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Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics

Overview of attention for article published in PeerJ, October 2016
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  • Good Attention Score compared to outputs of the same age (66th percentile)
  • Above-average Attention Score compared to outputs of the same age and source (51st percentile)

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Title
Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics
Published in
PeerJ, October 2016
DOI 10.7717/peerj.2603
Pubmed ID
Authors

Elena R. Schroeter, Caroline J. DeHart, Mary H. Schweitzer, Paul M. Thomas, Neil L. Kelleher

Abstract

Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different "extractomes" will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 66 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Japan 1 2%
Canada 1 2%
Unknown 64 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 15 23%
Student > Master 11 17%
Student > Bachelor 9 14%
Researcher 9 14%
Professor > Associate Professor 4 6%
Other 7 11%
Unknown 11 17%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 16 24%
Chemistry 9 14%
Agricultural and Biological Sciences 9 14%
Arts and Humanities 4 6%
Pharmacology, Toxicology and Pharmaceutical Science 3 5%
Other 13 20%
Unknown 12 18%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 4. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 03 November 2016.
All research outputs
#7,220,743
of 23,821,324 outputs
Outputs from PeerJ
#5,864
of 13,980 outputs
Outputs of similar age
#105,952
of 316,632 outputs
Outputs of similar age from PeerJ
#149
of 309 outputs
Altmetric has tracked 23,821,324 research outputs across all sources so far. This one has received more attention than most of these and is in the 69th percentile.
So far Altmetric has tracked 13,980 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 17.3. This one has gotten more attention than average, scoring higher than 57% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 316,632 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 66% of its contemporaries.
We're also able to compare this research output to 309 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 51% of its contemporaries.