Waters 2998 Operating manual

2998 Photodiode Array Detector
Overview and Maintenance Guide
715004753
Revision B Copyright © Waters Corporation 2015 – 2017
All rights reserved

December 5, 2017, 715004753 Rev. B
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General Information
Copyright notice
© 2015 – 2017 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF AMERICA
AND IN IRELAND. ALL RIGHTS RESERVED. THIS DOCUMENT OR PARTS THEREOF MAY
NOT BE REPRODUCED IN ANY FORM WITHOUT THE WRITTEN PERMISSION OF THE
PUBLISHER.
The information in this document is subject to change without notice and should not be construed
as a commitment by Waters Corporation. Waters Corporation assumes no responsibility for any
errors that may appear in this document. This document is believed to be complete and accurate
at the time of publication. In no event shall Waters Corporation be liable for incidental or
consequential damages in connection with, or arising from, its use. For the most recent revision of
this document, consult the Waters website (waters.com).
Trademarks
Waters, Waters Quality Parts, “THE SCIENCE OF WHAT’S POSSIBLE.”, ACQUITY, ACQUITY
Arc, Alliance, Empower, and MassLynx are registered trademarks of Waters
Corporation, and eSAT/IN and TaperSlit are trademarks of Waters Corporation.
PEEK is a trademark of Victrex PLC.
TWEEN is a trademark of ICI Americas Inc.
Tygon is a registered trademark of Saint-Gobain Performance Plastics Corporation.
All other trademarks are property of their respective owners.
Customer comments
Waters’ Technical Communications organization invites you to report any errors that you
encounter in this document or to suggest ideas for otherwise improving it. Help us better
understand what you expect from our documentation so that we can continuously improve its
accuracy and usability.
We seriously consider every customer comment we receive. You can reach us at
[email protected].

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Contacting Waters
Contact Waters with enhancement requests or technical questions regarding the use,
transportation, removal, or disposal of any Waters product. You can reach us via the Internet,
telephone, or conventional mail.
Safety considerations
Some reagents and samples used with Waters instruments and devices can pose chemical,
biological, or radiological hazards (or any combination thereof). You must know the potentially
hazardous effects of all substances you work with. Always follow Good Laboratory Practice (GLP),
and consult your organization’s standard operating procedures as well as your local requirements
for safety.
Safety hazard symbol notice
Documentation needs to be consulted in all cases where the symbol is used to find out the
nature of the potential hazard and any actions which have to be taken.
Considerations specific to the 2998 Photodiode Array Detector
Power cord replacement hazard
Waters contact information
Contacting medium Information
Internet The Waters Web site includes contact information for Waters
locations worldwide. Visit www.waters.com.
Telephone and fax From the USA or Canada, phone [phone], or fax
508-872-1990.
For other locations worldwide, phone and fax numbers appear in
the Waters Web site.
Conventional mail Waters Corporation
Global Support Services
34 Maple Street
Milford, MA 01757
USA
Warning: To avoid electric shock, use SVT-type power cords in the United States and
HAR-type (or better) cords in Europe. The power cords must be replaced only with ones of
adequate rating. For information regarding which cord to use in other countries, contact
your local Waters distributor.

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FCC radiation emissions notice
Changes or modifications not expressly approved by the party responsible for compliance, could
void the user's authority to operate the equipment. This device complies with Part 15 of the FCC
Rules. Operation is subject to the following two conditions: (1) this device may not cause harmful
interference, and (2) this device must accept any interference received, including interference that
may cause undesired operation.
Electrical power safety notice
Do not position the instrument so that it is difficult to disconnect the power cord.
Equipment misuse notice
If equipment is used in a manner not specified by its manufacturer, protections against personal
injury inherent in the equipment’s design can be rendered ineffective.
Safety advisories
Consult Appendix A for a comprehensive list of warning advisories and notices.
Operating this instrument
When operating the device, follow standard quality-control (QC) procedures and the guidelines
presented in this section.
Applicable symbols
Symbol Definition
Manufacturer
Date of manufacture
Authorized representative of the European Community
Confirms that a manufactured product complies with all applicable
European Community directives
or
Australia EMC compliant

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Audience and purpose
Tis guide is intended for personnel who install, operate, and maintain the Waters 2998 Photodiode
Array (PDA) detector.
Intended use of the 2998 Photodiode Array Detector
Waters designed the 2998 PDA detector to analyze and monitor various types of compounds. The
2998 PDA detector is not intended for use with in vitro diagnostic applications.
Calibrating
To calibrate LC systems, follow acceptable calibration methods using at least five standards to
generate a standard curve. The concentration range for standards must include the entire range of
QC samples, typical specimens, and atypical specimens.
Quality control
Routinely run three QC samples that represent subnormal, normal, and above-normal levels of a
compound. If sample trays are the same or very similar, vary the location of the QC samples in the
trays. Ensure that QC sample results fall within an acceptable range, and evaluate precision from
day to day and run to run. Data collected when QC samples are out of range might not be valid. Do
not report these data until you are certain that the instrument performs satisfactorily.
Confirms that a manufactured product complies with all applicable
United States and Canadian safety requirements
Consult instructions for use
Alternating current
Electrical and electronic equipment with this symbol may contain
hazardous substances and should not be disposed of as general
waste.
For compliance with the Waste Electrical and Electronic Equipment
Directive (WEEE) 2012/19/EU, contact Waters Corporation for the
correct disposal and recycling instructions.
Serial number
Part number catalog number
Symbol Definition
5()

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EMC considerations
Canada spectrum management emissions notice
This class A digital product apparatus complies with Canadian ICES-001.
Cet appareil numérique de la classe A est conforme à la norme NMB-001.
ISM Classification: ISM Group 1 Class B
This classification has been assigned in accordance with CISPR 11 Industrial Scientific and
Medical (ISM) instrument requirements.
Group 1 products apply to intentionally generated and/or used conductively coupled
radio-frequency energy that is necessary for the internal functioning of the equipment.
Class B products are suitable for use in both commercial and residential locations and can be
directly connected to a low voltage, power-supply network.
EC authorized representative
Waters Corporation
Stamford Avenue
Altrincham Road
Wilmslow SK9 4AX UK
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

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General Information ............................................................................................... iii
Copyright notice ......................................................................................................................... iii
Trademarks ................................................................................................................................ iii
Customer comments .................................................................................................................. iii
Contacting Waters ..................................................................................................................... iv
Safety considerations ................................................................................................................ iv
Safety hazard symbol notice........................................................................................ iv
Considerations specific to the 2998 Photodiode Array Detector ................................. iv
FCC radiation emissions notice .................................................................................... v
Electrical power safety notice ....................................................................................... v
Equipment misuse notice.............................................................................................. v
Safety advisories .......................................................................................................... v
Operating this instrument ............................................................................................................ v
Applicable symbols ....................................................................................................... v
Audience and purpose................................................................................................. vi
Intended use of the 2998 Photodiode Array Detector.................................................. vi
Calibrating.................................................................................................................... vi
Quality control.............................................................................................................. vi
EMC considerations .................................................................................................................. vii
Canada spectrum management emissions notice...................................................... vii
ISM Classification: ISM Group 1 Class B ................................................................... vii
EC authorized representative ................................................................................................... vii
1 2998 PDA Detector Optics Principles ................................................................. 15
1.1 Detector optics .......................................................................................................................... 15
1.1.1 Calculating absorbance ................................................................................................. 16
1.2 Flow cell operating principles .................................................................................................... 17
1.3 Resolving spectral data ............................................................................................................. 18
1.4 Measuring light at the photodiode array .................................................................................... 18
1.4.1 Optimizing the signal-to-noise ratio ............................................................................... 19
1.4.2 Selecting the appropriate sampling rate ........................................................................ 19
1.4.3 Filtering data .................................................................................................................. 20
1.5 Computing absorbance data points ........................................................................................... 22
1.5.1 Dark current ................................................................................................................... 23
Table of Contents

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1.5.2 Reference spectrum ...................................................................................................... 23
1.5.3 Data averaging .............................................................................................................. 23
1.5.4 Reference wavelength compensation............................................................................ 25
2 Setting Up the Detector ........................................................................................ 27
2.1 Before you begin ....................................................................................................................... 27
2.2 Unpacking and inspecting ......................................................................................................... 27
2.3 Selecting a laboratory site ......................................................................................................... 28
2.4 Stacking system modules .......................................................................................................... 28
2.5 Connecting to the electricity source .......................................................................................... 29
2.6 Connecting signal cables .......................................................................................................... 30
2.6.1 Connecting the Ethernet cable ...................................................................................... 32
2.6.2 Network installation guidelines ...................................................................................... 33
2.6.3 Connecting to other devices .......................................................................................... 34
2.7 Plumbing the 2998 PDA detector .............................................................................................. 38
2.7.1 Connecting the detector to the gas supply .................................................................... 39
2.8 Starting up and shutting down the 2998 PDA detector .............................................................. 40
2.8.1 Starting the detector....................................................................................................... 40
2.8.2 Monitoring LEDs ............................................................................................................ 41
2.8.3 Shutting down the detector ............................................................................................ 41
2.9 Using a cuvette .......................................................................................................................... 41
2.9.1 Before you begin............................................................................................................ 42
2.9.2 Cuvette measurement procedure .................................................................................. 42
3 Maintaining the Detector ...................................................................................... 45
3.1 Contacting Waters technical service ......................................................................................... 45
3.2 Maintenance considerations ...................................................................................................... 45
3.2.1 Safety and handling ....................................................................................................... 45
3.2.2 Spare parts..................................................................................................................... 46
3.3 Routine maintenance ................................................................................................................ 46
3.4 Maintaining the flow cell ............................................................................................................ 46
3.4.1 Flushing the flow cell ..................................................................................................... 47
3.4.2 Replacing the flow cell ................................................................................................... 47
3.5 Replacing the lamp .................................................................................................................... 49
3.6 Replacing the fuses ................................................................................................................... 51

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4 Diagnostic Tests and Troubleshooting ............................................................... 53
4.1 Diagnostic tests ......................................................................................................................... 53
4.1.1 Verifying the detector calibration.................................................................................... 53
4.1.2 How to read lamp energy............................................................................................... 54
4.1.3 Performing the erbium calibration.................................................................................. 54
4.1.4 How to read the calibration values................................................................................. 54
4.1.5 Displaying the rear-panel interface connections............................................................ 55
4.1.6 Changing the rear-panel interface connections ............................................................. 56
4.2 General troubleshooting ............................................................................................................ 56
4.2.1 Troubleshooting lamps................................................................................................... 56
4.2.2 Power surges................................................................................................................. 56
4.2.3 Clearing bubbles from the flow cell................................................................................ 57
4.2.4 Detector troubleshooting................................................................................................ 58
5 Spectral Contrast Theory ..................................................................................... 61
5.1 Comparing absorbance spectra ................................................................................................ 61
5.2 Representing spectra as vectors ............................................................................................... 62
5.2.1 Vectors derived from two wavelengths .......................................................................... 62
5.2.2 Vectors derived from multiple wavelengths ................................................................... 63
5.3 Spectral contrast angles ............................................................................................................ 63
5.3.1 Spectra with different shapes......................................................................................... 63
5.3.2 Differences between spectra of the same compound.................................................... 65
5.4 Undesirable effects .................................................................................................................... 65
5.4.1 Detector noise................................................................................................................ 66
5.4.2 Photometric error ........................................................................................................... 66
5.4.3 Solvent changes ............................................................................................................ 66
5.4.4 Threshold angle ............................................................................................................. 67
A Safety Advisories ................................................................................................. 69
A.1 Warning symbols ....................................................................................................................... 69
A.1.1 Specific warnings........................................................................................................... 70
A.2 Notices ...................................................................................................................................... 71
A.3 Bottles Prohibited symbol ......................................................................................................... 71
A.4 Required protection ................................................................................................................... 71
A.5 Warnings that apply to all Waters instruments and devices ...................................................... 72
A.6 Warnings that address the replacing of fuses ........................................................................... 75

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A.7 Electrical and handling symbols ................................................................................................ 76
A.7.1 Electrical symbols.......................................................................................................... 76
A.7.2 Handling symbols .......................................................................................................... 77
B Specifications ....................................................................................................... 79
B.1 Physical specifications .............................................................................................................. 79
B.2 Environmental specifications ..................................................................................................... 79
B.3 Electrical specifications ............................................................................................................. 79
B.4 Performance specifications ....................................................................................................... 80
B.5 Optical component specifications ............................................................................................. 81
B.6 Flow cell specifications ............................................................................................................. 82
C Solvent Considerations ....................................................................................... 83
C.1 Introduction ............................................................................................................................... 83
C.1.1 Clean solvents............................................................................................................... 83
C.1.2 Solvent quality............................................................................................................... 83
C.1.3 Preparation checklist..................................................................................................... 83
C.1.4 Water............................................................................................................................. 83
C.1.5 Use buffers.................................................................................................................... 84
C.1.6 Tetrahydrofuran ............................................................................................................. 84
C.2 Solvent miscibility ..................................................................................................................... 84
C.2.1 How to use miscibility numbers..................................................................................... 85
C.3 Buffered solvents ...................................................................................................................... 86
C.4 Head height .............................................................................................................................. 86
C.5 Minimum bend radius for tubing ............................................................................................... 86
C.6 Solvent viscosity ....................................................................................................................... 87
C.7 Mobile phase solvent degassing ............................................................................................... 87
C.7.1 Gas solubility................................................................................................................. 87
C.8 Solvent degassing methods ...................................................................................................... 88
C.8.1 Sparging ........................................................................................................................ 88
C.8.2 Vacuum degassing........................................................................................................ 88
C.8.3 Solvent degassing considerations................................................................................. 89
C.9 Wavelength selection ................................................................................................................ 89
C.9.1 UV cutoffs for common solvents.................................................................................... 89
C.9.2 Mixed mobile phases .................................................................................................... 90

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C.9.3 Wavelength selection for chromophore detection ......................................................... 91
C.9.4 Mobile phase absorbance ............................................................................................. 92

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12998 PDA Detector Optics
Principles
To use the 2998 Photodiode Array (PDA) detector effectively, you must understand the principles
that underlie operation of the detector’s optics and electronics.
1.1 Detector optics
The detector is an ultraviolet/visible light (UV/Vis) spectrophotometer. With a photodiode array of
512 photodiodes and an optical resolution of 1.2 nm/pixel, the detector operates within a range of
190 to 800 nm.
The figure below illustrates the light path through the optics assembly of the detector.
Figure 1–1: Optics assembly light path
The following table describes the optics assembly components.
TP02819
Grating
Photodiode
array
Spectrograph
mirror and mask
Flow cell
Window
Filter
flag/shutter
Lamp
Order
filter
M1 mirror Slit

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1.1.1 Calculating absorbance
The detector computes absorbance by subtracting the dark current (see “Dark current” on
page 23) from the reference spectrum (reference energy) and the acquired spectrum (sample
energy). Absorbance is based on the principles of Beer’s law.
1.1.1.1 Beer’s law
The Beer-Lambert law (commonly called Beer’s law) describes the relationship between the
quantity of light of a particular wavelength arriving at the photodiode and the concentration of the
sample passing through the flow cell. Beer’s law is expressed as A= lc where
A= dimensionless quantity measured in absorbance units
= constant of proportionality known as the molar absorptivity
l= path length in centimeters (1.0 cm in the detector’s normal flow cell)
c= concentration in moles per liter
Beer’s law applies only to well-equilibrated dilute solutions. It assumes that the refractive index of
the sample remains constant, that the light is monochromatic, and that no stray light reaches the
detector element. As concentration increases, the chemical and instrumental requirements of
Beer’s law are sometimes violated, resulting in a deviation from (absorbance versus
concentration) linearity. The absorbance of mobile phase can reduce the linear range.
Table 1–1: Optics assembly components
Component Function
Lamp Deuterium source lamp.
M1 mirror Focuses light from the deuterium source lamp.
Window Used to help minimize air infiltration into the lamp housing.
Filter flag/shutter Flag positions for measuring open (sample) and blocked (dark) beam
energies and a third for wavelength verification.
Flow cell Houses the segment of the flow path (containing eluent and sample)
through which the polychromatic light beam passes.
Spectrograph mirror and
mask
The mirror focuses light transmitted through the flow cell onto the slit
at the entrance to the spectrographic portion of the optics. The mirror
mask defines the size of the beam at the grating.
Slit Determines wavelength resolution and intensity of light striking the
photodiodes. The width of the slit is 50 µm.
Grating Disperses light into bands of wavelengths and focuses them onto the
plane of the photodiode array.
Order filter Reduces the contribution of second-order diffraction of UV light (less
than 370 nm) to the light intensity observed at visible wavelengths
(greater than 370).
Photodiode array A linear array of 512 photodiodes. The diode width (50 µm), together
with a 50-µm slit, yields single wavelength resolution of 1.2 nm.

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Figure 1–2: Absorbance as a function of concentration
1.2 Flow cell operating principles
The Waters®TaperSlit™ flow cell used in the PDA detector renders the detector baseline
essentially insensitive to changes in mobile phase refractive index (RI). RI changes occur during
gradient separations or result from temperature or pump-induced pressure fluctuations.
To achieve RI immunity, a combination of a spherical mirror, a lens at the entrance of the flow cell,
and a taper to the internal bore of the flow cell prevents light rays from striking the internal walls of
the flow cell. The Waters TaperSlit flow cell, so-called because of the shape of the flow cell exit
face, matches the shape of the spectrograph slit. Compared to a conventional flow cell with a
cylindrical shape, the PDA detector achieves higher light throughput for a given spectral resolution
with the TaperSlit cell design.
Figure 1–3: Comparison of flow cell characteristics:
Concentration
Absorbance
Ideal
Actual
Linear range for
analyte
Window
Window
UV light
Conventional flow cell:
TaperSlit analytical flow cell:
Window
Lens
UV light

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1.3 Resolving spectral data
Together with photodiode spacing, the detector’s 50-µm slit determines the intensity and
bandwidth of the light that strikes the photodiode array. Reducing the bandwidth increases the
resolving power of the detector. As a result, similar spectra are more effectively distinguished.
The grating images the slit onto the photodiode array. The angle of diffraction from the grating
determines the wavelength that strikes a particular photodiode in the array.
The following figure shows an absorbance spectrum of benzene. Note that the wavelength
resolution is sufficient to resolve five principal absorption peaks.
Figure 1–4: Benzene spectrum at different resolutions
1.4 Measuring light at the photodiode array
The detector measures the amount of light striking the photodiode array, to determine the
absorbance of the sample in the flow cell.
The array consists of a row of 512 photodiodes. Each photodiode acts as a capacitor initially
holding a fixed amount of charge.
Light striking a photodiode discharges the diode. The magnitude of the discharge depends on the
amount of light striking the photodiode.
Absorbance
nm
230.00 250.00 270.00
1.2 nm
3.6 nm

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Figure 1–5: Photodiodes discharged by light
The detector measures the amount of charge required to recharge each photodiode. The charge is
proportional to the amount of light transmitted through the flow cell over the interval specified by
the diode exposure time.
1.4.1 Optimizing the signal-to-noise ratio
To optimize signal-to-noise ratios, choose an acquisition wavelength range that includes only the
wavelengths of interest. It is also important that the range be one in which the mobile phase
absorbs only minimally. You can also improve the signal-to-noise ratio by increasing the spectral
resolution value. For example, you can choose to operate at 3.6 nm instead of at 1.2 nm
resolution. The signal-to-noise ratio is also affected by the filter-time constant and the sampling
rate.
1.4.2 Selecting the appropriate sampling rate
A sufficient number of points must fall across a peak, to define its shape. Thus the definition
between peaks is lost at very low sampling rates. Empower®uses the end time minus the start
time to calculate the points-across-peak value for each integrated peak in the chromatogram.
Tip: The points-across-peak value appears in the Peaks table, at the bottom of the Review Main
window. If the Points Across Peak field is not visible, right-click anywhere in the table, and then
click Table Properties. Click the Columns tab, and then scroll down to find the Points Across Peak
field. Clear the Points Across Peak check box, and then click OK.
If the points-across-peak value for the narrowest peak of interest is less than 25, specify a higher
sampling rate in the instrument method. If the value is greater than 50, specify a lower sampling
rate in the instrument method.
Mirror
Grating
Flow cell
Deuterium lamp
Light from grating
dispersed onto diodes.
Sample in flow cell
absorbs at specific
wavelengths.
Slit

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Figure 1–6: Example of how baseline noise increases with higher sampling rates
1.4.3 Filtering data
On the General tab of the PDA Instrument Method Editor you can apply an optional noise filter to
the data acquired.
See also: the Empower or MassLynx®online Help.
The detector uses a Hamming filter to minimize noise. The filter is a digital finite-impulse-response
filter that creates peak-height degradation and enhances the filtering of high frequency noise.
The performance of the filter depends on the filter-time constant that you select. Increasing the
filter-time constant reduces baseline noise, improving the signal-to-noise ratio. Nevertheless,
increasing the constant too much artificially broadens a peak and reduces chromatographic
resolution.
You can choose among these options when programming a filtering time: Fast, Slow, Normal, or
Other. If you select a fast, slow, or normal filtering time, you need not specify a value, because the
filtering constant is determined by the sampling rate. If you select the Other option, you can specify
a value. Nevertheless, the value that you specify is rounded up or down to a value based on the
sampling rate. Selecting Other and entering a value of 0.0 disables all filtering.
5 Hz
10 Hz
20 Hz
40 Hz