Dataset Information

Sequential Phosphoproteomic Enrichment by Complementary Metal-directed Immobilized Metal Ion Affinity Chromatography: Case Study on Kinase Substrate Mapping in Human Lung Cancer Tissue

ABSTRACT: Abstract: Despite recent advances in instrumentation and analytical strategies for identification and quantitation of protein phosphorylation, methodologies to enrich the heterogeneous types of phosphopeptides are critical towards comprehensive mapping of the under-explored phosphoproteome. Taking advantage of the distinctive binding affinity of Ga3+ and Fe3+ towards phosphopeptides, we designed a tip-based metal-directed immobilized metal ion affinity (MD-IMAC) chromatography for sequential enrichment of phosphopeptides. On the analysis of Raji B cell, this sequential Ga3+-Fe3+-IMAC strategy demonstrated 1.5-3.5 fold superior phosphoproteomic coverage compared to the single IMAC (Fe3+, Ti4+, Ga3+ and Al3+). In addition, as high as 92% among the 6283 phosphopeptides was uniquely enriched by either 1st Ga3+-IMAC fraction (41%) or 2nd Fe3+-IMAC fraction (51%). The complementary property of Ga3+ and Fe3+ was further shown on the exclusively superior efficiency to enriched almost all the 1214 multiply phosphorylated peptides (99.4%) by 1st Ga3+-IMAC, while as low as 10% of 5069 monophosphorylated phosphopeptides was commonly enriched by both fractions. Application of our sequential Ga3+-Fe3+-IMAC approach to a human lung cancer tissue allowed the identification of 2560 unique phosphopeptides with only 8% overlapping. The fractionation ability was shown not only on the mono phosphopeptides and multiply phosphopeptides but also on the basic and acidic phosphopeptides; acidiphilic phosphorylation sites were predominately present in 1st Ga3+-IMAC (72%) and 85% Pro-directed and 79% basophilic phosphorylation sites were enriched by 2nd Fe3+-IMAC. Most interestingly, this strategy complementarily mapped different kinase substrate on the protein as well as site levels in multiple cellular pathways related to cancer invasion and metastasis of lung cancer ., Given the demonstrated fractionation ability, reproducibility, sensitivity and ease of tip preparation, we hope that this Ga3+-Fe3+-IMAC allow more comprehensive characterization of phosphoproteome in vitro and in vivo. Database search: The raw MS/MS data obtained by TripleTOF 5600 were processed using AB_SCIEX MS Data Converter with default parameters. All MS/MS files were analyzed using Mascot (Matrix Science, London, UK; version 2.3) against the SwissPort database (version 57.8) with the following constraints: an allowance for tryptic peptides of up to two missed cleavage sites, a fragment ion mass tolerance of 0.05 Da, and a parent ion tolerance of 10 ppm. Phosphorylation (S, T, Y) and oxidation (M) were selected as variable modifications. Searching on a randomized decoy database created by Mascot was required to evaluate the false discovery rate associated with protein identification. The false discovery rates with a Mascot score (p< 0.05) ranged between 0% and 1% in this study.

REANALYSED by: PAe005323PAe005320

INSTRUMENT(S): instrument model

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Lung, Cell Culture

SUBMITTER: Chia-Feng Tsai

PROVIDER: PXD000314 | Pride | 2014-01-29

REPOSITORIES: Pride

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Publications

Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography.

Tsai Chia-Feng CF Hsu Chuan-Chih CC Hung Jo-Nan JN Wang Yi-Ting YT Choong Wai-Kok WK Zeng Ming-Yao MY Lin Pei-Yi PY Hong Ruo-Wei RW Sung Ting-Yi TY Chen Yu-Ju YJ

Analytical chemistry 20131217 1

Methodologies to enrich heterogeneous types of phosphopeptides are critical for comprehensive mapping of the under-explored phosphoproteome. Taking advantage of the distinct binding affinities of Ga(3+) and Fe(3+) for phosphopeptides, we designed a metal-directed immobilized metal ion affinity chromatography for the sequential enrichment of phosphopeptides. In Raji B cells, the sequential Ga(3+)-Fe(3+)-immobilized metal affinity chromatography (IMAC) strategy displayed a 1.5-3.5-fold superior ph ...[more]

PMID: 24313913

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Project description:Phosphosites cluster, a set of co-regulation sites, extends a variety of protein function via the distinct combination of phosphorylation events. The coordination of proximal multisite phosphorylation is a universal mechanism to regulate protein function, activity, and interaction pattern. The common method for efficiently separating heterogeneous types of phosphopeptides is insufficient thereby hampering the complete mapping of phosphoproteome. By taking the advantages of distinct binding affinities of Ga2O3 and TiO2 toward phosphopeptides under the same buffer condition, we present a simple and rapid strategy, metal-directed metal oxide chromatography (MD-MOC), for sequential separation of singly and multiply phosphorylated peptides. Among the 6,585 phosphopeptides identified from PC9 cells, up to 92% was uniquely enriched in either the first Ga2O3 or subsequent TiO2 fractions and more than 90 % of phosphopeptides in Ga2O3 fraction were multiply phosphorylated peptide, demonstrating the high complementary properties of these two materials. The high separation efficiency (<10% overlapping of identified phosphopeptides) results in a 1.9-fold superior phosphoproteomic coverage compared to conventional TiO2-based MOC in PC9 cells. Finally, the MD-MOC approach was applied to the large-scale phosphoproteomic profiling of ten mouse organ tissues allowed the identification of 42,086 unique phosphopeptides from 6,669 phosphoproteins using single-shot LC/MS/MS analysis. To our knowledge, the identification of 14,854 multiply phosphorylated peptides presented the largest dataset for multiply phosphorylated peptide from rodent tissues to date. Also, around half identified novel phosphosites (n=2,752) were uniquely came from the multiply phosphorylated peptide dataset further emphasizing the need of improving the detection sensitivity of multiply phosphorylated peptides. Given the good separation ability, stable reproducibility, and ease of tip-based preparation, this MD-MOC presents a sensitive approach for deep phosphoproteome identification and quantification from limited sample for shedding light on in vivo phosphoregulations.

Dataset Information

Sequential Phosphoproteomic Enrichment by Complementary Metal-directed Immobilized Metal Ion Affinity Chromatography: Case Study on Kinase Substrate Mapping in Human Lung Cancer Tissue

Publications

Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography.

Similar Datasets

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