PXD039268

PXD039268 is an original dataset announced via ProteomeXchange.

Title	Alkaline-SDS cell lysis with acetone protein precipitation for proteomic sample preparation of microbes in 96-well plate format
Description	Automated proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes (e.g Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_06:47:26.504.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Petzold
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Rhodotorula toruloides NP11; NCBI TaxID: 1130832; scientific name: Pseudomonas putida KT2440; NCBI TaxID: 160488; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-05 02:08:40	ID requested
1	2023-06-23 08:38:53	announced
⏵ 2	2023-11-14 06:47:26	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Sample preparation, High-throughput, Biotechnology, Synthetic microbial communities, Automation, Proteomics, Bacteria, Microbes, Fungi

Chris Petzold
contact affiliation	Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720
contact email	cjpetzold@lbl.gov
lab head
Christopher Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/06/PXD039268

PRIDE project URI

• PRIDE
  1. PXD039268
     1. Label: PRIDE project
     2. Name: Alkaline-SDS cell lysis with acetone protein precipitation for proteomic sample preparation of microbes in 96-well plate format