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X Demographics
Mendeley readers
Attention Score in Context
| Title |
QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure
|
|---|---|
| Published in |
BMC Bioinformatics, December 2014
|
| DOI | 10.1186/s12859-014-0403-1 |
| Pubmed ID | |
| Authors |
Joseph P Salisbury, Qian Liu, Jeffrey N Agar |
| Abstract |
BackgroundHydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13. Recent studies demonstrated that high-performance mass spectrometers could resolve isotopic fine structure and eliminate this peak overlap, allowing direct detection and quantification of deuterium incorporation.ResultsHere, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure. Given a peptide sequence (or elemental formula) and charge state, the mass-to-charge ratios of deuterium-associated peaks of the specified ion is determined. Intensities of peaks in an experimental mass spectrum within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated based on the estimated distribution of deuterium exchange to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter. A tool is also incorporated into QUDeX-MS to help in assigning ion signals from peptides arising from enzymatic digestion of proteins. MATLAB-deployable and standalone versions are available for academic use at qudex-ms.sourceforge.net and agarlabs.com.ConclusionIsotopic fine structure HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mass accuracy and deconvolution of overlapping ion signals. As previously demonstrated, however, the data analysis workflow for HDX-MS data with resolved isotopic fine structure is distinct. QUDeX-MS we hope will aid in the adoption of isotopic fine structure HDX-MS by providing an intuitive workflow and interface for data analysis. |
X Demographics
The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Norway | 1 | 50% |
| Unknown | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 1 | 50% |
| Members of the public | 1 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 26 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Germany | 1 | 4% |
| Unknown | 25 | 96% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 7 | 27% |
| Student > Ph. D. Student | 6 | 23% |
| Student > Bachelor | 3 | 12% |
| Other | 3 | 12% |
| Student > Master | 2 | 8% |
| Other | 3 | 12% |
| Unknown | 2 | 8% |
| Readers by discipline | Count | As % |
|---|---|---|
| Chemistry | 7 | 27% |
| Biochemistry, Genetics and Molecular Biology | 5 | 19% |
| Agricultural and Biological Sciences | 4 | 15% |
| Computer Science | 3 | 12% |
| Engineering | 2 | 8% |
| Other | 2 | 8% |
| Unknown | 3 | 12% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. 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 11 December 2014.
All research outputs
#18,345,702
of 23,577,761 outputs
Outputs from BMC Bioinformatics
#6,094
of 7,418 outputs
Outputs of similar age
#252,071
of 365,150 outputs
Outputs of similar age from BMC Bioinformatics
#110
of 135 outputs
Altmetric has tracked 23,577,761 research outputs across all sources so far. This one is in the 19th percentile – i.e., 19% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,418 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one is in the 12th percentile – i.e., 12% of its peers scored the same or lower than it.
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 365,150 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 27th percentile – i.e., 27% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 135 others from the same source and published within six weeks on either side of this one. This one is in the 9th percentile – i.e., 9% of its contemporaries scored the same or lower than it.