Many factors influence H/DX such as temperature, pH, salt, and buffer composition (18). As a result, in a typical H/DX–MS
experiment, the exchange reaction is carried out under conditions where these and other factors are well controlled (see Figure
2). The most common type of H/DX experiment is a continuous–labeling experiment where deuterium is added in 10– to 20–fold
excess, and the reaction is allowed to incubate. As the reaction incubates, aliquots are removed over time (usually ranging
from 10 s to more than 8 h) from the reaction and quenched to slow the labeling reaction. To quench the labeling, the pH is
reduced to 2.5–2.6, where the hydrogen–exchange rate for a typical backbone amide is at a minimum (18). For the average backbone
amide hydrogen, dropping the pH from 7.0 to 2.5–2.6 reduces the exchange by 4 orders of magnitude. In addition, lowering the
temperature from 25 °C to 0 °C reduces the rate of exchange by another order of magnitude (18).
Figure 2: A schematic representation of the workflow for a continuous labeling H/DX–MS experiment (arrows indicate the order
in which each step in an H/DX-MS experiment is carried out). In the initial step, a protein solution is incubated at ambient
temperature in its formulated buffer. The protein is then diluted ~20 fold with deuterated formulation buffer. The protein
is then incubated and at predetermined time points, a sample is taken from the reaction and quenched by dropping the pH to
~2.5-2.6 and the temperature to 0 °C. This quenched protein is then digested with an acidic protease (pepsin), and the resulting
peptides are separated at 0 °C under acidic conditions chromatographically before they are introduced into the mass spectrometer.
The mass of each peptide is determined for each deuterium time point, and the deuterium incorporation is plotted versus time.
If the structure of the protein is known, it can be plotted onto this structure, otherwise different data analysis and display
formats can be used to interpret the H/DX–MS data.
The insertion of a digestion step just after quenching (17), but prior to LC–MS (see Figure 2) cuts the protein into smaller
pieces (peptides). During the digestion step, quench conditions must be maintained to preserve the deuterium label; therefore
an acid protease (usually pepsin) is used for proteolytic digestion. After digestion, the peptic peptides are separated by
reversed phase LC, and the mass of each peptide is measured by the mass spectrometer. Both digestion and chromatographic separation
steps are carried out on–line. The reversed phase chromatography step not only functions to separate peptides, it also serves
the important function of removing buffer salts and other excipients not compatible with MS.
Following the chromatographic separation, the peptides are analyzed by mass spectrometry, and the amount and location of the
deuterium are determined (electrospray is most commonly used, although MALDI has also been used (21)). Typically, the protein
and amino-acid sequence are known, and the resulting pepsin peptides are unambiguously identified by tandem MS. The solvent
used in the digestion and chromatography steps are pure (100%) H2 O. As a result, deuterium that was incorporated in the protein starts to exchange back to hydrogen during these steps. To
minimize this, and to supply enough time for analysis, the temperature of the quench, digestion, and separation steps is dropped,
and the chromatography is done as quickly as possible under acidic pH conditions. At 0 °C and pH 2.5–2.6, in a properly controlled
experiment, only about 20%–30% of the deuterium is lost during analysis. If desired, control experiments can be performed
to correct for this loss (17).
Using the deuterium uptake information, a comparison study can be conducted on a protein and its variant forms (i.e., a protein
with and without different oligosaccharides). The main feature monitored in such comparisons is the difference in the locations
and extent of deuterium incorporation as a function of time. These results provide indirect information concerning conformational
changes in the polypeptide backbone of a protein as a result of a PTM. We have noted that protein deglycosylation can result
in greater deuterium incorporation in some areas, and less in others.