Analysis of Quantitative Proteomic Data Generated via Multidimensional Protein Identification Technology

2002 ◽  
Vol 74 (7) ◽  
pp. 1650-1657 ◽  
Author(s):  
Michael P. Washburn ◽  
Ryan Ulaszek ◽  
Cosmin Deciu ◽  
David M. Schieltz ◽  
John R. Yates
Keyword(s):  
Protein Identification ◽  
Proteomic Data ◽  
Multidimensional Protein Identification Technology

Parallel Channels-Multidimensional Protein Identification Technology

2020 ◽  
Vol 31 (7) ◽  
pp. 1440-1447
Author(s):  
Nan Zhang ◽  
Xiaojing Liu ◽  
Shuaixin Gao ◽  
Catherine Chiulan Wong
Keyword(s):  
Protein Identification ◽  
Multidimensional Protein Identification Technology ◽  
Parallel Channels

Arabidopsis cell wall proteome defined using multidimensional protein identification technology

PROTEOMICS ◽  
2006 ◽  
Vol 6 (1) ◽  
pp. 301-311 ◽  
Author(s):  
Emmanuelle M. Bayer ◽  
Andrew R. Bottrill ◽  
John Walshaw ◽  
Marielle Vigouroux ◽  
Mike J. Naldrett ◽  
...  
Keyword(s):  
Cell Wall ◽  
Protein Identification ◽  
Multidimensional Protein Identification Technology ◽  
Cell Wall Proteome

scholarly journals Comparative Proteomic Analysis of Listeria monocytogenes Strains F2365 and EGD

2008 ◽  
Vol 75 (2) ◽  
pp. 366-373 ◽  
Author(s):  
Janet R. Donaldson ◽  
Bindu Nanduri ◽  
Shane C. Burgess ◽  
Mark L. Lawrence
Keyword(s):  
Listeria Monocytogenes ◽  
Protein Identification ◽  
Altered Expression ◽  
Genetic Lineages ◽  
Multidimensional Protein Identification Technology ◽  
Food Borne ◽  
Flagellar Biosynthesis ◽  
Serotype 1 ◽  
Serotype 4B ◽  
Biological Differences

ABSTRACT Listeria monocytogenes is a gram-positive, food-borne pathogen that causes disease in both humans and animals. There are three major genetic lineages of L. monocytogenes and 13 serovars. To further our understanding of the differences that exist between different genetic lineages/serovars of L. monocytogenes, we analyzed the global protein expression of the serotype 1/2a strain EGD and the serotype 4b strain F2365 during early-stationary-phase growth at 37°C. Using multidimensional protein identification technology with electrospray ionization tandem mass spectrometry, we identified 1,754 proteins from EGD and 1,427 proteins from F2365, of which 1,077 were common to both. Analysis of proteins that had significantly altered expression between strains revealed potential biological differences between these two L. monocytogenes strains. In particular, the strains differed in expression of proteins involved in cell wall physiology and flagellar biosynthesis, as well as DNA repair proteins and stress response proteins.

scholarly journals The Landscape of Pseudomonas aeruginosa Membrane-Associated Proteins

Cells ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 2421
Author(s):  
Sara Motta ◽  
Davide Vecchietti ◽  
Alessandra M. Martorana ◽  
Pietro Brunetti ◽  
Giovanni Bertoni ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Outer Membrane ◽  
Protein Identification ◽  
Bacterial Species ◽  
Outer Membrane Proteins ◽  
Protein Domains ◽  
Host Cells ◽  
Inner Membrane ◽  
Proteomic Data ◽  
Associated Proteins

Background: Pseudomonas aeruginosa cell envelope-associated proteins play a relevant role in infection mechanisms. They can contribute to the antibiotic resistance of the bacterial cells and be involved in the interaction with host cells. Thus, studies contributing to elucidating these key molecular elements are of great importance to find alternative therapeutics. Methods: Proteins and peptides were extracted by different methods and analyzed by Multidimensional Protein Identification Technology (MudPIT) approach. Proteomic data were processed by Discoverer2.1 software and multivariate statistics, i.e., Linear Discriminant Analysis (LDA), while the Immune Epitope Database (IEDB) resources were used to predict antigenicity and immunogenicity of experimental identified peptides and proteins. Results: The combination of 29 MudPIT runs allowed the identification of 10,611 peptides and 2539 distinct proteins. Following application of extraction methods enriching specific protein domains, about 15% of total identified peptides were classified in trans inner-membrane, inner-membrane exposed, trans outer-membrane and outer-membrane exposed. In this scenario, nine outer membrane proteins (OprE, OprI, OprF, OprD, PagL, OprG, PA1053, PAL and PA0833) were predicted to be highly antigenic. Thus, they were further processed and epitopes target of T cells (MHC Class I and Class II) and B cells were predicted. Conclusion: The present study represents one of the widest characterizations of the P. aeruginosa membrane-associated proteome. The feasibility of our method may facilitates the investigation of other bacterial species whose envelope exposed protein domains are still unknown. Besides, the stepwise prioritization of proteome, by combining experimental proteomic data and reverse vaccinology, may be useful for reducing the number of proteins to be tested in vaccine development.

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