Proteomic profiling and protein identification by 2-DE-MS in the liver ofCarassius auratusexposed to Yongcheng coalmine subsidence area

An increasingly popular and promising field in functional proteomics is the isolation of proteome subsets based on small molecule-protein interactions. One platform approach in this field are Capture Compounds that contain a small molecule of interest to bind target proteins, a photo-activatable reactivity function to covalently trap bound proteins, and a sorting function to isolate captured protein conjugates from complex biological samples for direct protein identification by liquid chromatography/mass spectrometry (nLC-MS/MS). In this study we used staurosporine as a selectivity group for analysis in HepG2 cells derived from human liver. In the present study, we combined the functional isolation of kinases with different separation workflows of automated split-free nanoflow liquid chromatography prior to mass spectrometric analysis. Two different CCMS setups, CCMS technology combined with 1D LC-MS and 2D LC-MS, were compared regarding the total number of kinase identifications. By extending the chromatographic separation of the tryptic digested captured proteins from 1D LC linear gradients to 2D LC we were able to identify 97 kinases. This result is similar to the 1D LC setup we previously reported but this time 4 times less input material was needed. This makes CCMS of kinases an even more powerful tool for the proteomic profiling of this important protein family.

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Proteomic profiling of human urine using multi-dimensional protein identification technology

Journal of Chromatography A ◽

10.1016/j.chroma.2005.06.081 ◽

2006 ◽

Vol 1111 (2) ◽

pp. 166-174 ◽

Cited By ~ 29

Author(s):

Qinhua Cindy Ru ◽

Richard A. Katenhusen ◽

Luwang Andy Zhu ◽

Jordan Silberman ◽

Song Yang ◽

...

Keyword(s):

Human Urine ◽

Protein Identification ◽

Proteomic Profiling

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Proteomic profiling of platelet proteins by trypsin immobilized self-assembled monolayers digestion chip and protein identification using electrospray ionization tandem mass spectrometry

Journal of Biomedical Materials Research ◽

10.1002/jbm.a.30129 ◽

2004 ◽

Vol 71A (1) ◽

pp. 90-97 ◽

Cited By ~ 7

Author(s):

Yu-Chang Tyan ◽

Jiunn-Der Liao ◽

Shiang-Bin Jong ◽

Pao-Chi Liao ◽

Ming-Hui Yang ◽

...

Keyword(s):

Mass Spectrometry ◽

Tandem Mass Spectrometry ◽

Electrospray Ionization ◽

Protein Identification ◽

Self Assembled Monolayers ◽

Tandem Mass ◽

Proteomic Profiling ◽

Assembled Monolayers ◽

Ionization Tandem Mass Spectrometry ◽

Platelet Proteins

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A hybrid spectral library combining DIA-MS data and a targeted virtual library substantially deepens the proteome coverage

10.1101/2020.01.16.909952 ◽

2020 ◽

Author(s):

Ronghui Lou ◽

Pan Tang ◽

Kang Ding ◽

Shanshan Li ◽

Cuiping Tian ◽

...

Keyword(s):

Mouse Brain ◽

Protein Identification ◽

Transmembrane Protein ◽

Peptide Identification ◽

Protein Family ◽

Virtual Library ◽

Proteomic Profiling ◽

Spectral Library ◽

Proteome Coverage ◽

Brain Tissues

AbstractData-independent acquisition mass spectrometry (DIA-MS) is a rapidly evolving technique that enables relatively deep proteomic profiling with superior quantification reproducibility. DIA data mining predominantly relies on a spectral library of sufficient proteome coverage that, in most cases, is built on data-dependent acquisition-based analysis of the same sample. To expand the proteome coverage for a pre-determined protein family, we report herein on the construction of a hybrid spectral library that supplements a DIA experiment-derived library with a protein family-targeted virtual library predicted by deep learning. Leveraging this DIA hybrid library substantially deepens the coverage of three transmembrane protein families (G protein coupled receptors; ion channels; and transporters) in mouse brain tissues with increases in protein identification of 37-87%, and peptide identification of 58-161%. Moreover, of the 412 novel GPCR peptides exclusively identified with the DIA hybrid library strategy, 53.6% were validated as present in mouse brain tissues based on orthogonal experimental measurement.

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Proteomic Analysis of Maternal Urine for the Early Detection of Preeclampsia and Fetal Growth Restriction

Journal of Clinical Medicine ◽

10.3390/jcm10204679 ◽

2021 ◽

Vol 10 (20) ◽

pp. 4679

Author(s):

Emmanuel Bujold ◽

Alexandre Fillion ◽

Florence Roux-Dalvai ◽

Marie Pier Scott-Boyer ◽

Yves Giguère ◽

...

Keyword(s):

Fetal Growth ◽

Fetal Growth Restriction ◽

Protein Identification ◽

False Positive Rate ◽

Growth Restriction ◽

Urine Samples ◽

Proteomic Profiling ◽

Maternal Urine ◽

Liquid Chromatography Tandem Mass ◽

Protein Discovery

Background: To explore the use of maternal urine proteome for the identification of preeclampsia biomarkers. Methods: Maternal urine samples from women with and without preeclampsia were used for protein discovery followed by a validation study. The targeted proteins of interest were then measured in urine samples collected at 20–24 and 30–34 weeks among nine women who developed preeclampsia, one woman with fetal growth restriction, and 20 women with uncomplicated pregnancies from a longitudinal study. Protein identification and quantification was obtained using liquid chromatography–tandem mass spectrometry (LC–MS/MS). Results: Among the 1108 urine proteins quantified in the discovery study, 21 were upregulated in preeclampsia and selected for validation. Nineteen (90%) proteins were confirmed as upregulated in preeclampsia cases. Among them, two proteins, ceruloplasmin and serpin A7, were upregulated at 20–24 weeks and 30–34 weeks of gestation (p < 0.05) in cases of preeclampsia, and could have served to identify 60% of women who subsequently developed preeclampsia and/or fetal growth restriction at 20–24 weeks of gestation, and 78% at 30–34 weeks, for a false-positive rate of 10%. Conclusions: Proteomic profiling of maternal urine can differentiate women with and without preeclampsia. Several proteins including ceruloplasmin and serpin A7 are upregulated in maternal urine before the diagnosis of preeclampsia and potentially fetal growth restriction.

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Transcriptomic and Proteomic Analyses of Nepenthes ampullaria and Nepenthes rafflesiana Reveal Parental Molecular Expression in the Pitchers of Their Hybrid, Nepenthes × hookeriana

Frontiers in Plant Science ◽

10.3389/fpls.2020.625507 ◽

2021 ◽

Vol 11 ◽

Author(s):

Muhammad Mu’izzuddin Zulkapli ◽

Nur Syatila Ab Ghani ◽

Tiew Yik Ting ◽

Wan Mohd Aizat ◽

Hoe-Han Goh

Keyword(s):

Protein Identification ◽

Dietary Habits ◽

Lipid Transfer Protein ◽

Average Length ◽

Protein Composition ◽

Lipid Transfer ◽

Proteomic Profiling ◽

Molecular Physiology ◽

Pathogenesis Related Protein ◽

Species Specific

Nepenthes is a genus comprising carnivorous tropical pitcher plants that have evolved trapping organs at the tip of their leaves for nutrient acquisition from insect trapping. Recent studies have applied proteomics approaches to identify proteins in the pitcher fluids for better understanding the carnivory mechanism, but protein identification is hindered by limited species-specific transcriptomes for Nepenthes. In this study, the proteomics informed by transcriptomics (PIT) approach was utilized to identify and compare proteins in the pitcher fluids of Nepenthes ampullaria, Nepenthes rafflesiana, and their hybrid Nepenthes × hookeriana through PacBio isoform sequencing (Iso-Seq) and liquid chromatography-mass spectrometry (LC-MS) proteomic profiling. We generated full-length transcriptomes from all three species of 80,791 consensus isoforms with an average length of 1,692 bp as a reference for protein identification. The comparative analysis found that transcripts and proteins identified in the hybrid N. × hookeriana were more resembling N. rafflesiana, both of which are insectivorous compared with omnivorous N. ampullaria that can derive nutrients from leaf litters. Previously reported hydrolytic proteins were detected, including proteases, glucanases, chitinases, phosphatases, nucleases, peroxidases, lipid transfer protein, thaumatin-like protein, pathogenesis-related protein, and disease resistance proteins. Many new proteins with diverse predicted functions were also identified, such as amylase, invertase, catalase, kinases, ligases, synthases, esterases, transferases, transporters, and transcription factors. Despite the discovery of a few unique enzymes in N. ampullaria, we found no strong evidence of adaptive evolution to produce endogenous enzymes for the breakdown of leaf litter. A more complete picture of digestive fluid protein composition in this study provides important insights on the molecular physiology of pitchers and carnivory mechanism of Nepenthes species with distinct dietary habits.

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