Q.C.); and NIH P01 HD067244 and support from the Starr Cancer Consortium I13-0037 (S.S.G.). |
| Publications: | Under revision |
| Contributors: | Jason G. Dumelie, Qiuying Chen, Dawson Miller, Nabeel Attarwala, Steven S. Gross and Samie R. Jaffrey1 |
Subject:
| Subject ID: | SU002851 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | fraction | Extraction from condensate |
|---|---|---|---|
| SA289160 | MED1 Aqueous Sample 6 | aqueous | No heat step |
| SA289161 | MED1 Aqueous Sample 5 | aqueous | No heat step |
| SA289162 | MED1 Aqueous Sample 4 | aqueous | No heat step |
| SA289163 | MED1 Aqueous Sample 9 | aqueous | standard |
| SA289164 | MED1 Aqueous Sample 8 | aqueous | standard |
| SA289165 | MED1 Aqueous Sample 7 | aqueous | standard |
| SA289166 | MED1 Condensate Sample 6 | condensate | No heat step |
| SA289167 | MED1 Condensate Sample 5 | condensate | No heat step |
| SA289168 | MED1 Condensate Sample 4 | condensate | No heat step |
| SA289169 | MED1 Condensate Sample 9 | condensate | standard |
| SA289170 | MED1 Condensate Sample 7 | condensate | standard |
| SA289171 | MED1 Condensate Sample 8 | condensate | standard |
| SA289172 | MED1 Input Sample 4 | input | No heat step |
| SA289173 | MED1 Input Sample 6 | input | No heat step |
| SA289174 | MED1 Input Sample 5 | input | No heat step |
| SA289175 | MED1 Input Sample 9 | input | standard |
| SA289176 | MED1 Input Sample 7 | input | standard |
| SA289177 | MED1 Input Sample 8 | input | standard |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO002844 |
| Collection Summary: | Mouse metabolites were collected from the liver of female mice using methanol extraction. After euthanizing a mouse, the liver was immediately frozen in liquid nitrogen. We then used cold 80% methanol to extract metabolites. First, 1 ml of 80% methanol was added to the liver and incubated for 10 min at -20oC. Glass beads were added to the liver and then the liver was lysed by bead-beating for 45 s using a Tissuelyser cell disrupter (Qiagen). The lysate was incubated for 10 min at -20oC and centrifuged (13200 rpm, 5 min) to separate metabolites from macromolecules. The supernatant was collected and 200 µl of 80% methanol was added to the pellet. The incubation, shaking and centrifugation steps were repeated twice to extract more metabolites from the pellet. The three supernatants were combined and centrifuged (14000 rpm, 10 min) to separate any remaining macromolecules from the metabolites. The combined supernatants were dried using a SpeedVac Concentrator (Savant, SPD131DDA) at 25oC and the dried metabolite samples were stored at -80oC. The amount of protein in the pellet was measured using the Quick Start Bradford assay to calculate the metabolites’ protein equivalent mass. Mouse metabolites were initially re-suspended in condensate buffer (50 mM NH4HCO3 pH 7.5, 50 mM NaCl, 1 mM DTT) to a protein equivalent concentration of 938 g/l. The chosen final concentration of metabolites is slightly lower than the 200-300 g/l protein concentration observed in cells. Metabolites that were not fully soluble in condensate buffer were removed by centrifugation (2x5 min, 16,000 g each), in which only the supernatant was retained. Purified mCherry tagged MED1 low-complexity domain (37.5 μM) was centrifuged (1 min, 1,000 g) to disrupt any existing condensates and to remove any precipitated proteins. The MED1 (final concentration, 30 μM) was then combined with metabolites (final concentration, 150 g/l protein equivalent) and then phage lambda RNA (final concentration, 0.15 μM) in a total volume of 300 µl. An input sample (10 µl) was saved and then the sample was allowed to incubate for 10 min at 25oC. Condensates were then separated from the aqueous environment by centrifugation (10 min, 12,500 g, 25oC). The aqueous phase was removed from the condensate phase and then equal volumes (usually ~ 2 µl) of the aqueous fraction, condensate fraction and input sample were processed for metabolomics using identical approaches as described below. First the samples were diluted in ammonium bicarbonate buffer (50 mM NH4HCO3 pH 7.5) and briefly heated (2 min, 65oC) to disrupt condensates before being added immediately to 4x volume of ice-cold 100% methanol to precipitate protein and RNA. This heating step was excluded for some samples where noted. Protein and RNA were separated from metabolites by vortexing the samples (2 min), followed by incubation at -25oC (10 min) and then centrifugation (5 min, 13,000 rpm). The supernatant was saved and the process was repeated on the pellet two more times after adding 200 µl of 80% methanol each time to the pellet. The three supernatants were combined and centrifuged (10 min, 14000 rpm) to remove any additional macromolecules. The final supernatant was collected and dried using a SpeedVac Concentrator run at 25oC. Notably, in a subset of experiments, metabolites were added to MED1 condensates after the 10 min incubation rather than prior to the incubation. |
| Sample Type: | Liver |
| Collection Method: | 80% methanol |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002860 |
| Treatment Summary: | Mouse liver metabolites were combined with the condensate-forming low-complexity domain of MED1. Condensates were stimulated with 150 nM RNA and then incubated for 10 min. In a subset of samples, RNA addition occurred 10 min before metabolite addition. Next, condensates were centrifuged to the bottom of a 600 ul tube. Equal fractions from the input sample, aqueous phase and condensate phases were collected separately. Metabolites were extracted from each fraction using 80% methanol in steps that involved disrupting condensates with heat. In a subset of samples, this heat step was omitted. |
Sample Preparation:
| Sampleprep ID: | SP002857 |
| Sampleprep Summary: | Dried-down extracts were reconstituted in 150 µl 70% acetonitrile, at a relative protein concentration of ~ 2 µg/µl. These were stored at -20C until used. In these LC-MS experiments, 4 µl of reconstituted extract was injected for LC/MS-based targeted metabolite profiling for each sample. |
| Processing Storage Conditions: | Described in summary |
| Extract Storage: | -20℃ |
Combined analysis:
| Analysis ID | AN004449 | AN004450 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6550 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Ion abundance | Ion abundance |
Chromatography:
| Chromatography ID: | CH003342 |
| Chromatography Summary: | This reversed phase platform was adapted with minor modifications from a previously reported Agilent application note (A Comprehensive, Curated, High-Throughput Method for the Detailed Analysis of the Plasma Lipidome, https://www.agilent.com/cs/library/applications/an-plasma-lipidomics-6495-lc-ms-ms-5994-3747en-agilent.pdf) and showed similar lipid retention times for fatty acids and other lipids, as reported. This platform was comprised of an Agilent Model 1290 Infinity II liquid chromatography system coupled to an Agilent 6550 iFunnel time-of-flight MS analyzer. An Agilent ZORBAX Eclipse Plus C18, 100 × 2.1 mm, 1.8 μm reversed phase column was used for the separation. Mobile phases consisted of (A) 10 mM ammonium formate with 5 μM Agilent deactivator additive in 5:3:2 water:acetonitrile:2-propanol and (B) 10 mM ammonium formate in 1:9:90 water:acetonitrile:2-propanol. Column temperature was set at 55°C and autosampler temperature was at 20°C. The flow rate was 0.4 mL/min. The following gradient was applied: 0 min, 15% B; 0-2.5 min, to 50% B; 2.5-2.6 min, to 57%, 2.6-9 min, to 70% B; 9-9.1 min, to 93% B; 9.1-11.1 min, to 96%; 11.1- 15min, 100% B; 15-20 min, 15% B. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) |
| Column Temperature: | 55 |
| Flow Gradient: | 0 min, 15% B; 0-2.5 min, to 50% B; 2.5-2.6 min, to 57%, 2.6-9 min, to 70% B; 9-9.1 min, to 93% B; 9.1-11.1 min, to 96%; 11.1- 15min, 100% B; 15-20 min, 15% B. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 50% water/30% acetonitrile/20% isopropanol;10 mM ammonium formate with 5 µM Agilent deactivator additive |
| Solvent B: | 1% water/9% acetonitrile/90% isopropanol;10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004196 |
| Analysis ID: | AN004449 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Raw data were analyzed using Mass Hunter Qualitative analysis (10.0), MassHunter Profinder 8.0 and MassProfiler Professional (MPP) 15.1 software (Agilent technologies). Lipid identification was confirmed in the original samples by comparison with the retention times and masses in a lipidomics PCDL of 665 metabolites developed as recommended by the manufacturer (Agilent). |
| Ion Mode: | POSITIVE |
| MS ID: | MS004197 |
| Analysis ID: | AN004450 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Raw data were analyzed using Mass Hunter Qualitative analysis (10.0), MassHunter Profinder 8.0 and MassProfiler Professional (MPP) 15.1 software (Agilent technologies). Lipid identification was confirmed in the original samples by comparison with the retention times and masses in a lipidomics PCDL of 665 metabolites developed as recommended by the manufacturer (Agilent). |
| Ion Mode: | NEGATIVE |
