PXD039453-2
PXD039453 is an original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: online alkaline-pH reverse phase, mass spectrometry, proteomics, amino acid variant |
Contact List
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 |
Full Dataset Link List
iProX dataset URI |