Page 15 - Oligonucleotide Therapeutics Solution Guide

Characteristic analysis
Quality Control

Sequence Confirmation MALDI-8020

Features
Simple Sequence Confirmation by
The MALDI-8020 is the latest in a long line of MALDI-TOF products from Shimadzu. It is used for quality control and profiling of peptides, proteins, Modification
MALDI-TOF MS polymers and oligonucleotides. In order to maintain equipment performance for a long period of time, even benchtop types use large diameter ion Target selection
optics to reduce the risk of ion stain reduction. In addition, it is equipped with a UV laser quick automatic ion source cleaning function (TrueClean)
click here that can clean the ion extraction electrode without dropping the vacuum. It also provides tools to centrally manage data and support strict
adherence to 21 CFR Part 11.

• Rapid and easy nucleic acid analysis is possible with minimal pretreatment.
• MALDI-ISD allows simple sequencing of synthetic nucleic acids. • Linear mode (positive ion) MALDI-TOF
benefits • Benchtop MS can be used with high maintainability and low running cost. • 200 Hz solid-state laser, 355 nm
• Load-lock chamber for fast sample introduction Excision
• UV laser-based source cleaning (Pat. US 10340131) Unprotected
Methods and Results • Small footprint/benchtop design Oligomer synthesis
• Quiet operation (<55 dB)
Sample 5’-CTGAGACACTGAAGGTAGGA-3’
Conc., Volume 100 pmol/µL, 10 µL
Preparation After activation with 1 N hydrochloric acid, approximately 200
µL slurry of cation exchange resin (Dowex 50 w 100-200 mesh,
Dow chemical) washed with water was added to the Empty
microspin column (BioRad), and the solution was removed by
gentle centrifugation. Then, 10 µL of the sample was added to
the Dowex cation exchange resin column prepared above, and Sample Target Solutions
the flow-through was recovered by centrifugation.
Mass 1 µL of the collected solution was deposited onto a MALDI target Compatible with the FlexiMass series of microscope slide-format sample targets, Purification
spectrometry plate, and the matrix solution (0.5 µL) was overlaid and dried.
Measurements were performed in the positive-ion mode. these slides provide researchers with options depending on their experimental
Results As a result of MS analysis, a singly-charged ion was detected at workflow.
m/z 6214.5 (Figure 1). The individually barcoded, single-use FlexiMass-DS slides provide a convenient
The ISD spectrum of the nucleic acid was obtained as shown solution for more routine or defined workflows. Ready-to-use, these disposable
in Figure 2. The ISD in the positive-ion mode measurement of
nucleic acid produces a very simple spectrum because of the targets eliminate the need for cleaning and the risk of carryover. Alternatively, the
preferential cleavage producing w-series ions (Figure 3). Figure 1 MALDI-TOF mass spectrum of the synthetic nucleic acid. reusable stainless steel FlexiMass-SR sample targets provide a cost-effective, longer-
Sequence information of the nucleic acid can be easily obtained term solution to sample preparation.
by assigning fragment ions of the ISD spectrum.

Automated Source Cleaning
TrueClean Quality Control

To maintain instrument performance over time, the MALDI-8020 features wide-bore ion optics Characteristic analysis
which minimize the risk of source contamination and provide a robust platform. TrueClean, an
automated source cleaning function, cleans the extraction electrode in-situ quickly within 10 min by
using UV laser without breaking instrument vacuum. DDS

Figure 2 MALDI-ISD mass spectrum with the annotation of w-series ions of the nucleic acid. Figure 3 Cleavage site by ISD Pharmacokinetics
High Quality with Low-running Cost Database Management
For improving product performance and the longevity, components Operating under the control of MALDI Solutions software, the
were carefully selected, which realized a robust platform capable of software features a centralized, secure Microsoft SQL database which
delivering outstanding performance in a small footprint. Simple design can be used to store everything from sample lists and acquisition
provides easy maintenance and contribute to maintaining the quality Parameter Sets to acquired MALDI data. The system is managed by
of analysis over time. an administrator and customizable user profiles provide control over
Conclusions access to the database and operation of the instrument. Along with a Other
full audit trail, the software provides the tools to help achieve 21 CFR
By using the benchtop MALDI-TOF MS “MALDI-8020 ” dedicated to positive linear mode, it is possible to easily confirm the molecular
part 11 regulatory compliance.
weight and sequence of nucleic acids.

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