Summary of Study ST002730

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 PR001694. The data can be accessed directly via it's Project DOI: 10.21228/M8R136 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	ST002730
Study Title	Multi-Omics profiling of Candida albicans from agar plate and suspension media
Study Type	LC/MS/MS
Study Summary	Candida albicans is an opportunistic pathogen that is a significant challenge to healthcare facilities worldwide, commonly found in the human gastrointestinal, respiratory, and genitourinary systems. Morphological transition allows yeast cells to diffuse through bloodstream to colonize internal organs, whilst filamentous forms is related to penetration of host mucosa and epidermal surfaces. With the help of novel analytical techniques and instruments developed in the past years, which enabled accurate, simultaneous detection and quantification of proteins and metabolites. We investigated and compared the proteome and metabolome of C. albicans grown on agar plate verses suspension culture to gain insight into the different environmental adaptation and response to stress. Multi-omics (proteomics & metabolomics) analyses were performed using a high-resolution timsTOF mass spectrometer. From the findings reported in this experiment it is worth highlighting that ease of nutritional access in suspension media favours core growth metabolism and increased translation, while impeded access in solid media favours more diverse metabolic pathways. Core growth and replication machinery are enhanced in suspension media, with several terms related to protein translation and core metabolism increased in this media. In contrast, pathogenic cell wall proteins and proteins related to cell surface were increased in cells grown on solid media.
Institute	University of Sharjah
Department	Research institute of medical and health science
Laboratory	Biomarker Discovery Group
Last Name	Facility
First Name	Core
Address	M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
Email	tims-tof@sharjah.ac.ae
Phone	+971 6 5057656
Submit Date	2023-06-08
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2023-06-25
Release Version	1

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Project:

Project ID:	PR001694
Project DOI:	doi: 10.21228/M8R136
Project Title:	Multi-Omics profiling of Candida albicans from agar plate and suspension media
Project Type:	LC-MS/MS
Project Summary:	Candida albicans is an opportunistic pathogen that is a significant challenge to healthcare facilities worldwide, commonly found in the human gastrointestinal, respiratory, and genitourinary systems. Morphological transition allows yeast cells to diffuse through bloodstream to colonize internal organs, whilst filamentous forms is related to penetration of host mucosa and epidermal surfaces. With the help of novel analytical techniques and instruments developed in the past years, which enabled accurate, simultaneous detection and quantification of proteins and metabolites. We investigated and compared the proteome and metabolome of C. albicans grown on agar plate verses suspension culture to gain insight into the different environmental adaptation and response to stress. Multi-omics (proteomics & metabolomics) analyses were performed using a high-resolution timsTOF mass spectrometer. From the findings reported in this experiment it is worth highlighting that ease of nutritional access in suspension media favours core growth metabolism and increased translation, while impeded access in solid media favours more diverse metabolic pathways. Core growth and replication machinery are enhanced in suspension media, with several terms related to protein translation and core metabolism increased in this media. In contrast, pathogenic cell wall proteins and proteins related to cell surface were increased in cells grown on solid media.
Institute:	University of Sharjah
Department:	Research institute of medical and health science
Laboratory:	Biomarker Discovery Group
Last Name:	Facility
First Name:	Core
Address:	M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
Email:	tims-tof@sharjah.ac.ae
Phone:	+971 6 5057656

Subject:

Subject ID:	SU002836
Subject Type:	Yeast
Subject Species:	Candida albicans
Taxonomy ID:	5476

Factors:

Subject type: Yeast; Subject species: Candida albicans (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA274756	Liquid Media 1-01-4784	Liquid Media
SA274757	Liquid Media 3-02-4789	Liquid Media
SA274758	Liquid Media 3-01-4788	Liquid Media
SA274759	Liquid Media 1-02-4785	Liquid Media
SA274760	Liquid Media 2-01-4786	Liquid Media
SA274761	Liquid Media 2-02-4787	Liquid Media
SA274762	Solid Media 5-02-4799	Solid Media
SA274763	Solid Media 5-01-4798	Solid Media
SA274764	Solid Media 1-01-4790	Solid Media
SA274765	Solid Media 1-02-4791	Solid Media
SA274766	Solid Media 4-01-4796	Solid Media
SA274767	Solid Media 4-02-4797	Solid Media

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO002829
Collection Summary:	In this study, WT Candida albicans strain DK318 was used and cultured in two different types of growth media, broth (liquid medium) and agar plate (solid medium). Yeast Potato Dextrose agar (YPD) and YPD broth (HiMedia, India) were used for growing the strain. Briefly, a pure culture of Candida albicans was started from a single isolated colony in YPD agar and incubated 24 hrs at 37ºC for 200 rpm. For the liquid culture, 100ml of YPD broth was used to start a culture and incubated 24 hrs at 37ºC for 200 rpm.
Sample Type:	Yeast cells

Treatment:

Treatment ID:	TR002845
Treatment Summary:	Collect all the yeast growth from agar plate using sterile loop in a pre-weighed tube. Suspension broth was centrifuge at 4000 rpm for 10 minutes to collect the biomass in a pre-weighed tube. Later, the pellets were washed to remove the culture media using Phosphate Buffer Saline (PBS) then air dried to measure the biomass.

Sample Preparation:

Sampleprep ID:	SP002842
Sampleprep Summary:	The extraction method started by adding add 400 µl of protease inhibitor (dissolved in lysis buffer) to each pellet. Then were mixed and incubated for 10 minutes in room temperature, vortex each sample for 30 seconds. Cell lysates then were sonicated using COPLEY sonicator (Qsonica, Newtown, CT, USA) at 30% AMP for 30 seconds for 3 rounds until pellets dissolved homogenously. The samples were transferred to a new Eppendorf tube then centrifuge at 14000 rpm for 5 minutes. The supernatants, which contain the proteins and metabolites, were transferred to a new Eppendorf. Afterwards, 400µl of methanol were added to the transferred supernatant, followed by 300 µl of chloroform, then vortexed. Centrifuged again at 14000 rpm for 5 minutes to get eventually an upper layer (contains metabolites), an interphase of white disk (proteins) and lower layer. The supernatants that contained the metabolites were transferred carefully to a new tube, without disturbing the white disk. The interphase and the lower phase were mixed with 300µl of methanol. Vortexed well then centrifuged for 5 minutes at 14000 RPM and the new supernatants were added to the previously collected one. Later, the metabolites were completely dried using EZ-2 Plus (GeneVac, Ipswich, UK) at 45 ºC. After that, the samples were reconstituted in 200 µl of 0.1% Formic acid with water v/v. Finally, samples were filtered using 0.22µm filters and transferred into micro-insert to be analysed by TIMS-TOF MS.

Sampleprep ID:

SP002842

Sampleprep Summary:

The extraction method started by adding add 400 µl of protease inhibitor (dissolved in lysis buffer) to each pellet. Then were mixed and incubated for 10 minutes in room temperature, vortex each sample for 30 seconds. Cell lysates then were sonicated using COPLEY sonicator (Qsonica, Newtown, CT, USA) at 30% AMP for 30 seconds for 3 rounds until pellets dissolved homogenously. The samples were transferred to a new Eppendorf tube then centrifuge at 14000 rpm for 5 minutes. The supernatants, which contain the proteins and metabolites, were transferred to a new Eppendorf. Afterwards, 400µl of methanol were added to the transferred supernatant, followed by 300 µl of chloroform, then vortexed. Centrifuged again at 14000 rpm for 5 minutes to get eventually an upper layer (contains metabolites), an interphase of white disk (proteins) and lower layer. The supernatants that contained the metabolites were transferred carefully to a new tube, without disturbing the white disk. The interphase and the lower phase were mixed with 300µl of methanol. Vortexed well then centrifuged for 5 minutes at 14000 RPM and the new supernatants were added to the previously collected one. Later, the metabolites were completely dried using EZ-2 Plus (GeneVac, Ipswich, UK) at 45 ºC. After that, the samples were reconstituted in 200 µl of 0.1% Formic acid with water v/v. Finally, samples were filtered using 0.22µm filters and transferred into micro-insert to be analysed by TIMS-TOF MS.

Combined analysis:

Analysis ID	AN004427
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Bruker timsTOF
Column	Hamilton Intensity Solo 2 C18
MS Type	ESI
MS instrument type	QTOF
MS instrument name	Bruker timsTOF
Ion Mode	POSITIVE
Units	AU

Chromatography:

Chromatography ID:	CH003326
Chromatography Summary:	10 µL aliquot of the sample was injected and the separation was performed on a Hamilton® Intensity Solo C18 column (2.1 × 100 mm, 1.8 µm) (Bruker Daltonik) in a column oven temperature set at 35 ◦C , using solvent A (0.1% formic acid in deionized Water) and solvent B (0.1% formic acid in acetonitrile) with the following gradient elution mode: 0 to 2 min, 1% B; 2 to 17 min, 1–99% B; 17 to 20 min, 99% B; 20 to 20.1 min, 99–1% B; 20.1 to 30 min, 1% B. The flow rate was 0.25 mL/min from 0 to 20 min, 0.35 mL/min from 20 min to 28.3 min, and 0.25 mL/min from 28.3 to 30 min.
Instrument Name:	Bruker timsTOF
Column Name:	Hamilton Intensity Solo 2 C18
Column Temperature:	35
Flow Gradient:	gradient elution mode: 0 to 2 min, 1% B; 2 to 17 min, 1–99% B; 17 to 20 min, 99% B; 20 to 20.1 min, 99–1% B; 20.1 to 30 min, 1% B
Flow Rate:	250 uL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004174
Analysis ID:	AN004427
Instrument Name:	Bruker timsTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The ESI source conditions for every injection were as follows: the drying gas flow rate was 10.0 L/min at a temp of 220 ◦C; the capillary voltage was set at 4500 V; the End Plate offset was set at 500 V; the nebulizer pressure of 2.2 bar. The acquisition involved two segments; auto MS scan, which ranged from 0 to 0.3 min for the calibrant sodium formate, and auto MS/MS scan with CID acquisition, which included fragmentation and ranged from 0.3 to 30 min. The acquisition in both segments was performed using the positive mode at 12 Hz. The automatic in-run mass scan range was from 20 to 1300 m/z, the width of the precursor ion was ±0.5, the number of precursors was 3, the cycle time was 0.5 sec., and the threshold was 400 cts. Active exclusion was excluded after 3 spectra and released after 0.2 min. For MS2 acquisition the data dependent acquisition (DDA) was used, and the collision energy stepping fluctuated between 100 and 250% set at 20 eV. m/z measurements were externally calibrated using 10 mM of sodium formate before sample analysis. In addition, sodium formate solution was injected at the beginning of each sample run and used for internal calibration during data processing.
Ion Mode:	POSITIVE