Evidence map›Paper›PMID 16934998›Full record

ArticleJournal of the American Society for Mass Spectrometry2006

Extraction of local hydrogen exchange data from HDX CAD MS measurements by deconvolution of isotopic distributions of fragment ions.

Rinat R Abzalimov, Igor A Kaltashov

Abstract read
PubMed Publisher
In one paragraph

Article in Journal of the American Society for Mass Spectrometry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
1.4field-weighted citation impact, top 21% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 37 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Review
  6. Analytical Aspects of Hydrogen Exchange Mass Spectrometry.Annual review of analytical chemistry (Palo Alto, Calif.) · 2015
    Review
  7. Review
  8. Article
  9. Article
  10. Conformer-specific characterization of nonnative protein states using hydrogen exchange and top-down mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America · 2013
    Article
  11. HDX workbench: software for the analysis of H/D exchange MS data.Journal of the American Society for Mass Spectrometry · 2012
    Article
  12. Article
  13. Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. HD desktop: an integrated platform for the analysis and visualization of H/D exchange data.Journal of the American Society for Mass Spectrometry · 2009
    Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors at 1 institution in 1 country.

Rinat R AbzalimovDepartment of Chemistry, University of Massachusetts-Amherst, 710 North Pleasant Street, 01003, Amherst, MA, USA.
Igor A KaltashovDepartment of Chemistry, University of Massachusetts-Amherst, 710 North Pleasant Street, 01003, Amherst, MA, USA. kaltashov@chem.umass.edu.
University of Massachusetts Amherst · US

Funding

PROTEIN FOLDING DYNAMICS BY MASS SPECTROMETRYR01GM061666 · NIGMS · UNIVERSITY OF MASSACHUSETTS AMHERST · PI KALTASHOV, IGOR A · 2000 to 2013
$3.4M
NIGMS NIH HHS R01 GM061666
6 · The paper itself

Abstract

Hydrogen/deuterium exchange (HDX) coupled to protein fragmentation either in solution (by means of proteolysis) or in the gas phase (using collisional activation of protein ions) and followed by mass spectral measurements of deuterium content of individual fragments has become one of the major experimental tools to probe protein structure and dynamics. One difficulty, which often arises in the course of interpretation of HDX MS data, is a need to separate deuterium contribution to the observed isotopic patterns from that of naturally occurring isotopes. Another frequently encountered problem, especially when HDX in solution is followed by protein ion fragmentation in the gas phase, is a need to determine the deuterium content of an internal protein segment based on the measured isotopic distributions of overlapping fragments. While several algorithms were developed in the past several years to address the first problem, the second one did not enjoy as much attention. Here we report a new algorithm based on a maximum entropy principle, which is capable of extracting local exchange data form the isotope distribution of overlapping fragments, as well as subtracting the background due to the presence of natural isotopes and residual deuterium in exchange buffers. The new method is tested with several proteins and appears to generate stable solutions even under unfavorable circumstances, e.g., when the resolving power of a mass analyzer is not sufficient to avoid signal interference or when the isotopic distributions of individual fragments are complex and cannot be approximated with simple binomial distributions. The latter feature makes the algorithm particularly useful when the exchange in solution is correlated or semicorrelated, paving the way to precise structural characterization of non-native protein states in solution.

Indexed as

Deuterium Exchange MeasurementAlgorithmsHydrogenProtein ConformationProteinsSpectrometry, Mass, Electrospray IonizationUbiquitinHydrogenProteinsUbiquitin

Identifiers

PMID16934998
OpenAlexW2048923022

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.