Intact protein profiling in breast cancer biomarker discovery: Protein identification issue and the solutions based on 3D protein separation, bottom-up and top-down mass spectrometry

PROTEOMICS ◽  
2013 ◽  
Vol 13 (7) ◽  
pp. 1053-1058 ◽  
Author(s):  
Pavel Bouchal ◽  
Monika Dvorakova ◽  
Alexander Scherl ◽  
Spiros D. Garbis ◽  
Rudolf Nenutil ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Mass Spectrometry ◽  
Protein Separation ◽  
Protein Identification ◽  
Biomarker Discovery ◽  
Cancer Biomarker ◽  
Protein Profiling ◽  
Intact Protein ◽  
Top Down ◽  
Bottom Up

A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery

2015 ◽  
Vol 14 (7) ◽  
pp. 2807-2818 ◽  
Author(s):  
Martin Sjöström ◽  
Reto Ossola ◽  
Thomas Breslin ◽  
Oliver Rinner ◽  
Lars Malmström ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Mass Spectrometry ◽  
Biomarker Discovery ◽  
Cancer Biomarker

scholarly journals Mass spectrometry‐based top‐down and bottom‐up approaches for proteomic analysis of the Moroccan Buthus occitanus scorpion venom

FEBS Open Bio ◽  
2021 ◽  
Author(s):  
Khadija Daoudi ◽  
Christian Malosse ◽  
Ayoub Lafnoune ◽  
Bouchra Darkaoui ◽  
Salma Chakir ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Scorpion Venom ◽  
Top Down ◽  
Bottom Up

Contributions of Proteome Profiling to the Molecular Analysis of Cancer

2002 ◽  
Vol 1 (4) ◽  
pp. 237-245 ◽  
Author(s):  
Hong Wang ◽  
S. M. Hanash
Keyword(s):  
Mass Spectrometry ◽  
Tumor Cell ◽  
Cell Lines ◽  
Molecular Analysis ◽  
Protein Separation ◽  
Protein Identification ◽  
Tumor Cell Lines ◽  
Transcriptomic Profiling ◽  
Proteome Profiling

The proteome is the most functional compartment encoded for in the genome. Technologies for protein separation and quantitation, coupled with mass spectrometry for protein identification, have provided the means for proteome profiling of tumor cell lines and tissues that complement genomic and transcriptomic profiling. The application of established and novel proteomic technologies to the molecular analysis of cancer is reviewed.

Management and Analysis of Mass Spectrometry Proteomics Data on the Grid

2011 ◽  
pp. 206-227
Author(s):  
Mario Cannataro ◽  
Pietro Hiram Guzzi ◽  
Giuseppe Tradigo ◽  
Pierangelo Veltri
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
Biomarker Discovery ◽  
Integrated Management ◽  
Molecular Signature ◽  
Proteomics Data ◽  
Computational Proteomics ◽  
Manual Inspection ◽  
A Cell ◽  
Grid Based

Recent advances in high throughput technologies analysing biological samples enabled the researchers to collect a huge amount of data. In particular, mass spectrometry-based proteomics uses the mass spectrometry to investigate proteins expressed in an organism or a cell. The manual inspection of spectra is unfeasible, so the need to introduce a set of algorithms, tools and platforms to manage and analyze them arises. Computational Proteomics regards the computational methods for analyzing spectra data in qualitative (i.e. peptide/protein identification in tandem mass spectrometry), and quantitative proteomics (i.e. protein expression in samples), as well as in biomarker discovery (i.e. the identification of a molecular signature of a disease directly from spectra). This chapter presents main standards, tools, and technologies for building scalable, reusable, and portable applications in this field. The chapter surveys available solutions for computational proteomics and includes a deep description of MS-Analyzer, a Grid-based software platform for the integrated management and analysis of spectra data. MS-Analyzer provides efficient spectra management through a specialized spectra database, and supports the semantic composition of pre-processing and data mining services to analyze spectra on the Grid.

Proteomics: current techniques and potential applications to lung disease

2004 ◽  
Vol 287 (1) ◽  
pp. L1-L23 ◽  
Author(s):  
Jan Hirsch ◽  
Kirk C. Hansen ◽  
Alma L. Burlingame ◽  
Michael A. Matthay
Keyword(s):  
Posttranslational Modifications ◽  
Protein Separation ◽  
Protein Identification ◽  
Cell Types ◽  
Protein Profiling ◽  
Complex Samples ◽  
Potential Value ◽  
Potential Applications ◽  
Tissue Specimens ◽  
Different Cell Types

Proteomics aims to study the whole protein content of a biological sample in one set of experiments. Such an approach has the potential value to acquire an understanding of the complex responses of an organism to a stimulus. The large vascular and air space surface area of the lung expose it to a multitude of stimuli that can trigger a variety of responses by many different cell types. This complexity makes the lung a promising, but also challenging, target for proteomics. Important steps made in the last decade have increased the potential value of the results of proteomics studies for the clinical scientist. Advances in protein separation and staining techniques have improved protein identification to include the least abundant proteins. The evolution in mass spectrometry has led to the identification of a large part of the proteins of interest rather than just describing changes in patterns of protein spots. Protein profiling techniques allow the rapid comparison of complex samples and the direct investigation of tissue specimens. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. These methodologies have made the application of proteomics on the study of specific diseases or biological processes under clinically relevant conditions possible. The quantity of data that is acquired with these new techniques places new challenges on data processing and analysis. This article provides a brief review of the most promising proteomics methods and some of their applications to pulmonary research.

Mass spectrometry-based proteomics: The road to lung cancer biomarker discovery

2012 ◽  
Vol 32 (2) ◽  
pp. 129-142 ◽  
Author(s):  
Paola Indovina ◽  
Eleonora Marcelli ◽  
Francesca Pentimalli ◽  
Piero Tanganelli ◽  
Giulio Tarro ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Lung Cancer ◽  
Biomarker Discovery ◽  
Cancer Biomarker ◽  
The Road ◽  
Lung Cancer Biomarker
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