Background -- The instrument
is really two intrumental modules combined to make one very powerful
analytical tool, managed by software called, MassLynx. The opening
screen for MassLynx software used for instrument
control and data analysis is shown at the left. There
are several modules.
The first module is a high-performance liquid
chromatograph (HPLC). Waters Alliance 2690 Separations Module
has the following capabilities:
HPLC is a chemistry based tool for quantifying
and analyzing mixtures of chemical compounds. It's used to find
the amount of a chemical compound within a mixture of other chemicals.
An example would be to find out how much caffeine there is in
the cup of coffee (or tea, or cola). First dissolve the sample
in a solvent (like water or alcohol), thus the term LIQUID chromatography
and then a detector measures response changes between the solvent
itself, and the solvent plus the sample when passing through.
The electrical response is digitized and sent to a data system.
A solvent delivery System - pushes the solvent
stream through the instrument at constant flow rate
into a column - a stainless steel tube packed with silicon beads
that separates an analyte
(the caffeine) from other compounds (like sugar), a detector -
or an optical sensor that detects changes in the characteristics
of the solvent stream, plus a data system which controls the system
components followed by storing, processing, and displaying data.
In a liquid chromatographic process a liquid permeates through
a porous solid stationary phase and elutes the solutes into a
The stationary phase is usually in the form
of small-diameter (5-10 mm) uniform particles, packed into a cylindrical
column. The typical column is constructed
from a rigid material (such as stainless steel or plastic) and
is generally 5-30 cm long and the internal diameter is in the
range of 1-9 mm. Column - A tube which contains the stationary
phase. The stationary phase differentially interacts with the
sample's constituent compounds as they are carried along in the
mobile phase. The most efficient columns produce the sharpest
peaks, which gives better separation by minimizing band spreading.
A tight narrow sample "band" is produced when a columns'
stationary phase is uniformly packed (mechanical). The packing
material adds "chemical" band spreading (tailing, pore
An other Detector
(in series or parallel to the MS) is a UV/VIS: Waters 996 photodiode
array detector. Detector - Instrument in the chromatographic system
which senses the presence of a compound passing through, and provides
an electronic signal to a recorder or computer data station. Output
is usually peaks, that is, the chromatogram. The detector consists
o UV Ultraviolet light
o Grating/Lens - Wave length
The Waters integrated system allows identification
of peaks in HPLC separations. It separates complex mixtures and
identifies peaks of interest. The integrated photodiode array
(PDA) detection and mass spec detection is the heart of the unit.
The combination PDA and MS data from a single HPLC injection for
productes positive compound identification. The PDA detector also
helps to ascertain peak homogeneity. Each chromatographic peak
generates a positive Electron Ionization (EI) mass spectra. These
spectra are characteristic "fingerprints" for compounds,
which, unlike ambiguous molecular weight information, can identify
compounds. Automated library search for compounds to match both
mass spec and PDA spectra against commercially available and/or
user libraries for sample identification of analysis.
The MASSLYNX.INI file contains current settings
for all MassLynx windows and dialog
boxes. When a new user logs on a new Username.INI file is created.
Each time this user uses MassLynx any changes to the current settings
are saved to this file. It is possible under some conditions that
one of the settings in Username.INI may become corrupted causing
problems with the operation of MassLynx. A default INI file is
present in the C:\MASSLYNX directory saved under the name MASSLYNX.SAV.
In cases where the INI file has become corrupted this backup file
can be copied to Username.INI to restore a set of uncorrupted
To restore MASSLYNX.SAV using Windows Explorer
1. Save any parameter files needed in MassLynx e.g. tuning
2. Close down MassLynx.
3. Press Start button, choose Windows NT Explorer from the Programs
4. Select the MassLynx directory
5. Highlight the MASSLYNX.SAV file and select Copy from the Edit
6. Choose Paste from the Edit menu. This
will give a file called Copy of MassLynx.sav.
Delete the USERNAME.INI file , e.g. Administrator.ini,
and select the copy of Masslynx.sav. Click on the name of the
file until a rectangular box appears around the name, then type
in USERNAME.INI, or choose rename from the Edit menu.
8. Restart MassLynx.
9. This will set the MassLynx system, for this user, back to a
default state, for example the current raw data file will be V50 etc.
A nitrogen generator is used to produce a constant supply of high purity gas to the
instrument. The nitrogen generator is an alternative to traditional
gas supply (cylinders, or Dewars of liquid nitrogen).
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