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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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.