PXD039453

PXD039453 is an original dataset announced via ProteomeXchange.

Title	Online alkaline-pH reverse phase nanoelectrospray-tandem mass spectrometry complements conventional low-pH method for global proteomic analysis
Description	The global proteome analysis was limited by the identification of peptides with low abundance or specific physiochemical properties. Here, a one-dimensional online alkaline-pH reverse phase nanoelectrospray-tandem mass spectrometry (AlkalinepH-MS/MS) method was developed and optimized for global proteomic analysis. In this method, peptides were separated on a nanoflow C18 column with an alkaline-pH mobile phase (pH=8) and directly introduced to the mass spectrometer through nanoelectrospray ionization. The identified peptides overlapped between AlkalinepH-MS/MS and conventional online low-pH reverse phase nanoelectrospray-tandem mass spectrometry (LowpH-MS/MS) were as low as 45%, indicating that these two methods were complementary to each other. In addition, the AlkalinepH-MS/MS method showed identification capacity for a higher proportion of peptides with low molecular weight (MW), positive grand average of hydropathy (GRAVY), or high isoelectric point (pI). Moreover, the AlkalinepH-MS/MS method had a bias toward histidine, lysine, methionine, and proline- containing peptides. The complementarity of AlkalinepH-MS/MS and LowpH-MS/MS was further demonstrated for the analysis of tryptic digests from 15 intrahepatic cholangiocarcinoma (iCCA) cell lines. The alternating of 60-min AlkalinepH-MS/MS and 60-min LowpH-MS/MS method outperformed the conventional 120-min LowpH-MS/MS method in the identification of amino acid variants and protein groups. Our AlkalinepH-MS/MS method was an excellent complementary and alternative method to the LowpH-MS/MS method for global proteomic analysis.
HostingRepository	iProX
AnnounceDate	2023-01-15
AnnouncementXML	Submission_2023-12-25_19:57:31.298.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yuqiu Wang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-15 19:18:37	ID requested
1	2023-01-15 19:20:12	announced
⏵ 2	2023-12-25 19:57:32	announced	2023-12-26: Update information.

Gao J, Wang Y, Zhang S, Yang Z, Zhu H, Luo X, Lu D, Gao Q, Zhou H, Online Alkaline-pH Reverse Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Conventional Low-pH Method for Global Proteomic Analysis. J Proteome Res, 22(5):1446-1454(2023) [pubmed]

submitter keyword: online alkaline-pH reverse phase, mass spectrometry, proteomics, amino acid variant

Hu Zhou
contact affiliation	Shanghai Institute of Materia Medica
contact email	zhouhu@simm.ac.cn
lab head
Yuqiu Wang
contact affiliation	Shanghai Institute of Materia Medica
contact email	995752924@qq.com
dataset submitter

iProX dataset URI