{"database":"iProX","file_versions":[],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Hu Zhou"],"species":["Homo Sapiens"],"full_dataset_link":["http://www.iprox.org/page/project.html?id=IPX0004181000"],"submitter_email":["zhouhu@simm.ac.cn"],"submitter_affiliation":["Shanghai Institute of Materia Medica"],"sample_protocol":[""],"repository":["iProX"],"data_protocol":[""],"pubmed_abstract":["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 (alkaline-pH-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 = 8.0) and directly injected into the mass spectrometer. The unique peptides overlapped between alkaline-pH-MS/MS and conventional online low-pH reverse phase nanoelectrospray-tandem mass spectrometry (low-pH-MS/MS) were as low as 45%, strongly indicating that these two methods were complementary to each other. In addition, alkaline-pH-MS/MS showed identification capacity for a higher proportion of peptides with negative grand average of hydropathy (GRAVY) or high isoelectric point (p<i>I</i>). Compared to low-pH-MS/MS, alkaline-pH-MS/MS enabled enrichment preference toward histidine-, lysine-, methionine-, and proline-containing peptides. The complementarity of alkaline-pH-MS/MS and low-pH-MS/MS was further demonstrated for the analysis of tryptic digests from 15 intrahepatic cholangiocarcinoma (iCCA) cell lines. The alternating 60 min alkaline-pH-MS/MS plus 60 min low-pH-MS/MS method outperformed the conventional 120 min low-pH-MS/MS method in both the identification of amino acid variants and protein groups. Therefore, we established the alkaline-pH-MS/MS method as a simple, competitive, alternative method to low-pH-MS/MS for global proteomic analysis."],"pubmed_title":["Online Alkaline-pH Reverse Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Conventional Low-pH Method for Global Proteomic Analysis."],"pubmed_authors":["Gao Jing J, Wang Yuqiu Y, Zhang Shu S, Yang Zhicheng Z, Zhu Hongwen H, Luo Xuanyang X, Lu Dayun D, Gao Qiang Q, Zhou Hu H"],"additional_accession":[]},"is_claimable":false,"name":"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.","dates":{"publication":"Sun Jan 15 00:00:00 GMT 2023"},"accession":"PXD039453","cross_references":{"TAXONOMY":["9606"],"pubmed":["36751022"]}}