PXD018074

PXD018074 is an original dataset announced via ProteomeXchange.

Title	One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale.
Description	The additional experimental results obtained by the conventional capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis with a 15 cm long, 3 μm diameter, C(18) silica particle-packed column of JPST000059. We successfully identified the proteome expressed in Escherichia coli (E. coli) cells on a microarray scale using one-dimensional capillary LC-MS/MS with a 350 cm long, 100 μm i. d., monolithic silica-C(18) capillary column. E. coli tryptic digest (4 μg) was injected onto the column, and a 41 h gradient was applied with a flow rate of 500 nL/min at less than 20 MPa. In total, 22,196 nonredundant tryptic peptides from 2602 proteins, including 830 membrane proteins, were identified from the E. coli cells (triplicate analysis), in which an equivalent number of genes was detected by transcriptome analysis. Approximately, a 5-fold larger peak response on average was obtained in this system, compared with that obtained by conventional capillary LC-MS/MS analysis with a 15 cm long, 3 μm diameter C(18) silica particle-packed column. The higher response suggests that the influence of ionization suppression was drastically reduced by the high-efficiency separation on the long monolithic silica column coupled with the shallow gradient. Because this high-resolution system does not require any additional separation prior to LC-MS/MS, this "one-shot" proteomics approach can simplify the workflow of shotgun proteomics and minimize the sample amount, as well as reduce the total analysis time, despite the use of prolonged shallow gradient elution.
HostingRepository	jPOST
AnnounceDate	2021-03-06
AnnouncementXML	Submission_2022-09-18_03:20:10.638.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pasrawin Taechawattananant
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-17 02:00:00	ID requested
1	2021-03-05 07:00:03	announced
⏵ 2	2022-09-18 03:20:11	announced	2022-09-18: Updated FTP location.

Taechawattananant P, Yoshii K, Ishihama Y, Peak Identification and Quantification by Proteomic Mass Spectrogram Decomposition. J Proteome Res, 20(5):2291-2298(2021) [pubmed]

submitter keyword: E. coli

Yasushi Ishihama
lab head
Pasrawin Taechawattananant
contact affiliation	Kyoto University
dataset submitter

jPOST dataset URI

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.jpostdb.org/JPST000765/