Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein‐Profiling Technologies

Bruce, Can; Stone, Kathryn L.; Gulcicek, Erol E.; Williams, K. R.

doi:10.1002/0471250953.bi1321s41

Cited by 16 publications

(17 citation statements)

References 122 publications

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“…Also, a conservative search engine (Protein-Pilot) was applied in our studies, which was reflected by the very low FDR reported. It is known that the choice of search engine influences the detection of proteins (Bruce et al, 2013). Applying a search engine with a low FDR obviously decreases the number of positive hits (Elias and Gygi, 2007).…”

Section: Total Detection Of Proteins By 2d-lc-ms/msmentioning

confidence: 99%

Colostrum and milk protein rankings and ratios of importance to neonatal calf health using a proteomics approach

Nissen

Andersen

Bendixen

et al. 2017

Journal of Dairy Science

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Administration of colostrum to the newborn calf before gut closure is pivotal to its health, because of the transfer of passive immunity. Traditionally, passive immunity has been attributed to the transfer of immunoglobulins although it is increasingly clear that multiple other factors contribute, including innate immune proteins, developmental factors, immunomodulatory factors, and the presence of cellular immunity. The objective of this study was to produce a comprehensive comparison of the bovine colostrum proteome and the milk proteome by applying 2-dimensional liquid chromatography-tandem mass spectrometry. Further, the objectives were to rank proteins mutually and generate protein ratios from the spectral counts of the 2 proteomes and ELISA to gain insight into which proteins could be of most relevance to neonatal calf health. To obtain an in-depth picture of the bovine colostrum and milk proteome, we compared the contents of different fractions from bovine colostrum and milk from our 2 previous studies. A total of 140 colostrum fluid-phase proteins and 103 milk fluid-phase proteins were detected. In the cellular fraction, 324 and 310 proteins were detected in colostrum and milk, respectively. In total, 514 proteins were detected, of which 162 were in the fluid phase. Of these, 50 proteins were exclusively seen in colostrum, 13 were exclusively seen in milk, and 99 were common to colostrum and milk. Ranking of proteins mutually and calculating protein ratios based on spectral counts and ELISA resulted in new information on how proteins were associated with the fluid or cellular fraction of the samples. Interestingly, despite lower counts/concentrations than the classical proteins such as immunoglobulins, β-lactoglobulin, and lactotransferrin, several proteins appeared in higher or similar colostrum:milk spectral count ratios as these. Using this approach indicated, for example, that osteopontin, haptoglobin, milk amyloid A, and gelsolin may be interesting molecules to study in detail in their relation to calf health. Although the sensitivity, identification, and ranking of proteins varied between the 2 methods, and proteome analysis clearly suffers from low sensitivity, we believe that this idea and approach of generating ratios and ranking proteins can contribute new information and perspectives on how to prioritize the importance of multiple proteins, beyond immunoglobulins, in relation to neonatal calf health.

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Section: Total Detection Of Proteins By 2d-lc-ms/msmentioning

confidence: 99%

Colostrum and milk protein rankings and ratios of importance to neonatal calf health using a proteomics approach

Nissen

Andersen

Bendixen

et al. 2017

Journal of Dairy Science

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“…Comparison to a proteome database allows the assignment of the tandem mass spectrum to its most likely peptide sequence and, ultimately, parent protein of origin. 11,75,76 Despite successes, glycoproteomics remains challenging for a number of reasons. Glycosylation is a labile PTM and requires technical expertise to ensure that the glycan is preserved in its entirety during sample handling or during MS analysis.…”

Section: Glycosylation Is An Important Ptm That Influences Proteinmentioning

confidence: 99%

Chemical Glycoproteomics

Palaniappan

Bertozzi²

2016

Chem. Rev.

233

205

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Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.

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“…With recent advances in mass spectrometry technology, a single analysis can contain more than 100,000 tandem mass spectra, and a means to efficiently process the results becomes a necessity (Bruce et al., 2013). STRAP PTM is a software program with the capability to rapidly sift through large amounts of proteomics data in the search for differential PTMs based on spectral counting (Spencer et al, 2013a).…”

Section: Basic Protocolmentioning

confidence: 99%

STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post‐Translational Modifications

Spencer

Bhatia

Whelan

et al. 2013

CP in Bioinformatics

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The identification of protein post‐translational modifications (PTMs) is an increasingly important component of proteomics and biomarker discovery, but very few tools exist for performing fast and easy characterization of global PTM changes and differential comparison of PTMs across groups of data obtained from liquid chromatography–tandem mass spectrometry experiments. STRAP PTM (Software Tool for Rapid Annotation of Proteins: Post‐Translational Modification edition) is a program that was developed to facilitate the characterization of PTMs using spectral counting and a novel scoring algorithm to accelerate the identification of differential PTMs from complex data sets. The software facilitates multi‐sample comparison by collating, scoring, and ranking PTMs, and by summarizing data visually. The freely available software (beta release) installs on a PC and processes data in protXML format obtained from files parsed through the Trans‐Proteomic Pipeline. The easy‐to‐use interface allows examination of results at protein, peptide, and PTM levels, and the overall design offers tremendous flexibility that provides proteomics insight beyond simple assignment and counting. Curr. Protoc. Bioinform. 44:13.22.1‐13.22.36. © 2013 by John Wiley & Sons, Inc.

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Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein‐Profiling Technologies

Cited by 16 publications

References 122 publications

Colostrum and milk protein rankings and ratios of importance to neonatal calf health using a proteomics approach

Colostrum and milk protein rankings and ratios of importance to neonatal calf health using a proteomics approach

Chemical Glycoproteomics

STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post‐Translational Modifications

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