Improvements in protein identification confidence and proteome coverage for human liver proteome study by coupling a parallel mass spectrometry/mass spectrometry analysis with multi-dimensional chromatography separation

2006 ◽  
Vol 566 (2) ◽  
pp. 147-156 ◽  
Author(s):  
Jie Zhang ◽  
Mingxia Gao ◽  
Jia Tang ◽  
Pengyuan Yang ◽  
Yinkun Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Liver ◽  
Protein Identification ◽  
Mass Spectrometry Analysis ◽  
Proteome Coverage ◽  
Spectrometry Analysis ◽  
Identification Confidence ◽  
Liver Proteome ◽  
Mass Spectrometry Mass Spectrometry

scholarly journals Gel Electrophoresis/Electroelution Sorting Fractionator combined with Filter Aided Sample preparation (FASP) for deep proteomic analysis

2021 ◽  
Author(s):  
Yassel Ramos ◽  
Alexis Almeida ◽  
Jenis Carpio ◽  
Arielis Rodríguez-Ulloa ◽  
Yasser Perera ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Protein Identification ◽  
Protein Extraction ◽  
Complex Mixture ◽  
Fold Increase ◽  
Mass Spectrometry Analysis ◽  
Protein Fractionation ◽  
Spectrometry Analysis ◽  
Sds Page

AbstractSample preparation and protein fractionation are important issues in proteomic studies in spite of the technological achievements on protein mass spectrometry. Protein extraction procedures strongly affect the performance of fractionation methods by provoking protein dispersion in several fractions. The most notable exception is SDS-PAGE-based protein fractionation due to its extraordinary resolution and the effectiveness of SDS as a solubilizing agent. Its main limitation lies in the poor recovery of the gel-trapped proteins, where protein electro-elution is the most successful approach to overcome this drawback. We created a device to separate complex mixture of proteins and peptides (named “GEES fractionator”) that is based on the continuous Gel Electrophoresis/Electro-elution Sorting of these molecules. In an unsupervised process, complex mixtures of proteins or peptides are fractionated into the gel while separated fractions are simultaneously and sequentially electro-eluted to the solution containing wells. The performance of the device was studied for SDS-PAGE-based protein fractionation in terms of reproducibility, protein recovery and loading capacity. In the SDS-free PAGE setup, complex peptide mixtures can also be fractionated. More than 11 700 proteins were identified in the whole-cell lysate of the CaSki cell line by using the GEES fractionator combined with the Filter Aided Sample Preparation (FASP) method and mass spectrometry analysis. GEES-based proteome characterization shows a 1.7 fold increase in the number of identified proteins compared to the unfractionated sample analysis. Proteins involved in the co-regulated transcription activity, as well as cancer related pathways such as apoptosis signaling, P53 and RAS pathways are more represented in the protein identification output of GEES-based fractionation approaches.

scholarly journals Unraveling endometriosis-associated ovarian carcinomas using integrative proteomics

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 189
Author(s):  
Felix Leung ◽  
Marcus Q. Bernardini ◽  
Kun Liang ◽  
Ihor Batruch ◽  
Marjan Rouzbahman ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cell Carcinoma ◽  
Protein Identification ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Mass Spectrometry Analysis ◽  
Ovarian Carcinomas ◽  
Spectrometry Analysis ◽  
Proteomic Data ◽  
Fresh Frozen

Background: To elucidate potential markers of endometriosis and endometriosis-associated endometrioid and clear cell ovarian carcinomas using mass spectrometry-based proteomics. Methods: A total of 21 fresh, frozen tissues from patients diagnosed with clear cell carcinoma, endometrioid carcinoma, endometriosis and benign endometrium were subjected to an in-depth liquid chromatography-tandem mass spectrometry analysis on the Q-Exactive Plus. Protein identification and quantification were performed using MaxQuant, while downstream analyses were performed using Perseus and various bioinformatics databases. Results: Approximately 9000 proteins were identified in total, representing the first in-depth proteomic investigation of endometriosis and its associated cancers. This proteomic data was shown to be biologically sound, with minimal variation within patient cohorts and recapitulation of known markers. While moderate concordance with genomic data was observed, it was shown that such data are limited in their abilities to represent tumours on the protein level and to distinguish tumours from their benign precursors. Conclusions: The proteomic data suggests that distinct markers may differentiate endometrioid and clear cell carcinoma from endometriosis. These markers may be indicators of pathobiology but will need to be further investigated. Ultimately, this dataset may serve as a basis to unravel the underlying biology of the endometrioid and clear cell cancers with respect to their endometriotic origins.

Determination of cocaine in postmortem human liver exposed to overdose. Application of an innovative and efficient extraction/clean up procedure and gas chromatography–mass spectrometry analysis

2013 ◽  
Vol 1309 ◽  
pp. 15-21 ◽  
Author(s):  
Elisângela Jaqueline Magalhães ◽  
Maria Eliana Lopes Ribeiro de Queiroz ◽  
Marcus Luiz de Oliveira Penido ◽  
Marco Antônio Ribeiro Paiva ◽  
Janaína Aparecida Reis Teodoro ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Human Liver ◽  
Mass Spectrometry Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Spectrometry Analysis ◽  
Chromatography Mass Spectrometry ◽  
Efficient Extraction

Integrated plant proteomics — putting the green genomes to work

2003 ◽  
Vol 30 (5) ◽  
pp. 471 ◽  
Author(s):  
Joshua L. Heazlewood ◽  
A. Harvey Millar
Keyword(s):  
Mass Spectrometry ◽  
Data Storage ◽  
Large Scale ◽  
Protein Identification ◽  
Mass Spectrometry Analysis ◽  
Plant Science ◽  
Genomic Information ◽  
Plant Proteomics ◽  
Spectrometry Analysis ◽  
Complete Set

Protein analysis has been at the heart of plant science for many years, but with new questions emerging from an abundance of genomic information and further improvements in technology, there are now new opportunities to undertake large-scale analyses and to move to more complex systems than has been possible previously. This explosion of interest and data is often referred to simply as proteomics, which is the study of the complete set of proteins expressed at a given time and place, the proteome. As its name suggests proteomics is intricately linked to allied technologies such as genomics, transcriptomics and metabolomics. In this review of plant proteomics we outline a series of issues that face the practical user, particularly the largest problem that currently faces researchers, the myriad of options to choose from. The choices, problems and pitfalls of entering into gel-based and non-gel-based arraying techniques are discussed together with advances in pre-fractionation of samples, liquid chromatography separations and subcellular analyses. Issues relating to mass spectrometry analysis and the eventual protein identification are outlined, and the dilemmas of data storage and analysis are highlighted. During this tour we provide a series of references to the literature — experimental, theoretical and technical — to illustrate the breadth of current investigations using these techniques.

scholarly journals Unraveling endometriosis-associated ovarian carcinomas using integrative proteomics

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 189
Author(s):  
Felix Leung ◽  
Marcus Q. Bernardini ◽  
Kun Liang ◽  
Ihor Batruch ◽  
Marjan Rouzbahman ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cell Carcinoma ◽  
Protein Identification ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Mass Spectrometry Analysis ◽  
Ovarian Carcinomas ◽  
Spectrometry Analysis ◽  
Proteomic Data ◽  
Fresh Frozen

Background: To elucidate potential markers of endometriosis and endometriosis-associated endometrioid and clear cell ovarian carcinomas using mass spectrometry-based proteomics. Methods: A total of 21 fresh, frozen tissues from patients diagnosed with clear cell carcinoma, endometrioid carcinoma, endometriosis and benign endometrium were subjected to an in-depth liquid chromatography-tandem mass spectrometry analysis on the Q-Exactive Plus. Protein identification and quantification were performed using MaxQuant, while downstream analyses were performed using Perseus and various bioinformatics databases. Results: Approximately 9000 proteins were identified in total, representing the first in-depth proteomic investigation of endometriosis and its associated cancers. This proteomic data was shown to be biologically sound, with minimal variation within patient cohorts and recapitulation of known markers. While moderate concordance with genomic data was observed, it was shown that such data are limited in their abilities to represent tumours on the protein level and to distinguish tumours from their benign precursors. Conclusions: The proteomic data suggests that distinct markers may differentiate endometrioid and clear cell carcinoma from endometriosis. These markers may be indicators of pathobiology but will need to be further investigated. Ultimately, this dataset may serve as a basis to unravel the underlying biology of the endometrioid and clear cell cancers with respect to their endometriotic origins.

scholarly journals In situ protein identification and mapping using secondary ion mass spectrometry

2019 ◽  
Author(s):  
Anna M. Kotowska ◽  
Philip M. Williams ◽  
Jonathan W. Aylott ◽  
Alexander G. Shard ◽  
Morgan R. Alexander ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
Secondary Ion Mass Spectrometry ◽  
Ion Beam ◽  
Mass Spectrometry Analysis ◽  
Protein Film ◽  
Spectrometry Analysis ◽  
Ion Mass Spectrometry ◽  
Secondary Ion

AbstractProtein characterisation at surfaces currently requires digestion prior to either liquid extraction of the protein for mass spectrometry analysis or in situ matrix-assisted desorption/ionisation. Here, we show that direct assignment of individual proteins and mixtures at surfaces can be achieved by employing secondary ion mass spectrometry (SIMS) with gas cluster ion beam (GCIB) bombardment and an Orbitrap™ analyser. Potential applications of the method are illustrated by demonstrating imaging of a protein film masked by a gold grid and the analysis of a protein monolayer biochip.

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