An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics

2001 ◽  
Vol 73 (23) ◽  
pp. 5683-5690 ◽  
Author(s):  
Dirk A. Wolters ◽  
Michael P. Washburn ◽  
John R. Yates
Keyword(s):  
Protein Identification ◽  
Shotgun Proteomics ◽  
Multidimensional Protein Identification Technology

scholarly journals Shotgun Proteomics and Biomarker Discovery

2002 ◽  
Vol 18 (2) ◽  
pp. 99-105 ◽  
Author(s):  
W. Hayes McDonald ◽  
John R. Yates
Keyword(s):  
Large Scale ◽  
Protein Identification ◽  
Biomarker Discovery ◽  
Dynamic Range ◽  
Shotgun Proteomics ◽  
Sequence Information ◽  
Protein Biomarkers ◽  
Post Translational Modifications ◽  
Multidimensional Protein Identification Technology ◽  
Shotgun Approach

Coupling large-scale sequencing projects with the amino acid sequence information that can be gleaned from tandem mass spectrometry (MS/MS) has made it much easier to analyze complex mixtures of proteins. The limits of this “shotgun” approach, in which the protein mixture is proteolytically digested before separation, can be further expanded by separating the resulting mixture of peptides prior to MS/MS analysis. Both single dimensional high pressure liquid chromatography (LC) and multidimensional LC (LC/LC) can be directly interfaced with the mass spectrometer to allow for automated collection of tremendous quantities of data. While there is no single technique that addresses all proteomic challenges, the shotgun approaches, especially LC/LC-MS/MS-based techniques such as MudPIT (multidimensional protein identification technology), show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range. Advances in the ability to quantitate differences between samples and to detect for an array of post-translational modifications allow for the discovery of classes of protein biomarkers that were previously unassailable.

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

Optimizing Shotgun Proteomics Analysis for a Confident Protein Identification and Quantitation in Orphan Plant Species: The Case of Holm Oak (Quercus ilex)

2020 ◽  
pp. 157-168
Author(s):  
Isabel Gómez-Gálvez ◽  
Rosa Sánchez-Lucas ◽  
Bonoso San-Eufrasio ◽  
Luis Enrique Rodríguez de Francisco ◽  
Ana M. Maldonado-Alconada ◽  
...  
Keyword(s):  
Plant Species ◽  
Protein Identification ◽  
Quercus Ilex ◽  
Shotgun Proteomics ◽  
Holm Oak ◽  
Proteomics Analysis ◽  
Protein Identification And Quantitation

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

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

scholarly journals Putative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database

Antibiotics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 757 ◽  
Author(s):  
Daniela Almeida ◽  
Dany Domínguez-Pérez ◽  
Ana Matos ◽  
Guillermin Agüero-Chapin ◽  
Hugo Osório ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Salivary Glands ◽  
Protein Identification ◽  
Inflammatory Responses ◽  
Shotgun Proteomics ◽  
Octopus Vulgaris ◽  
Protein Database ◽  
Venom Protein ◽  
Protein Toxin ◽  
Proteomics Approach

Cephalopods, successful predators, can use a mixture of substances to subdue their prey, becoming interesting sources of bioactive compounds. In addition to neurotoxins and enzymes, the presence of antimicrobial compounds has been reported. Recently, the transcriptome and the whole proteome of the Octopus vulgaris salivary apparatus were released, but the role of some compounds—e.g., histones, antimicrobial peptides (AMPs), and toxins—remains unclear. Herein, we profiled the proteome of the posterior salivary glands (PSGs) of O. vulgaris using two sample preparation protocols combined with a shotgun-proteomics approach. Protein identification was performed against a composite database comprising data from the UniProtKB, all transcriptomes available from the cephalopods’ PSGs, and a comprehensive non-redundant AMPs database. Out of the 10,075 proteins clustered in 1868 protein groups, 90 clusters corresponded to venom protein toxin families. Additionally, we detected putative AMPs clustered with histones previously found as abundant proteins in the saliva of O. vulgaris. Some of these histones, such as H2A and H2B, are involved in systemic inflammatory responses and their antimicrobial effects have been demonstrated. These results not only confirm the production of enzymes and toxins by the O. vulgaris PSGs but also suggest their involvement in the first line of defense against microbes.

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.

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