Time Series Proteome Profiling To Study Endoplasmic Reticulum Stress Response

Mintz, Michelle; Vanderver, Adeline; Brown, Kristy J.; Lin, Joseph; Wang, Zuyi; Kaneski, Christine R.; Schiffmann, Raphael; Nagaraju, Kanneboyina; Hoffman, Eric P.; Hathout, Yetrib

doi:10.1021/pr700842m

Cited by 32 publications

(24 citation statements)

References 47 publications

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“…8). Calreticulin (CRT), which is also a chaperone with sugar binding activity, and EDEM, which participates in the ER-associated degradation, are also induced with ER stress (20,21). Again, these proteins showed the same expression levels among 1F12-, 3F1-, 5A3-, 1G4-, 1A4-, and 1H7-scFv-Fc-transfected COS-7 cells (Fig.…”

Section: Detection Of Er Stress-inducible Gene Expression By Rt-pcr-mentioning

confidence: 78%

Production of Anti-carbohydrate Antibodies by Phage Display Technologies

Yuasa

Zhang

Goto

et al. 2010

Journal of Biological Chemistry

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Anti-mannotriose (Man3) antibodies were previously isolated from a Keio phage library displaying human single chain variable fragments (scFvs) using a neoglycolipid, Man3-dipalmitoylphosphatidylethanolamine. Of three genes constructed, the 5A3 clone was expressed in mouse myeloma NS0 cells as a conjugate with human IgG 1 Fc (scFv-Fc) and characterized (Sakai, K., Shimizu, Y., Chiba, T., MatsumotoTakasaki, A., Kusada, Y., Zhang, W., Nakata, M., Kojima, N., Toma, K., Takayanagi, Since the human genome project was completed, our understanding of structure-function relationships among proteins has made significant advances. In contrast, elucidating the role of carbohydrate modification on the functions of glycoproteins, glycolipids, and peptide glycans remains elusive. The project that was to produce a variety of carbohydrate-specific antibodies by the phage display technology was thus launched in 2003 with the hope that the resulting antibodies could not only provide tools for carbohydrate research but also be applied to diagnostic or therapeutic uses. In vitro production of anti-carbohydrate antibodies is seemingly a logical strategy because carbohydrate moieties are self-antigens by nature. Thus far, researchers have most often preferred to use phage display technologies because they have been successful to a certain extent, in producing antibodies against varieties of carbohydrate moieties of glycoconjugates (1-6). The phage display strategy readily provides genes encoding recombinant antibodies against antigens of interest, which then need to be introduced into prokaryotic or eukaryotic cells for translation of the obtained antibody genes to produce proteins. Unless other in vitro translation systems are employed, this technology cannot provide an absolute in vitro system for production of anti-carbohydrate antibodies.Previously, we reported on producing and characterizing anti-mannotriose (Man3) 4 antibodies (7,8). The objectives of our first study (7) were to establish a new methodology so that single chain variable fragments (scFvs) against desired carbohydrate moieties could be readily isolated, and the objectives of our second paper (8) were to produce soluble scFv proteins in quantity so that purification and characterization of isolated scFvs could be readily accomplished.

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Section: Detection Of Er Stress-inducible Gene Expression By Rt-pcr-mentioning

confidence: 78%

Production of Anti-carbohydrate Antibodies by Phage Display Technologies

Yuasa

Zhang

Goto

et al. 2010

Journal of Biological Chemistry

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“…A concerted action of all parties, albeit difficult to achieve, is mandatory and will lead to even greater advances in the field. Other researchers seem to think along the same line by emphasizing the modularity of their approach and also extend this idea by integrating methods from related fields such as micro array analysis Bellew et al 2006;Mintz et al 2008). Developing an open toolbox consisting of many different modules works best if the individual Fig.…”

Section: Resultsmentioning

confidence: 99%

Existing bioinformatics tools for the quantitation of post-translational modifications

Allmer

2010

Amino Acids

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Mass spectrometry (MS)-based proteomics, by itself, is a vast and complex area encompassing various mass spectrometers, different spectra, and search result representations. When the aim is quantitation performed in different scanning modes at different MS levels, matters become additionally complex. Quantitation of post-translational modifications (PTM) represents the greatest challenge among these endeavors. Many different approaches to quantitation have been described and some of these can be directly applied to the quantitation of PTMs. The amount of data produced via MS, however, makes manual data interpretation impractical. Therefore, specialized software tools meet this challenge. Any software currently able to quantitate differentially labeled samples may theoretically be adapted to quantitate differential PTM expression among samples as well. Due to the heterogeneity of mass spectrometry-based proteomics; this review will focus on quantitation of PTM using liquid chromatography followed by one or more stages of mass spectrometry. Currently available free software, which either allow analysis of PTM or are easily adaptable for this purpose, is briefly reviewed in this paper. Selected studies, especially those related to phosphoproteomics, shall be used to highlight the current ability to quantitate PTMs.

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“…The software presented is furthermore suitable for label-free quantitation for any number of experiments thus also allowing analysis of time series which is important for the investigation of protein expression dynamics (Mintz et al 2008). The robustness of the results can be increased by providing peptides that can serve as standards.…”

Section: Resultsmentioning

confidence: 99%

“…The quantitation software, Serac, by Old et al (2005) for instance directly depends on a commercial software package. Other studies directly use commercial software packages for quantitation (Mintz et al 2008). Census (Park et al 2008) is a software for quantitation, currently more powerful than the one presented in this study, but with the drawback of working directly from measured data and therefore not as flexible in its application.…”

Section: Discussionmentioning

confidence: 99%

Label-free quantitation, an extension to 2DB

Allmer

2009

Amino Acids

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Determining the differential expression of proteins under different conditions is of major importance in proteomics. Since mass spectrometry-based proteomics is often used to quantify proteins, several labelling strategies have been developed. While these are generally more precise than label-free quantitation approaches, they imply specifically designed experiments which also require knowledge about peptides that are expected to be measured and need to be modified. We recently designed the 2DB database which aids storage, analysis, and publication of data from mass spectrometric experiments to identify proteins. This database can aid identifying peptides which can be used for quantitation. Here an extension to the database application, named MSMAG, is presented which allows for more detailed analysis of the distribution of peptides and their associated proteins over the fractions of an experiment. Furthermore, given several biological samples in the database, label-free quantitation can be performed. Thus, interesting proteins, which may warrant further investigation, can be identified en passant while performing high-throughput proteomics studies.

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Time Series Proteome Profiling To Study Endoplasmic Reticulum Stress Response

Cited by 32 publications

References 47 publications

Production of Anti-carbohydrate Antibodies by Phage Display Technologies

Production of Anti-carbohydrate Antibodies by Phage Display Technologies

Existing bioinformatics tools for the quantitation of post-translational modifications

Label-free quantitation, an extension to 2DB

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