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HS20-22 User’s Manual V1.2

Document Control

Author

Systems Engineer

Review Panel

Test and Installation Manager

Sales Administrator

Technical Director

Version History

Version Author Notes Date

1.0 NL Draft June 2013

1.1 DJMC Release Aug 2013

1.2 BSLC Update Sept 2013

2.0 JOC Release March 2018

Sercon operate a policy of continuous product development and therefore reserve the right to

alter product design and specifications without prior notice.

The names of various manufacturers, their instruments and their products referred to herein

may be protected by trademark or other law, and are used herein solely for purpose of

reference.

Sercon expressly disclaims any affiliation with them or sponsorship by them.

Registered Office:

Sercon Ltd

Unit 3B Crewe Trade Park

Gateway, Crewe

Cheshire

CW1 6JT

Registered in England and Wales No 4290072

VAT Registration No GB771 1100 74


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Contents

1. INTRODUCTION ............................................................................................................................. 4

1.1 STABLE ISOTOPE MEASUREMENT NOTATION ..................................................................................... 5 1.2 STABLE ISOTOPE STANDARDS ........................................................................................................... 5

2. PRINCIPLE OF OPERATION ......................................................................................................... 7

2.1 SAMPLE INLETS ................................................................................................................................ 7 Dual Inlet .......................................................................................................................................... 8 Split Continuous Flow ...................................................................................................................... 8

2.2 ION SOURCE .................................................................................................................................... 9 Source Control ............................................................................................................................... 11 HT .................................................................................................................................................. 11 Half Plates ..................................................................................................................................... 12 Focus ............................................................................................................................................. 12 Trap ............................................................................................................................................... 12 eV .................................................................................................................................................. 12 IR ................................................................................................................................................... 12 Emission ........................................................................................................................................ 12

2.3 MAGNETIC SECTOR ........................................................................................................................ 13 Isotopic Separation ........................................................................................................................ 13 Mass Range................................................................................................................................... 14 Ion Beam Focus ............................................................................................................................ 14

2.4 COLLECTOR ARRAYS...................................................................................................................... 15 2.5 STANDARD AND UNIVERSAL COLLECTOR ARRAYS ............................................................................ 16 2.6 HYDROGEN COLLECTOR ................................................................................................................. 16 2.7 HEAD AMPLIFIERS .......................................................................................................................... 17 2.8 VACUUM SYSTEM ........................................................................................................................... 17

3. SERCON HS20-22 SYSTEM OVERVIEW .................................................................................... 19

3.1 MAIN POWER MODULE SWITCHES................................................................................................... 19 3.2 SYSTEM CONTROLLER ................................................................................................................... 19 3.3 FLIGHT TUBE ................................................................................................................................. 20 3.4 MAGNET ........................................................................................................................................ 20

Switching between magnet settings .............................................................................................. 21 3.5 VALVES AND TRAPPING LOOP ......................................................................................................... 21

Isolation valves .............................................................................................................................. 22 Reference Gas System ................................................................................................................. 22 Trapping Loop................................................................................................................................ 23

4. GETTING STARTED ..................................................................................................................... 24

4.1 STANDBY MODE ............................................................................................................................. 24 4.2 BACKGROUND SCAN ....................................................................................................................... 24 4.3 INTRODUCTION TO PEAK SHAPES AND STABILITY ............................................................................. 26 4.4 DAILY TUNING ................................................................................................................................ 28 4.5 TUNING THE SOURCE FOR SULPHUR ANALYSIS ................................................................................ 30 4.6 TUNING THE SOURCE FOR HYDROGEN ANALYSIS ............................................................................. 31 4.7 ADVANCED TUNING ........................................................................................................................ 32

5. REFERENCE GAS PULSES ........................................................................................................ 33

5.1 PRECISION TEST ............................................................................................................................ 33 5.2 LINEARITY TEST ............................................................................................................................. 34


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6. MAINTENANCE ............................................................................................................................ 35

6.1 VENTING AND PUMPING THE HS20-22 ............................................................................................ 35 Venting ........................................................................................................................................... 35 Pumping ......................................................................................................................................... 35

6.2 ROTARY PUMPS ............................................................................................................................. 35 Oil Change ..................................................................................................................................... 35 Ballasting ....................................................................................................................................... 36

6.3 CHANGING THE FILAMENT ............................................................................................................... 36 6.4 CONDITIONING THE FILAMENT ......................................................................................................... 46 6.5 CLEANING THE SOURCE ................................................................................................................. 46 6.6 SOURCE ASSEMBLY LISTING ........................................................................................................... 48

7. TROUBLESHOOTING .................................................................................................................. 49

7.1 INSTRUMENT WILL NOT SWITCH ON: ............................................................................................... 49 7.2 TURBO PUMPS WILL NOT ACTIVATE: ............................................................................................... 49 7.3 VACUUM WILL NOT REACH 1E-6MBAR: ............................................................................................. 49 7.4 VACUUM WILL NOT REACH 1E-8MBAR: ............................................................................................. 49 7.5 PUMPING SYSTEM NOISY OR ERRATIC ............................................................................................ 50 7.6 INCORRECT SOURCE PRESSURE ..................................................................................................... 50 7.7 OIL LEAKING FROM ROTARY PUMP .................................................................................................. 50 7.8 VALVES NOT ACTIVATING ............................................................................................................... 50 7.9 NO TRAP CURRENT ........................................................................................................................ 50 7.10 TRAP NOT REACHING SET POINT .................................................................................................. 51 7.11 NO HT OR INCORRECT HT ........................................................................................................... 51 7.12 NO SAMPLE PEAKS ...................................................................................................................... 51 7.13 LOW SENSITIVITY/SMALL PEAKS ................................................................................................... 51 7.14 SOFTWARE ERROR ...................................................................................................................... 51 7.15 COMMUNICATIONS ERROR/ANALYSER NOT RESPONDING .............................................................. 51 7.16 HIGH BACKGROUND ..................................................................................................................... 52 7.17 NOISY OR UNSTABLE 2/1 RATIO .................................................................................................... 52 7.18 MISSING BEAM(S) ........................................................................................................................ 53


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1. Introduction

The Sercon HS20-22 Isotope Ratio Mass Spectrometer (IRMS) is designed for the precise

measurement of the total element content and stable isotope ratio in a wide variety of gases

i.e. H2, N2, NO, N2O, O2, CO, CO2,CH4,SO and SO2. The Sercon HS20-22 IRMS uses novel

120˚ ion optics to give improved sensitivity for both continuous flow and dual inlet applications

and can be coupled with a wide variety of preparation systems to facilitate the measurement

of isotopes in a wide range of materials. The Sercon HS20-22 is fitted with a reference gas

injection port for easy source tuning and has the option of a trapping loop to capture gases

that the user may not want bottles of in the laboratory.

Figure 1-1: The Sercon HS20-22 Isotope Ratio Mass Spectrometer

The Sercon HS20-22, shown in Figure 1-1, forms the analyser stage of a modular stable

isotope system and can be fitted with up to 4 inlets for multiple sample preparation systems.

Available applications include:

Sercon Cyroprep – for the analysis of N2, NO, N2O, O2, CO, CH4 and CO2 at

atmospheric concentrations.

Sercon EA – gas, solid and liquid sample analysis.

Sercon NCS – for simultaneous analysis of nitrogen, carbon and sulphur from one solid

sample.

GEO – Dual inlet system (including carbonates and water samples).

GC-CP – For compound specific work.

HT-EA – Pyrolysis of solid and liquid samples.

TIC/TOC/TON – Carbon and nitrogen from water samples.

LCI – Liquid chromatograph interface.

The Sercon HS20-22 and prep systems are controlled by the Callisto software. It is designed

to control the available functions of the mass spectrometer and preparation systems, collect

data and process it to give the isotopic enrichment of the samples with respect to international

standards.


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1.1 Stable Isotope Measurement Notation

An IRMS measures the ratio of a stable isotope in a sample with respect to a standard

reference sample. It is difficult to measure the absolute abundance of the isotopes within a

sample because of the small differences being measured and problems such as sample

heterogeneity, sample preparation and fractionation within the preparation system. To

compensate for these variables, the isotope ratio for a sample (Rs) is measured with respect

to the ratio measured for a standard (Rstd), which is analysed in exactly the same way. The

ratio, R is defined as the ratio of heavy to light isotope. The differences in the isotopic ratios of

the sample and standard are calculated in delta, δ notation by

𝛿(‰) = [(𝑅𝑠

𝑅𝑠𝑡𝑑) − 1] × 1000

and has units of per mil or ‰.

The isotopic abundance, A, is calculated from the measured δ value and the absolute ratio of

the standard material, Rstd-abs by

𝐴 =100

[1

((𝛿 1000 ⁄ ) + 1)𝑅𝑠𝑡𝑑−𝑎𝑏𝑠] + 1

and is expressed as Atom %.

1.2 Stable isotope standards

All standards for nitrogen analysis are compared to atmospheric nitrogen which has a 15N/14N

ratio of 0.0036765. The natural abundance of 15N is 0.3663 atom % and 99.6337 atom % for 14N. A sample with less 15N than natural abundance (‘depleted’) will have a δ value of less than

1 while one with a greater amount (‘enriched’) will have a δ value greater than 1.

Most of the standards used for carbon analysis are compared to Pee Dee Belemnite (PDB)

which has a 13C/12C ratio 0.0112372. Canyon Diablo Triolite (CDT) is the isotopic standard for

sulphur and Vienna-Standard Mean Ocean Water (vSMOW) is the isotopic standard for

deuterium and oxygen. The ratio values for these primary reference standards are given in

Table 1-1.

Table 1-1: Isotopic ratios for primary reference standards

Reference Standard Isotope Isotope Ratio

V-SMOW 2H/1H 0.00015576

V-SMOW 18O/16O 0.00200520

PDB 13C/12C 0.0112372

PDB 18O/16O 0.0020671

Atmospheric N2 15N/14N 0.0036765

CDT 34S/32S 0.0450045


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As the majority of the primary reference standards are exhausted or in severely limited supply,

most laboratories use secondary or tertiary reference standards. For example, global supplies

of VSMOW are now exhausted so VSMOW2 must now be used. A secondary standard is one

that has been calibrated against a primary standard. A tertiary standard is one that has been

calibrated against a secondary standard and so on.

For convenience and consistency in analysing and reporting data, the IAEA calibrates and

distributes a range of secondary standards.

Table 1-2- Delta values, δ, for isotopic standards distributed by the IAEA.

Reference

Designation

Reference

Material

13C ‰

vs. PDB

15N ‰

vs. Air

34S ‰

vs. CDT

2H ‰ vs.

SMOW

18O ‰ vs.

SMOW

IAEA-N1 Ammonium

Sulphate - 0.40 - - -

NBS-127 Barium

Sulphate - - 20.30 - 9.30

NBS-30 Biotite - - - -66.00 5.10

NBS-19 Calcium

Carbonate 1.95 - - - -2.20

NBS-18 Carbonatite - - - - 27.42

NBS-22 Oil -29.81 - - -118.50 -

PEF-1 Poly-

ethylene -31.80 - - -100.30 -

IAEA-

NZ1/S1 Silver Sulphide - - -0.30 - -

IAEA-

NZ2/S2 Silver Sulphide - - 21.50 - -

IAEA-CH6

(ANU) Sucrose -10.40 - - - -

SLAP Water - - - -189.70 -24.80

GISP Water - - - -428.00 -55.50


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2. Principle of Operation

Each stage of the process from the sample entering the IRMS via the sample inlet to the

processing of data is described in detail in this chapter. A schematic of the Sercon HS20-22

mass spectrometer is shown in Figure 2-1.

Figure 2-1: A schematic of the Sercon HS20-22 IRMS

A schematic of the Sercon HS20-22 IRMS as seen from above. The gaseous sample passes

into the HS20-22 via the Sample Inlet, either in a stream of helium from a continuous flow

preparation unit or as sample gas from a dual inlet system. Once inside the ion source, the

sample gas is ionised and accelerated through an electrostatic potential into a narrow beam

of positively ionised molecules of a specific energy. This beam enters the magnetic sector of

the IRMS where it is split spatially into components of different molecular weights. The

component beams are focussed onto the faraday-cup collector arrays and the positive charge

of the ions produces an electric current which is amplified and passed to the data system.

2.1 Sample Inlets

There are two types of sample inlet systems available for the Sercon HS20-22 IRMS; the Dual

Inlet and Continuous Flow Split. The Dual Inlet is used in conjunction with the Geo preparation

unit for small samples and the Continuous Flow Split is used with preparation systems such

as the Sercon GSL and Cryoprep.


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Dual Inlet

The principle of a dual inlet is that a pure sample gas and pure reference gas are allowed into

variable volume bellows which are attached to the ion source inlet line via a switching or

change-over valve. This is shown schematically in Figure 2-2 below. During analysis, gas from

either the sample or reference is allowed to enter the ion source. The bellows that contain the

gases can be compressed or expanded such that both the sample and reference gas enter the

ion source at exactly the same pressure with the desired ion intensity. The source pressure is

determined by a crimp on either side restricting the gas flow.

Figure 2-2: A schematic of the dual inlet system.

For Sercon IRMS HS20-22 units fitted with Dual inlet capability the change-over block is

positioned on the IRMS HS20-22 unit next to the source block with a direct link into the ion

source.

Split Continuous Flow

A schematic of the continuous flow open-split inlet is shown in Figure 2-3. The continuous flow

split works by passing a continuous flow of helium past a restricted pathway to the ion source.

The helium carries the sample gas from a sample preparation system such as a GC or

elemental analyser. The helium carrier flow from the preparation unit can range from 1 to > 60

ml/min but the flow into the IRMS is only 0.07 ml/min and is set by a physical restriction or

crimp in the inlet capillary.

Figure 2-3: A schematic of the split inlet system.

The HS20-22 can be fitted with multiple continuous flow open split inlets depending on the

number of preparation units operating with the same IRMS.


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2.2 Ion Source

The Sercon ion source uses a type of ionisation is known as electron impact. The sample gas

is directed through an electron beam where it is ionised and then accelerated by an electric

field, as shown in Figure 2-4.

Figure 2-4: A simplified diagram of electron impact ionisation inside an ion source.

A detailed schematic of a Sercon ion source is represented in Figure 2-5. Inside the ion source,

the electron beam is formed by heating a wire filament (F), made from iridium coated in thoria,

to liberate electrons. The electrons are focused into a tight beam by a magnetic field created

by the Source Magnets (M). The electrons impact with the sample gas molecules, stripping off

an electron and forming positive ions. The ions are kicked into a region of high electrical field

by an ion repeller (IR). In the high electrical field, the ions are accelerated out of the ion source

through a series of focusing lenses (electrical). The ion beam exits the ion source through the

exit slit before entering the magnetic region of the mass spectrometer.

The atomic mass and concentration of the molecules that are being analysed will determine

the ion source conditions. If the gas is of a low concentration, more ions will need to be

produced; therefore, more electrons will need to be generated by the filament (F). The current

passed through the filament set by adjusting the Trap (T) current.


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Figure 2-5: A schematic diagram of Sercon Ion Source,

F – Filament.

T - Trap.

M - Magnets to collimate electron beam.

H1, H2 - Half plates, or ‘beam focus’. These help to draw out ions from the source box

and change focusing conditions.

S - Source slits act as collimators and are held at 0V.

A - Alpha Slit acts in conjunction with S as a collimator. It is so called as it constrains

the dispersive angle with which the ions may enter the mass spectrometer. It is held at

0V.

R - Repeller Plate is so called because it was traditionally used to repel ions toward the

ion exit slit. It is now more important in dispelling space charge effects within the source

block. When it is negative with respect to the source voltage, it attracts ions.

f - This is the focal object plane of the mass spectrometer, the point at which all ions

must appear if they are to be focused to a tight spot at the collector.


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Source Control

The source is controlled by the Callisto software in the Source Control Window, where the

source tuning parameters are set to the appropriate voltages and currents to obtain a stable

ion beam. The computer sends the set values to the microprocessors in the System Controller

which ultimately controls the voltages and currents at the source block. With the computer

disconnected, the source control will run independently at the last set values.

Figure 2-6: Ion Source Control

Figure 2-6 shows the Callisto ion source control window. The following source parameters can

be adjusted:

1. Acceleration Voltage (HT) - Sets the voltage of the source block (Vs).

2. Half Plates (HP) - Sets a differential voltage across the two half plates.

3. Focus - Sets the voltage of the half plates with respect to ground.

4. Trap Current- Controls the flux of electrons through the source chamber.

5. Electron Energy (eV) - Sets the voltage between the filament and the source block.

6. Ion Repeller (IR) - Sets the voltage difference between the ion repeller and source

block.

The Emission box is a readback and cannot be adjusted.

HT

High Tension refers to the voltage applied to the source block to give the charged ions enough

kinetic energy to pass through the magnetic field in the flight tube (maximum 5kV). The lower

the mass of the ion, the higher the voltage needed to get it round the flight tube to the collectors.

This is why N2 (masses 28, 29 and 30) needs a higher voltage than CO2 (masses 44, 45 and

46).

N.B. All other voltages in the source are set with respect to the HT.


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Half Plates

The two half plates are positioned just outside the source block in the direction of travel for the

ions. The voltages to them can be controlled independently and a potential difference between

the half plates can be used to steer the ion beam to the left or right after it has exited the source

slit.

Focus

Also known as the Accelerating Voltage, this is the mean voltage of then two half plates and

is a presented as a percentage of the HT. The potential difference between the source block

and the half plates accelerates the ions out of the source. If the Focus is set to 89, this means

that the voltage on the half plates is 89% of the HT.

Trap

Sometimes known as Electron Current or EC, the trap is on the opposite side of the source

block from the filament and consists of a small plate that is hit by the electrons that pass straight

through the source block without hitting a molecule of sample gas. These electrons form a

current that is measured in micro amps (μA) and forms a feedback loop that regulates the

filament current, i.e. if the trap current is changed from 150μA to 300μA, the filament current

is increased until the number of electrons hitting the trap plate produces a current of 300μA. If

the desired trap current cannot be reached, the filament’s ‘limit’ has been reached.

eV

Electron Volts. This negative voltage is applied to the filament and pushes the electrons

towards the source block and the trap. Because the voltage is with respect to the HT, an HT

setting of 4000V and an eV setting of -80V means that the actual voltage across the filament

is 3920V.

IR

Ion Repeller. The ion repeller acts together with the half plates as an electrostatic lens to focus

the ion beam. If the IR is set to -3 and the HT is set to 4000V, then the voltage on the ion

repeller is actually 3997V. IR settings can have a large effect on the source linearity and for

CO2, CO, SO2 and N2 are generally from -5 to +5V. For H2, however, the IR is much more

positive, typically 30-45V.

Emission

When the filament is producing electrons some go through the electron entrance hole and

across to the Trap to produce the set Trap current e.g.100µA. Most, however, do not pass

through the hole and impact the source block. This also produces a current called the Source

Current. The Emission is the sum of the Trap Current + Source Current.

With a trap current of 100µA, the emission is typically between 300µA and 500µA. A high

emission normally indicates an old, failing or misaligned filament. This is due to the filament

having to work a lot harder to produce the set Trap Current which also means a more electrons

impacting the source block, thus producing a higher source current.


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Consider the situation if the filament was in completely the wrong position and not adjacent to

the electron entrance hole. In this case, no electrons would reach the trap and more current

would be applied by the source controller. A large number of electrons would be produced but

all of these would hit the source block and the Emission reading would be very high. The

filament would be ‘In Limit’. Under conditions such as these, the filament could quite easily

bend or break.

2.3 Magnetic Sector

After being produced by the source, the beam enters the magnetic sector and the ions are

separated spatially into their different masses. Either a fixed-field permanent magnet or an

adjustable electromagnet are available for the HS20-22. The permanent magnet is used for a

limited mass range and is standard on systems that are for CO2, N2 and SO2 analysis. The

electromagnet however has a much broader mass range and is installed on systems capable

of analysing H2.

Isotopic Separation

The isotopic separation in a magnetic sector IRMS relies on the fact that an ion moving in a

magnetic field will experience a force perpendicular to the direction of propagation of the ion.

This is also known as a centripetal force and acts to pull the ion in a circular path with a radius

dependant on the mass and velocity of the ion as well as the strength of the magnetic field and

the charge of the ion.

Within the ion source the molecules ionised and given a charge Q (coulombs) by removing

one of the electrons. The electric field, V within the ion source then acts to accelerate the ions

with the electric potential energy, EELEC given by

𝑬𝑬𝑳𝑬𝑪 = 𝑽𝑸. [1]

Conservation of energy dictates that the electric potential energy is equal to kinetic energy

transferred to the ions as they are accelerated out of the source and into the magnet sector.

The kinetic energy gained by the electrons, EKIN is described by the mass of the ions, m and

the final velocity when they leave the electric field, v:

EKIN=𝟏

𝟐mv2. [2]

Combining equations 1 and 2 and solving for velocity gives the accelerated velocity of an ion

in the magnetic sector of the IRMS as

𝒗 = √𝟐𝑽𝑸

𝒎 [3]

An ion with this velocity and a charge, Q travelling in a magnetic field will experience a force,

FMAG given by

FMAG=BQv, [4]

where B is the strength of the magnetic field. The magnetic force acts perpendicularly to the

direction of the ion and is therefore a centripetal force. Centripetal force is defined as


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𝑭𝑪𝑬𝑵𝑻 =𝒎𝒗𝟐

𝑹, [5]

where R is the radius of an ion with mass, m and velocity, v. Since FMAG equals FCENT the radius

of the ion path is given by combining equations 4 and 5 as

𝑹 =𝒎𝒗

𝑩𝑸. [6]

By substituting for the velocity of the accelerated ion from the ion source given in equation 3

the radius can be expressed as

𝑹 =𝟏

𝑩√

𝟐𝑽𝒎

𝑸 [7]

If it is assumed that the voltage (V), magnetic field (B), and the molecular charge (Q) in are

constant for all molecules then the equation reduces such that the radius of the path is

proportional to the mass of the molecule, therefore the different isotopes will follow different

paths and can be measured separately.

NB The term m/z is commonly used in mass spectroscopy and is the molecular mass

divided by the number of electrons removed in ionisation.

Mass Range

Equation 7 demonstrates that by varying B or V we can effectively create a working range for

the IRMS for the measurement of molecules of different masses. The Sercon HS20-22 can

measure molecules in the m/z range 2 -66 when fitted with an electromagnet.

The analysis of heavier molecules such as CO2, N2 and SO2 are all performed with a constant

magnetic field (B) and using a fixed collector position; the acceleration voltage (V) must be

varied so that the molecules of interest are incident on to the collector. CO2 typically requires

an acceleration voltage of approximately 2000V. N2 is a lighter molecule and so for the same

position of collector will require a higher acceleration voltage of approximately 4000V.

Conversely, the heavier SO2 molecule will require a lower acceleration voltage than CO2.

The analysis of the light H2 molecule requires a much lower magnetic field for the beams to be

focussed within the geometry of the mass spectrometer. Systems used for the analysis of

hydrogen are fitted with an electromagnet and an additional collector position to achieve this.

Ion Beam Focus

Assuming perfect focussing by the IRMS, whatever is at the object plane will be reproduced at

the collector array, split into m/z units. In reality, no mass spectrometer is capable of perfect

focussing owing to effects such as energy spread, magnetic fringe fields and pole face shape.

The ion beam will therefore have a degree of dispersion and the ions follow a complex optical

path through the magnetic sector as demonstrated in Figure 2-7.


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Figure 2-7: Beam dispersion in a mass spectrometer

The position of the ion source is fixed in relationship to the flight tube and collector arrays so

the focussing of the ion beam is determined by the shape and position of the magnet and the

tuning of the ion source.

2.4 Collector Arrays

The HS20-22 is fitted with two collector array apertures at 120˚ and 98.8˚. The 120˚ aperture

can house either a standard collector array for the analysis of CO2 and N2 or the universal

collector array for the analysis of CO2, N2 and SO2. The standard array and the universal array

contain three individual Faraday cup collectors which collect the ion beams of the most

common and analytically interesting isotopes in these species: 28,29,30 (N2) 44,45,46 (CO2)

and 64,65,66 (SO2). A Faraday cup is simple metal ‘bucket’ coated with a specialised high

carbon content paint. When an ion strikes the cup, an amplification circuit measures the energy

release caused by the impact.

A schematic diagram of the data processing is shown in Figure 2-8. The amplification of each

collector or cup depends on the concentration of the isotopes being measured. For light stable

isotopes, the second and third collectors have around 50 times more signal amplification than

the first. This is because the first collector is used to measure the major isotope, which is in

high abundance, and the second and third collectors are used to measure the minor isotopes

with lower abundances.


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Figure 2-8: A Schematic diagram of the mass spectrometer Data Processing.

2.5 Standard and Universal Collector Arrays

The Sercon HS20-22 collector arrays are designed for the measurement of multiple isotopes.

The amount of m/z separation varies with mass so the placement of the faraday collectors

within the array have been carefully calculated to allow for good resolution and peak shapes

for the desired isotopic measurements. The standard collector is configured to give optimum

results for N2 and CO2 while the Universal collector allows for the measurement of a much

larger mass range including SO2 with 33S taken into account.

Figure 2-9 shows a visual representation of the standard and universal collector arrays. The

m/z separation is reduced for heavier masses, such as the SO2, so the width of the centre

collector is reduced to compensate.

Figure 2-9: Schematic diagrams of the Standard and Universal collectors, showing

where the ion beams are incident on the collector array.

2.6 Hydrogen Collector

The isotopes of hydrogen are measured in the form of the H2 molecule and have the m/z ratios

of 2 and 3. The separation between these isotopes is much larger than the heavier mass

isotopes and it is not possible to measure them within the geometry of the standard and

universal collectors. The HS20-22 achieves m/z =2 and 3 measurements via an additional

faraday collector at 98.8˚. The m/z=3 ions are focused into this specialised hydrogen collector

while the m/z=2 ions are focussed in the major collector of the standard or universal collector

at 120˚. The path of the hydrogen isotopes are represented in the schematic of the IRMS

shown in Figure 2-10.

Fixed Gain

Head Amplifier Variable

Gain

Amplifier

Voltage

Frequency

Converters

Counter

s Computer Data

Analysis


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Figure 2-10: A schematic of the Sercon HS20-22 IRMS as seen from above showing

the focusing of m/z= 2 and 3 isotopes of Hydrogen.

2.7 Head Amplifiers

Head amplifiers are attached to both the Standard and Hydrogen collector arrays and are

responsible for amplifying the signal from each faraday collector bucket. The values of the

resistors used to amplify the signal from each individual collector are varied based on the

amount of amplification required for the signal for that particular collector. The hydrogen

collector has a 100,000 MΩ resistor to amplify the relatively small HD signal. The standard

collector has a 100 MΩ resistor for collector 1, and 5000 MΩ resistors for collectors 2 and 3.

2.8 Vacuum System

For the ions to travel through the mass spectrometer to the collectors, the probability of them

colliding with other molecules should be as low as possible. For this reason it is essential to

generate a high vacuum. The HS20-22 IRMS uses a differential pumping system with one

turbomolecular pump located at the ion source and another near the collector array. The two

regions are separated by a baffle. This configuration reduces the number of unwanted ion and

gas collisions and creates a more sensitive and accurate IRMS than a singly pumped

alternative.


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Figure 2-11:A schematic diagram of the HS20-22 mass spectrometer diferential

pumping system.

A schematic of the Sercon pumping system is shown in Figure 2-11.The two turbomolecular

pumps in the Sercon HS20-22 run at speeds up to 94,000 rpm and create a vacuum of <1e-8

mbar when the isolation valves are closed. The turbomolecular pumps used are unable to

operate at pressures above 1e-3 mbar due to the fragile nature of their stator blades. In order

for the pumps to operate, the flight tube must be evacuated to a pressure below 1e-3 mBar.

This is accomplished through the use of a rotary ‘backing’ or ‘roughing’ pump. The vacuum

pressure is monitored by two cold cathode AIM gauges.


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3. Sercon HS20-22 System Overview

A diagram showing the layout of the HS20-22 is shown in Figure 3-1.

Figure 3-1: Layout of the Sercon HS20-22 Mass spectrometer, highlighting the ion

optics, the system controller, pumping system and reference gases.

3.1 Main Power Module Switches

There are four main power switches located inside the front right-hand door of the HS20-22.

The function of these switches is as follows:

• Magnet – Power to the electromagnet (if installed).

• Pumps – Power to the vacuum pumps.

• Electronics - Power to the system controller.

• Mains - Main power to whole instrument.

3.2 System Controller

The system controller contains the electronic circuitry for the mass spectrometer. It houses the

electronics boards for source control and readbacks, valve control, pressure and flow

readbacks and signal processing.

Figure 3-2 shows the lights and switches located on the front of the system controller.


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Figure 3-2: System controller.

• The Source power should only be switched on when the source standby file has been

loaded and the system has pumped down to < 3.2e-7 mbar source pressure.

• The HT needs to be on when running samples.

• If the Source switch is off, the HT switch LED will also go out. The HT will not be on

when source switch is off regardless of HT switch position.

• If there is no active connection between the USB port and the computer then the USB

LED will show Red.

• When the source is first switched on and the filament is firing then the Filament LED

will show solid red indicating the filament is in LIMIT, when the filament has fired and

the Trap Current is stable, the LED will turn green indicating an OK filament status.

• A flashing Red filament LED indicates that the filament is not connected e.g. the source

cable is not connected or the filament has broken.

3.3 Flight Tube

The flight tube is a hollow, airtight, stainless steel structure with a geometry designed to exactly

match the path of the sample ions through the magnetic field to the collectors. As well as being

airtight, the flight tube must be free of all contamination if the mass spectrometer is to function

properly.

3.4 Magnet

The Sercon HS20-22 is supplied with either an electromagnet or a permanent magnet,

depending on the gas species to be analysed. The magnet will be positioned during the

installation of the mass spectrometer and should not be moved unless under instruction from

a Sercon engineer. For systems fitted with an electromagnet, the current is controlled by setting

the ‘Emag’ parameter in the Callisto source window (Figure 2-6) where the current is displayed


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in mAmps. Typical values for the Emag current are 3.5 Amps for Hydrogen and 13.5 Amps for

all other gas species.

Switching between magnet settings

When the current is set to 13.5 Amps, the temperature of the magnet increases to about 50ºC.

If H2 parameters are selected, the lower current used means the magnet cools down

considerably. For this reason, it is recommended that when switching between low and high

Emag currents, sufficient time is given to allow the magnet temperature to stabilise before

analysing samples.

3.5 Valves and Trapping Loop

The inside of the main compartment of the HS20-22 mass spectrometer is shown in Figure

3-3. As well as housing the turbomolecular pumps and their controllers, the compartment is

the location of the system’s isolation and reference gas valves.

Figure 3-3: Inside the HS20-22 chassis.

The valves on the HS20-22 are divided into three types: isolation valves, trapping loop valves

and reference gas valves.

The usual configuration of valves is:

0: Nitrogen Reference/tuning gas

1: Carbon Dioxide Reference/tuning gas

2: Hydrogen Reference/tuning gas

4: Reference gas isolation valve

5 - 8: Isolation valves for prep units

9 and 10: Trapping loop valves


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Isolation valves

The isolation valves are pneumatic valves that open or shut the split from the sample prep unit

(or reference gas injections). When a sample isolation valve is closed, the sample stream from

the prep system flows to waste. When it is open, a small split of the carrier flow and sample

gas is drawn into the mass spectrometer. The amount of helium and sample that passes into

the mass spectrometer, and therefore the pressure within the instrument, is determined by a

crimp.

Each isolation valve is operated pneumatically by a corresponding SMC solenoid actuator

valve.

Reference Gas System

A variable number of ‘reference’ gases can be connected to the HS20-22, depending on the

customer’s requirements. The reference gases are typically nitrogen, carbon dioxide and

hydrogen (it is possible to use other gases such as carbon monoxide or sulphur dioxide but

most people prefer not to have noxious gases in their laboratory, hence the trapping loop) and

are connected to the bulkheads at the rear of the mass spectrometer unit labelled Ref 1, Ref

2 and Ref 3, respectively. These gases are in turn connected to the reference gas injection

assembly which consists of 3 SMC solenoid valves linked in series via a small manifold with a

common helium stream (typically 15ml/min). The typical layout of the reference gas system is

shown in Figure 3-4.

Figure 3-4: The layout of the reference gas system. The needle valve on the left is

used to control the Reference gas carrier flow. The central valves control the

reference gases and the valves on the right control the isolation valves.

There is a constant bleed of approximately 1-2 ml/min from the pigtails on top of the valves in

order to prevent any fractionation in the reference gas line.

When a reference gas valve is activated, the corresponding reference gas flow will enter the

common helium stream. If the reference gas isolation valve (valve 4) is open, the helium and

ref gas are carried passed the split inlet to the mass spectrometer. The helium flow is usually

set to 15ml/min.


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Figure 3-5: The Callisto software mimic of the reference gas and inlet system.

The reference gas valves are controlled via the Callisto software. Figure 3-5 shows the section

of the software mimic that represents the reference gas system. To activate valve 0, 1 or 2,

simply click in the boxes labelled N2, CO2 and HD, respectively. To allow the reference gas

into the mass spectrometer, both the appropriate reference gas valve and the reference gas

isolation valve (4) must be open.

Trapping Loop

A trapping loop is used to provide a fixed volume of sample gas for the purpose of tuning the

mass spectrometer and is particularly useful when noxious gases such as SO2 or CO are of

interest. As sample gas passes through the loop, valves 9 and 10 can be activated to trap the

gas.

Valves 9 and 10 are paired together so only one has to be activated to trap the gas. Drop a

sample into the prep unit and then watch the beam intensity on the main Callisto window. The

beams will begin to increase and, when a maximum intensity seems to have been reached,

activate the trap. The beams will usually decrease slightly before becoming stable.

The beam intensity will decrease over time as the trapped sample gas and helium are slowly

pumped away through the crimp by the source turbo pump.


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4. Getting started

This chapter is designed to guide the user through the process of getting the mass

spectrometer ready to run samples from the standby mode. It describes the process of setting

the mass spectrometer to run mode, tuning of the system using reference gases and checking

the peak shape and stability.

4.1 Standby mode

The system in standby mode should have the following settings and conditions:

• The preparation system isolation valves and the reference isolation valves are closed.

• The source pressure should be approximately 1e-8mbar.

• The standby source parameter file should be loaded. The standby parameters are

shown in Figure 4-1, and are designed to keep the filament warm whilst the system is

not in use.

Figure 4-1: Standby Source Control parameters.

4.2 Background scan

A background scan shows what is in the flight tube. It can reveal leaks or contamination. It can

also be a useful tool for finding certain gas species when tuning the mass spectrometer.

To scan the background, load the N2 source tuning file. Click on Background in the [Preset]

drop down menu on the Callisto graph window (shown in Figure 4-2) to start a scan across the

central collector over a HT range of 2000 to 4200 Volts. The scaling of the y-axis will

automatically be set to 1e-11. The range of the HT background scan can be altered by going

to Presets> Customise.


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Figure 4-2: A Section of the Callisto graph window showing the ‘Presets’ scan list

options.

As the HT increases, beams of ions with decreasing m/z ratios will pass across the central

collector creating peaks in the graph. The graph in Figure 4-3 shows an example of an

acceptable background scan. The mass 28 nitrogen peak, as observed in the central collector

(beam 2) should be less than 1e-11 Amps. Any higher than this might suggest a leak. The

presence of any additional peaks in the scan compared to the ones shown in the example

below may suggest that the flight tube has become contaminated. The contamination can be

identified by counting from a known peak such as nitrogen (28) or carbon (44).

Figure 4-3: A scan of the HT (x axis) showing the background in the mass

spectrometer. The scan shows the current in the central collector. Note that the mass

is from high to low.


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4.3 Introduction to Peak Shapes and Stability

In stable isotope mass spectrometry, the peak shape is a fundamental tool for finding the

correct HT settings for the ion source. The ion beams are swept across the collectors to show

which voltage gives full coincidence for all masses, i.e. where all 2 or 3 beams are hitting the

back of the collectors. The width of the beam 2 peak is essentially the width of the central

collector in volts (see Figure 4-4).

Figure 4-4: A schematic diagram to demonstrate the point of coincidence in the

source. As the HT is increased the beams are swept across the collectors from

collector 1 towards 3. The point of coincidence is the HT at which each beam falls in

the relevant collector

The stability of a source with specific tuning parameters is evaluated as a trace of the beam

intensities and ratios over time. Any noise or fluctuations of the ion ratio will affect the results

from real samples.

The peak shape(s) should be checked before running a batch samples to ensure the HT has

been correctly set.

Callisto contains four pre-set scans to easily evaluate the peak shape and stability of the

source tuning. The pre-set scans are located in the [Preset] menu on the graph window (shown

in Figure 4-2). The Peak 2/1 scans the beam intensities and the ratio of beam 2 to beam 1

across a range of HT ±30V either side of the set voltage (±60V for hydrogen). The Peak 3/1

scans the ratio of beam 3 to beam 1 which would be most commonly used for CO or SO2.


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Figure 4-5: A peak shape scan (Peak 2/1) of beam intensity over a range of ±30V from the set

value for N2 reference gas. For N2 beam 1 (red) is m/z = 28, beam 2 (green) is m/z =29 and beam

3 is m/z =30.

An example of a Peak 2/1 scan for N2 is shown in Figure 4-5 where beams 1, 2 and 3 are

shown in red, green and blue, respectively and the 2/1 ratio is in black. The set HT value is at

the centre of the scan.

The ratio stability 2/1 pre-set scan will produce a trace of the 3 beams (red, green and blue)

and the 2/1 beam ratio (black) at the current tuning parameters over 600 seconds. Similarly,

the ratio stability 3/1 scan will show the 3 beams and the 3/1 scan (black) over 600 seconds.

An example of ratio stability 2/1 pre-set scan for N2 reference gas is shown in Figure 4-6.

Figure 4-6: A stability scan of beam intensities and the 2/1 beam ratio (black) over time

(600s) for N2 reference gas. Beam 1 (red) is m/z = 28, beam 2 (green) is m/z =29 and

beam 3 is m/z =30.


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4.4 Daily Tuning

The fine tuning of the mass spectrometer will have been completed on installation but may

need to be repeated after the filament has been changed. The following steps describe how to

run a peak centre scan and how to determine the correct HT. This should be carried out for

each gas species of interest before a batch of samples is run. The example below is for CO2

with a reference gas injector. The procedure is the same for all other gas species.

1. Ensure that there is a flow of helium (approximately 15ml/min) across the reference

gas injector. The flow is controlled by the needle valve (see Figure 3-4).

2. Open the reference gas isolation valve.

3. Load the CO2 source file and then open the CO2 reference gas valve (valve 1). Watch

the beam intensities as they increase and wait for the values to stabilise.

4. Scan the 2/1 peak using the pre-set Peak 2/1 scan.

5. The peak shape scan uses automatic scaling. If the HT is not close to the centre of the

peak, scans can look confusing such as the example in Figure 4-7. In this example, the

shape of the scan suggests that the peak centre is approximately 10-20V higher (to the

right) than that currently set.

Figure 4-7: A peak 2/1 scan of CO2 when the HT is set 10-20V lower than the

peak centre. The auto scaling of the scan has caused the trace of beam 2 and

the 2/1 ratio to be outside the range of the axis.

6. Adjust the HT until the 2/1 ratio is consistent with CO2 (~ 0.112). A background scan

can be used to find the CO2 peak if the HT is completely wrong.

7. Repeat the Peak 2/1 scan until the mass 45 peak is in the centre of the screen (see

Figure 4-8). The dashed vertical lines on the scan indicate the original and new HT

settings.


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Figure 4-8: Peak shape for CO2, the dotted vertical line on the left shows the

original HT value. The dotted line to the right shows the new HT position in the

centre of the 2/1 peak.

8. Set the HT to the centre of the flat part of the peak, and save the new source

parameters.

9. Scan the stability using the Ratio Stability 2/1 pre-set scan. Figure 4-9 shows an

example of a stability scan for CO2.

Figure 4-9: A stability 2/1 scan for CO2

10. Close the CO2 reference gas valve (valve 1). The beams should decrease back to

background levels.


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The only variation of this procedure is if a trapping loop has been fitted. In this case, trap some

sample gas before following steps 4 to 10.

• The expected 2/1 ratio for nitrogen is 0.007.

• The expected 2/1 ratio for hydrogen can vary greatly, but is usually in the region of

0.0003.

• The expected 3/1 ratio for carbon monoxide is 0.002.

▪ The expected 3/1 ratio for sulphur dioxide is 0.04.

4.5 Tuning the Source for Sulphur Analysis

Due to the toxic nature, it is not advisable to use SO2 as a reference gas. Systems fitted with

a universal collector can be tuned for SO2 by trapping a sample in the trapping loop. A

percentage of SO2 breaks down to SO in the source so It is possible to tune for either SO or

SO2.

1. Use the preparation unit such as GSL or NCS to combust a sample containing a

minimum of 50µg of Sulphur.

2. When the SO2 peak reaches a maximum value, activate the trapping loop. If there is

no previous SO2 (or SO) tuning, the Peak Jump function can be used (please refer to

the Callisto manual).

3. Run a Peak 3/1 scan. A 3/1 ratio of 0.042 is expected for both SO2 and SO (see Figures

4-10 and 4-11).

4. Adjust the HT to the centre of the peak.

5. Check the stability of the system with a ratio stability 3/1 scan.

6. Deactivate the trapping loop and wait for the beams to return to background level.

Figure 4-10: SO2 2/1 peak shape.


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Figure 4-11: SO 3/1 peak shape

4.6 Tuning the Source for Hydrogen Analysis

The electromagnet current is lower for hydrogen than for the other gas species. The magnet

will cool down and takes a couple of hours to stabilise.

To tune for hydrogen:

1. Open the reference gas isolation valve.

2. Load the H2 source file and then open the H2 reference gas valve (valve 2). Wait for

the beams to stabilise.

3. Scan the 2/1 peak using the pre-set Peak 2/1 scan. An example of a H2 scan in shown

in Figure 4-12.

4. Evaluate the stability using the ratio stability 2/1 scan.

5. Close the H2 reference gas valve and watch the beams return to background levels.

6. If the hydrogen peak cannot be found by moving the HT up and down, run a background

scan. Please note that the Peak Jump function does not work for hydrogen due to the

different magnet current.

Figure 4-12: Hydrogen 2/1 peak shape.


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4.7 Advanced Tuning

After a filament change, more advanced tuning may be required. There are several factors to

consider and optimise when tuning the mass spectrometer:

• The Sensitivity of the source.

• Peak shape and stability.

• Precision- The repeatability of the result for identical samples.

• Linearity- The repeatability of the result for differently sized identical samples.

It is important to balance and evaluate all of the factors listed above whilst tuning the source.

The adjustable parameters are the half plates, ion repeller, focus and eVs. Descriptions of

each of these components of the source are given in Section 2.2. It is advisable to change

each parameter in turn and see how the peak shape and sensitivity respond with each

adjustment. A good starting point is to find the tuning parameters that give the highest

sensitivity. Altering the individual source parameters will have an effect on the other

parameters. The focus and the IR, in particular, have a large effect on each other which in turn

affects the source linearity.

Once a good peak shape, sensitivity and stability have been achieved, the precision and

linearity should be evaluated using reference gas pulses (see Chapter 5. Further tuning may

be required to improve their precision.)


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5. Reference Gas Pulses

Batches of reference gas pulses are an important tool for diagnosing any potential problems

with linearity and precision. It is a good way of determining whether a lack of precision is due

to the prep unit or the mass spectrometer itself.

Reference gas peaks are created by opening the relevant reference gas valves for a period of

time, between 1 and 10 seconds, and mimic real sample peaks.

5.1 Precision Test

To test the precision (reproducibility) of the mass spectrometer, a series of reference gas

pulses of the same duration are measured. The Setup groups required will have been created

during the instrument’s initial testing.

An example of a sample list for a reference gas batch to test for precision is shown in Figure

5-1.

Figure 5-1: A sample list to test for precision of the mass spectrometer.

The precision of the mass spectrometer is measured in terms of the standard deviation across

5 identical reference gas pulses. This can be determined by holding down the Ctrl button and

selecting the appropriate results from in the results window. The selected results will be

highlighted in red and the standard deviation will appear in a separate window as shown in

Figure 5-2.


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Figure 5-2: The results window for a precision reference gas batch of nitrogen

showing the standard deviation over 5 results.

For a mass spectrometer operating with good precision, a standard deviation of ≤0.1‰ is

expected for N2 and CO2 and a standard deviation of ≤2.0‰ is expected for H2.

5.2 Linearity Test

Reference gas pulses of different duration give different sized peaks and can be used to test

the linearity of the ion source. The Setup groups will have been created during the instrument’s

initial test.

The linearity of the mass spectrometer for each reference gas is measured in terms of the

standard deviation across 5 identical reference gas pulses. For a mass spectrometer operating

with minimal linearity effects, a standard deviation of ≤0.3‰ is expected for N2 and CO2 and a

standard deviation of ≤4.5‰ is expected for H2.


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6. Maintenance

Carrying out some simple routine maintenance procedures will increase the life span of the

mass spectrometer’s components and consumables. It is sensible to keep a journal with print

outs of peak shapes and stability scans to monitor any changes in performance.

6.1 Venting and Pumping the HS20-22

Venting

Observe the following procedure to vent the instrument:

1. Load the Standby source tuning file.

2. Turn the source off by toggling the HT and Source switches on the front of the system

controller (see Figure 3-2).

3. Close the isolation valves.

4. Turn off the pumps by pressing the Pumps switch on the front panel of the HS20-22.

5. Use the [Check Pump Speeds] window in Callisto (see Callisto manual) to watch the

pump speeds decrease. This may take up to 5 minutes. When the vent valves can be

heard clicking and the pump speeds read 0, it is safe to break the seals.

Pumping

Observe the following procedure to pump the instrument:

1. Check that the rotary pump has sufficient oil.

2. Turn on the pumps by pressing the Pumps switch on the front panel of the HS20-22.

3. Use the [Check Pump Speeds] window in Callisto to watch the pump speeds increase.

The pumps should reach their maximum (94krpm) within a few minutes.

4. When the pumps have reached 80% of their full speed, the Penning gauges are

automatically switched on. Monitor the pressure in the Callisto software.

5. The pressure in the Source side will decrease much faster than in the Analyser side as

the pump has a far smaller volume to evacuate.

6. Do not open an isolation valve or turn the ion source on until the pressure has reached

at least 4e-7mbar.

If any problems with the pumping system are experienced, please refer to the Troubleshooting

section and/or contact Sercon.

6.2 Rotary Pumps

Oil Change

The Oil Level and colour should be checked on a weekly basis. It is recommended that the oil

is changed every 6 months or when the oil shows signs of discolouration (dark brown). The

system must be vented to change the oil so this should be scheduled in with the workload.

When the instrument has vented, unscrew the ‘oil in’ cap on the upper surface of the pump.

Then loosen the plug to be found at the bottom of the front of the pump. Make sure that a

suitable receptacle is positioned near the pump when the plug is removed as the oil will flow

out quite quickly. Care should be taken as the oil may also be hot. Replace the plug and fill the


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pump with fresh oil. The window on the front of the pump has two marks. These are the

maximum and minimum fill levels.

Appropriate safety measures should be taken during this procedure: gloves, safety glasses,

correct disposal of waste oil, solvents, etc.

Ballasting

Ballasting is performed to remove any non-condensable gases which may have built up in the

oil. This is done by opening the ballast valve which allows a stream of atmosphere to bubble

through the oil reservoir removing the non-condensable gases. The ballast valve is usually

located on the top surface of the pump. This procedure produces a lot of oil vapour, so it is

recommended that an outlet tube is connected to the exhaust port and the vapours vented into

a fume cupboard. Alternatively an oil vapour trap can be used to contain the exhaust during

this process. The pump should be ballasted for at least 30 minutes whenever the oil is changed.

6.3 Changing the Filament

Sercon recommends that the filament be changed annually. It will also need to be replaced if

it is broken or if the emission reads >3000µA. To do this, use the following procedure:

Please refer to the exploded source diagram (Figure 6-2, Page 47).

1. Vent the instrument.

2. Undo the two thumbscrews and remove the white PTFE source connector. If this is

tight, gently pull it off using a flat-bladed screwdriver – do not twist the source connector

as this may damage the ceramic feedthroughs.


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3. Remove the stud guides and then the 1/16 capillary line connected to the source.

4. Using an 8mm hex key, undo the bolts holding the source flange. Support the source

flange as the last bolts are removed.


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5. Once the bolts have been removed, CAREFULLY pull the source from the flight tube.

DO NOT ROTATE.


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6. Whenever touching any source components, powderless nitrile or Latex gloves should

be worn. Work in a clean area. Cover the entrance of the flight tube with aluminium foil

to prevent any dust, particulate matter or other contamination from entering.

7. The filament is located behind one of the source magnets. Two steel legs reach down

from underneath the magnet.


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8. Remove the magnet by loosening the grub screw holding it in place. There is no need

to completely remove the grub screw.

9. Loosen the barrel connectors on the filament legs and carefully bend the connectors

out of the way.


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10. Undo the screw holding the filament and remove.

11. Carefully bend the legs of the new filament backwards slightly.

12. Slide the positioning slot over the screw - take care not to touch or scrape the filament

wire whilst doing this as it may damage the thoria coating. The edge of the wraparound

forms a slight ridge. The ceramic body of the filament assembly should be flush against

this ridge. This should place the filament in the centre of the small window in the

wraparound. One way to check the positioning is to remove the magnet on the other

side, loosen the screw and move the trap to one side so that the filament position can

be viewed from the opposite side.


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13. Once the filament position is set, tighten the screw. Do not allow the filament to twist.

14. Replace the magnet and tighten the grub screw to hold it in place.

15. Attach the barrel connectors to the legs of the filament, ensuring that they are tightly

held.

16. Check that the gas feedthrough tube is sitting correctly in the locating holes in the flange

and source block.


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17. Replace the copper gasket. A new one should be used each time the source is removed.

When removing the old gasket, be very careful not to damage the cutting edge of the

flange.

18. Carefully insert the source back into the flight tube.

19. The two locating pins on the source mounting flange fit into two corresponding holes in

the flight tube baffle. Press the source flange firmly into place, ensuring that the copper

gasket is correctly positioned.


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20. Holding the source flange in place, screw in two bolts to hold it in position. Do not allow

the copper gasket to slip out of place or a leak may occur.

21. Use a digital volt meter to perform a continuity test between the flange with each

feedthrough, then each feedthrough with each other. Only pins 6 and 7 (Filament - see

Figure 6-1) should show continuity.


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22. Replace the rest of the bolts but do not tighten. The bolts should be tightened gradually

and in opposite pairs e.g. bolt 1 then 5. Bolt 3 then 7. Bolt 2 then 6, etc. Failure to do

this may squash the gasket and cause a leak.

23. Replace the inlet capillary(ies). If necessary, replace the 1/8” - 1/16” PTFE reducing

ferrule(s).

24. Replace the stud guides, white PTFE block and the black ground wires and wingnuts.

25. Turn the pumps on and monitor the pump speeds and pressure readings.

Figure 6-1: Source Flange with white PTFE block removed


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6.4 Conditioning the Filament

If the filament is not conditioned gently, or is subjected to a large current before being

conditioned properly, it may bend or break and would need to be replaced again. It is, therefore,

best to take time over this procedure.

1. Ensure that the pressure inside the mass spectrometer is low enough, i.e. <4e-7 mbar.

2. Load the Standby source tuning file. Flick the Source power switch on the front of the

HS20-22 into the on position for 5 seconds then turn it off. The source pressure should

increase rapidly as the filament de-gasses.

3. Allow the pressure to return to approximately 4e-7mbar.

4. Repeat this routine 10 times, increasing the on time from 5 to 6 -7 -8 seconds etc. until

the source pressure stays in the e-7mbar range when the filament is left on. Allow 15

minutes for stabilisation and then check that the set and actual Trap values are the

same.

5. Slowly increase the trap current from 50-100µA. At this point the emission should read

less than 500µA, typically 300-400µA. If it is much higher, then there may be a problem

with the filament position.

6. Wait for the source vacuum pressure to improve. At 100µA wait for 15 minutes and

then start increasing the trap current by 100µA at a time, waiting for 5 minutes after

each increase until 600µA is reached.

7. Load the Standby source file and open the reference isolation valve. Check the Peak

shape and Stability for each gas species of interest.

6.5 Cleaning the Source

If the source has somehow become dirty or contaminated, it will need to be cleaned. It is

recommended that the source be sent to Sercon to be cleaned and evaluated by our engineers.

If this is not possible, please contact Sercon for advice.


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Figure 6-2: Exploded diagram of the Sercon Ion Source


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6.6 Source Assembly Listing

Refers to Figure 6-2:

1. Source mounting pillar x 1 SI 0141

2. Compression spring x 1 SI 1996

3. Location screw (M3 x 12mm pan head) x 3 SI 1985

4. Magnet x 2 SI 1981

5. Trap screw (M2 x 6mm pan head) x 2 SI 1994

6. Ceramic sleeve (3.5mm) x 1 SI 2003

7. Trap and boss x 1 SI 2013 & SI 1978

8. Ceramic spacer (2mm) x 12 SI 2002

9. Magnet grub screw (M3 x 4mm) x 4 SI 1989

10. Ceramic spacer (1.77mm) x 5 SI 2001

11. Ion repeller x 1 SI 1979

12. Ceramic tube (2.75OD x 1.6 ID x 25mm) x 1 SI 1999

13. Ion exit plate (wraparound) x 1 SI 2011

14. Half plate x 2 SI 2008

15. Slit plate x 2 SI 2009

16. Screw (M2 x 6mm pan head) x 2 SI 1994

17. Locating pin x 2 SI 1970

18. Ceramic rod x 4 SI 1998

19. End flange x 1 SI 1971

20. Slit support plate x 4 SI 2010

21. Metal spacer (7.8mm) x 4 SI 1972

22. Metal spacer (6.2mm) x 4 SI 1973

23. Metal spacer (2mm) x 4 SI 1974

24. Screw (M4 x 2mm) x 8 SI 1993

25. Ceramic tube (2.75OD x 1.6 ID x 25mm) x 1 SI 1999

26. Screw (M2 x 6mm pan head) x 1 SI 1994

27. Magnet block x 2 SI 1975

28. Filament x 1 SC0028

29. Ceramic sleeve (6.4mm) x 1 SI 2004

30. M2 washer x 10 SI 1992

31. M2 nut x 5 SI 1998

32. Source block x 1 SI 1976

33. Adjusting screw x 4 SI 1977

34. Wavy washers x 8 SI 1984

35. Circlip x 8 SI 1983


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7. Troubleshooting

This is by no means an exhaustive list but may be used to remedy some potential problems.

When in doubt, contact Sercon. Also, refer to Troubleshooting section in the prep system

manuals for more specific application advice.

7.1 Instrument Will Not Switch On:

• Check the mains socket for power.

• Check the fuses. These are located in the alcove around the back of the system. Make

sure the instrument is unplugged before removing the fuse carriers.

7.2 Turbo Pumps Will Not Activate:

• Check that the vent valve is connected and tightened to the turbo pump,

• Check that the rotary and turbo pumps have been properly connected with the o-rings

and clamps provided.

• Check that the rotary pump is operating.

• Check the LED on the pump controller is green.

• Check turbo pump cables are connected.

• Check for large analyser leaks. The turbo will shut down if there is a large enough leak.

• Tighten the flanges.

7.3 Vacuum will not reach 1e-6mbar:

• Tighten inlet capillary nut.

• Check turbo pump to rotary pump connections.

• Check that the turbo pump vent valves are tight.

• Check that the turbo pumps have reached full speed ([Check Turbo Speed] window

in Callisto).

• Inject small quantities of acetone into the gaps between the flanges. A large jump in

pressure will be observed if the leak has been discovered.

7.4 Vacuum will not reach 1e-8mbar:

Before carrying out any of the procedures below, it is advisable to run a background scan to

see what is preventing the system from pumping properly. Is it air, water or contamination?

Only turn the source on if the pressure is less than 2e-6mbar. If the problem is either moisture

or contamination, a heat gun may be used to bake the system. If it is air, the following

procedures can be carried out:

• Tighten all flanges.

• Check splitter/isolation valve is closing properly

• Tighten splitter/isolation valve.

• Vent the system and isolate the source with a blanking ferrule over the inlet. Pump

again and check for improvement.

• Tune the source to argon and use a small flow to check for leaks around all joins and

ferrules.


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7.5 Pumping System Noisy or Erratic

• Check that the rotary pump has oil. This should be changed regularly.

• Check connections to rotary and turbo pumps.

7.6 Incorrect Source Pressure

When the isolation valves have been closed for a period of time e.g. overnight, the source

pressure should be approximately 1e-8mbar. With the reference gas isolation valve open, the

pressure should be approximately 2e-7mbar. Depending on the prep system, the pressure with

the sample isolation valve open should be between 2e-6mbar and 5e-6mbar.

• Check that the Penning gauge is reading correctly. An inactive gauge will read 1e-8.

• If the pressures with the isolation open are incorrect, check that there is a helium flow.

• Open the nitrogen source file to check for air leaks.

• It is possible that the crimps need to be reset. Consult a Sercon engineer before altering

the crimps.

7.7 Oil Leaking from Rotary Pump

If oil is found around the pump, vent the system and have the rotary pump serviced/replaced.

7.8 Valves Not Activating

• Check that the ribbon cable(s) to the back of the system controller are properly

connected.

• Make sure that the preparation system is switched on.

• Check compressed air pressure for pneumatic valves is >55psi.

7.9 No Trap Current

• Turn the source off by toggling the Source and HT switches on the front of the system

controller. Remove the PTFE block from the source flange by unscrewing the two

wingnuts.

• Measure the resistance between pins 6 and 7 on the source flange. If the resistance is

approximately 0.6Ω, the filament is OK.

• If there is an open circuit between the pins, then the filament has blown and will need

to be replaced.

• If the filament is not open circuit, replace the PTFE block and turn the source on. Load

a normal source file and check the Electron Volts (eV) readback with the Source

Monitor. If the eV is near zero when set to -80 eV, then the most likely cause is that the

filament is bending and/or touching the source block. Refer to section 6.3.

• If the Trap current is still reading zero and the emission is close to zero it is unlikely but

possible that the filament drive circuit in the system controller is damaged. Contact

Sercon.


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7.10 Trap Not Reaching Set Point

• Observe the emission readback in the source control window. It should be

approximately three to four times the trap current set value. If the emission is well above

this value then the filament may be poorly positioned and requires repositioning.

7.11 No HT or Incorrect HT

• If the HT is not reaching the set point with the switched source on, contact Sercon. HT

voltages can exceed 4000 Volts, so do not attempt any troubleshooting unless advised

by Sercon.

• Check that the HT toggle switch on the front of the system controller is on and that the

red LED is lit.

N.B. The HT will not switch on if the Source/Filament switch is off.

7.12 No Sample Peaks

• Ensure the sample isolation valve is open. You should see the pressure rise to

approximately 5e-6 mbar when open. If the valve has not opened, check that there

is sufficient air/helium pressure to open the valve (50psi/3.5bar).

• Refer to the troubleshooting sections of the particular sample preparation unit.

• Check that the ion source is switched on.

• Ensure that the instrument has been correctly tuned. See section 4.4

• Check that the events/timings selected are correct. Please refer to the Callisto

manual.

7.13 Low Sensitivity/Small Peaks

• Check that the inlet pressure is near 5e-6 mbar when the split/isolation valve is

open with normal flow. The pressure may be less if the valve is not opening properly.

• Check the Trap Current setting. This is normally set to 600µA for N2, 100-200µA for

CO2 depending on sample size and composition.

• Ensure that the instrument has been correctly tuned. See section 4.4.

• Refer to the troubleshooting sections of the particular sample preparation unit.

• Check the events/timing sequences. Refer to the Callisto manual.

7.14 Software Error

If an error occurs that cannot be rectified by clicking ‘cancel’ or by restarting the software,

please refer to the Callisto manual or contact Sercon.

7.15 Communications Error/Analyser Not Responding

• Check that the USB cable between the PC and the HS20-22 and/or prep unit is

properly plugged in.

• If the red LED marked USB on the front of the system controller is illuminated, there

is no USB connection to the PC. Reboot the PC and/or the system controller.


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7.16 High Background

The N2 baseline value for Beam 1 should be less than 4e-10A with the isolation valve open. If

not:

• Check that the source pressure is between 2e-6 mbar and 5e-6 mbar when the

isolation valve is open with a normal helium carrier flow. If it is much higher, the

isolation valve crimp may need to be reset. Please contact a Sercon engineer.

• Refer to the prep system’s manual for leak checking protocols.

• Check that the carrier helium is the correct grade i.e. 99.998% purity.

• Use Snoop (SC8407) or a similar leak checking solution to see if there are any

leaks on the connections of the helium supply tubing, especially around bulkheads

and tees.

• Check the gas cylinder and regulator for leaks.

N.B. Be careful not to get leak detection fluid on any electrical connections.

7.17 Noisy or Unstable 2/1 Ratio

Figure 7-1 shows an example of a 2/1 ratio showing instability and noise caused by a faulty

head amp

Figure 7-1: Ratio stability noise caused by a faulty head amp.

• If ‘spikes’ occur on a regular basis, e.g. one every 20-60 seconds, it may a problem

with the rotary pump. The rotary pump may need to be ballasted or even replaced.

Ballast the pump for 15 minutes following the procedure in the maintenance section.

Perform a new 2/1 stability scan to look for improvement.

• If the 2/1 is very noisy, e.g. the noise is greater than 25% full scale on the scan

window, perform the following:

1. Save the poor 2/1 scan.

2. Unplug the head amp cable from the head amp (see Figure 7-2).

3. Remove the cover from the head amp, by removing the three screws to expose

the head amp circuit board and feedthrough connections.


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4. Disconnect the four PTFE connectors from the collector flange.

5. Put the cover back onto the head amp and plug the head amp cable (15 way

D-type) back in.

6. Perform a 2/1 stability scan and save the results.

7. Unplug the head amp cable again.

8. Perform a 2/1 stability scan and save the results.

9. Save and email all three scans to Sercon for diagnostics.

7.18 Missing Beam(s)

If the source control window in the software is displaying a missing beam(s) while all the source

parameters are working correctly, check the following.

• Unplug the head amplifier cable. If the beam returns, the problem is either the

collectors or head amplifier. Remove the head amp cover. Remove the 4 PTFE

connectors from the head amp assembly feedthroughs.

• Plug the head amp cable (15 way D-type) back in. If the beam returns, the problem

is most likely the collectors. Contact Sercon with this information.

• If the beam(s) are still missing with the head amplifier cable removed, the problem

is most likely a defective channel on the VFC card in the System Controller. Contact

Sercon.

Figure 7-2: Schematic of a head amplifier with the cover removed.

Beam 1 Beam 2

Beam 3 Suppressor

Head Amp

Issue No.

15 Way D-Type

Sercon Instruments & Applications - GC CP manuals...

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