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1. Purpose:
The purpose of this procedure is to provide the instructions of the user manual
Cobas 6000.

2. Definition:
c 501 (ISE): ISE unit of the c 501 module
c 501 (P): photometric unit of the c 501 module
CLAS 2 : Clinical Laboratory Automation System 2
CLIA: Clinical Laboratory Improvement Amendments
DIL: diluent
ECL: electrochemiluminescence
EMC: electromagnetic compatibility
HCFA: Health Care Financing Administration
IEC: International Electrical Commission
IS: internal standard (ISE module)
ISE: ion selective electrode
KVA: kilovolt-Ampere. Unit for expressing rating of AC electrical machinery.
LDL: lower detection limit see analytical sensitivity
LIS: laboratory information system
LLD: liquid level detection
MBC: matrix barcode
MSDS: material safety data sheet
n/a: not applicable
NCCLS:n National Committee for Clinical Laboratory Standards
PC/CC: ProCell M (ProCell) /CleanCell M (CleanCell)
PSM: process system manager (software)
REF: reference solution for ISE module
UL: Underwriters Laboratories Inc.

3. Responsibilities:
Chemistry section Technicians
Laboratory Physician

4. Policy:
Cobas® 6000 analyzer series

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5. Procedure:
The cobas 6000 analyzer series is a fully automated, random-access, software-
controlled system for immunoassay and photometric analysis intended for qualitative
and quantitative in vitro determinations using a wide variety of tests. The cobas 6000
analyzer series is a powerful tool for complete diagnostic laboratory automation. It is
optimized for high throughput workloads using an immunoassay analysis module (e 601
module).

5.1. Overview Modules

.

Figure 1: Cobas 6000

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Figure 2: A: Cobas link PC, B: Control unit computer

Figure 3: Core Unit

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Figure 4: e601 module

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Figure 5: STAT port

Figure 6: Water Supply

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Figure 7: Rack Rotor

5.1.1. Sample racks

The analyzer distinguishes the following categories of samples:
1- Patient samples
 Routine samples
 STAT samples
 Rerun samples
2- Calibrators
3- Quality controls.

Each sample category has its own type of sample rack. Each sample rack
holds a maximum of five samples. To load sample racks, they are either
inserted at the STAT port or placed on a tray and the tray is placed into
the rack loader.

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Figure 8:Sample Rack

Sample racks are color-coded and equipped with a barcode label and a label with a
unique rack number. Each rack is identified and registered when its barcode label is
scanned by the barcode reader of the rack sampler unit.
The following table explains the different types of racks, their color codes and
numbers:

Rack type Rack color Display in software Label on

rack

Routine rack Gray N00001-N03999 001-3999

STAT rack Red E00001-E00999 S001-S999

Rerun rack (a) Pink R00001-R00999 R001-R999

Calibrator rack Black S00001-S00999 C001-C999

QC rack White C00001-C00999 Q001-Q999

\Wash rack Green W00999 W999

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The table shows that each type of sample rack has its specific range of rack numbers.
The software allows subdividing the range of rack numbers of routine, rerun, and
STAT racks according to sample types (such as Ser/Pl, Urine, CSF…). This
assignment of sample types to rack numbers is displayed in the Rack Assignment
area on Utility > System.

Make sure the rack barcode label is on the right side, when inserting a rack into the
STAT port or when placing a rack into the rack loader. The barcode label can be read
only when racks are supplied in the correct orientation.

Figure 9: Reagent Area

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Figure 10: Pre-wash Area

Figure 11: Consumables Area

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5.2. Daily Operation:

Daily operation encompasses the routine tasks that are required to prepare
the analyzer, analyze samples, and maintain the analyzer. The layout of the
System Overview screen gives the operator an intuitive guide for the tasks
required for routine operation.
The following diagram gives an overview of daily operation.

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5.2.1. Routine operation:

5.2.1.1. Test selection

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Test selections for routine samples are downloaded from the Host.
However, these test selections can manually be changed—regardless
of the mode (Stand By, Stop, Operation, or Sample Stop) the
analyzer is in.
5.2.1.2. Loading routine samples
 To load patient samples
1. Prepare sample racks with the correct color and rack
numbers according to sample types (such as Ser/Pl,
Urine, CSF…).
 For all routine samples use gray racks.
 To verify the correct rack numbers for each sample type
refer to the Rack
Assignment area on the Utility > System screen.

2. Place the samples in the prepared sample racks. Ensure

the sample barcodes are facing the open slot in the rack
so the barcode reader can scan them.

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Figure 12: Sample Racks

3. Place the routine sample racks onto a rack tray in the

correct orientation: The barcode labels of the sample
racks have to be on the right side when placing the tray
into the rack loader. The rack loader is on the left side.

 To start processing
1. Choose Start (global button).

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Figure 13: Start Conditions Screen

2. Verify the settings on the Start Conditions screen.

3. Choose Start (on the Start Conditions screen). The analyzer
performs preparation routine and then begins to process the
samples.

 To process additional samples

1. Load the additional samples either from the STAT port or on the
rack loader (racks placed on a rack tray).
 If the analyzer is in operation, samples are processed without any further
action.
 If the analyzer is not already in operation, go to step 2.
2. Choose Start (global button).
3. Choose Start on the Start Conditions screen to initiate the run.

5.2.1.2. Processing STAT samples

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 Test selection
Test selection for STAT samples is the same as for routine samples. That is,
test selections for samples are downloaded from the Host in real time but can
still be changed from the analyzer’s control unit.

 Loading STAT samples

Once test selections have been made on your Host system or on the analyzer,
load the
STAT samples onto the analyzer using the STAT port observing the notes
below.

 To load STAT samples

1. Prepare red STAT racks with the correct rack numbers
according to sample types.
To verify the correct rack numbers for each sample type refer to the Rack
Assignment area on the Utility > System screen.
2. Set the samples in the prepared sample racks. Ensure the
sample barcodes are facing the open slot in the rack so the
barcode reader can scan them.

Figure 14: STAT rack

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3. Place the STAT rack in the STAT port carefully observing its
correct orientation:
The open slots in the racks must point to the rear of the rack sampler unit.
The side of the STAT rack with the barcode label must point to the
analyzer.

5.2.1.3. Checking results

As results are generated on the instrument, they are saved in the database
located on the internal hard disk of the control unit. When all results for all
the tests requested for a sample are available, the analyzer sends them to
the Host where they can be validated.
To view or edit results on the analyzer, use the Workplace > Data Review
screen; all test results in the database are displayed here.

When checking results, it can become necessary to locate a certain sample

for further inspection. If a sample is still on the analyzer, use System
Overview > Sample Tracking to locate it.
Statuses displayed in the Sample Tracking window comprise the following:

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Figure 15:Sample traching button

5.3. Reagents:

5.3.1. Reagent Setting Screen

To display This screen choose Reagent>Setting

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Figure 16: Reagent Setting Screen

 To manually register a cobas e pack

1 Select an e 601 from the Module box on the Reagent > Setting screen.
2 Choose Manual Registration to open the Manual Registration (e 601)
window.
3 Type the barcode of the cobas e pack to be registered.
3 Choose OK.

 To unload a reagent cassette

1 Put the module in standby.
2 Select a c 501module from the Module box on Reagent > Setting.
3 Select the position of the reagent cassette that is to be unloaded.
4 Choose Cassette Unloading to open the Cassette Unloading window.

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5 Choose either Unload (to send the cassette to the cassette loading port)
or Dump.Choose Execute.

5.3.2. Reagent Status screen

To display this screen, choose Reagent > Status.

Figure 17: Reagent Status Screen

5.3.3. Reagent Overview button

By changing its color, the Reagent Overview button indicates potentially insufficient
amounts of reagent on the module currently selected in the Module Overview area. It
also indicates when QC results are out of range and if there is no valid calibration
available:

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Figure 18: Button in module overview

Choose the reagent overview button to display the Reagent Overview window. This
window displays an overview of the consumables loaded on the module currently
selected.

5.3.4. Reagent Overview e 601 module

Select an e 601 module in the Module Overview area of the System Overview
screen and choose Reagent Overview to display this screen. It consists of 2
areas, the Reagent area and the Inventory area.

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Figure 19: Reagent overview windom (e 601)

5.4. Calibration
Calibration is the process that establishes a relation between measurement value
and the corresponding results.
This process may comprise the complete setting up of a new calibration curve or it
is only the update of one or two parameters of an existing calibration curve. In
either case the term calibration is appropriate.

5.4.1. Overview
The calibration menu contains three screens: Calibration > Status,
Calibration > Calibrator, and Calibration > Install.

The following sections explain certain tasks associated with the

Calibration > Status screen. Not all tasks are described, but the most
important ones.
To display this screen choose Calibration > Status.

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Figure 20: Calibration > Status screen

This screen shows detailed information about the calibration status of the tests on the
modules selected in the Module list box. This screen is used to select tests for start up,
timeout, changeover or manual calibrations.

5.4.2. Requesting and cancelling calibrations manually

According to the intended use, calibrations are automatically recommended
by the system and accepted by the operator via the System Overview
screen.
 To request calibration for a test manually
1 Choose Calibration > Status.
2 Select the test and reagent (Current or SBx) that needs to be
calibrated from the list.
The selected line is highlighted in blue.

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3 Select the appropriate button in the Method area for a Blank, 2

Point, Full, or Span calibration.
The selected option appears in the Method column highlighted in
green, the Cause column indicates Manual, and the Save button
turns yellow.
4 To request calibrations for additional reagents and tests repeat
steps 2 and 3.
5 Choose Save to save the changes.
All listed tests and reagents that have an entry in the Method column
are highlighted in green. This corresponds to a requested calibration.

5.4.3. Reviewing calibration data

After a calibration is completed it should be reviewed. Details for each
calibration performed on any of the analyzer’s modules can be
retrieved from the Calibration >
Status screen. The following sections describe the possibilities to
check calibration data according to the different kinds of test calibrated.

5.4.4. To view and compare results of previous e 601 calibrations

1 Choose Calibration > Status.
2 Select a cobas e pack and the corresponding measuring cell from the
list on
Calibration > Status.
3 Choose Calibration Trace to open the Calibration Trace window.

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Figure 21: Calibration Trace Window

The graph shows calibration results for the selected photometric test. It displays
the measured absorbance values for both the Std (1) calibrator and the
calibrator with the maximum concentration Std (2)-Std (6) on one plot.
The left and right y-axes are scaled independently:
o The left axis refers to the Std (1) calibrator represented by .
o The right axis refers to the maximum calibrator Std (2)-Std (6) represented
by

5.4.5. Calibration Calibrator screen

The following sections explain certain tasks associated with the
Calibration > Calibrator screen. Not all tasks are described, but the most
important ones.
To display this screen choose Calibration > Calibrator.

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Figure 22 : Calibrator screen

The Calibration > Calibrator screen is used to review information about
already
registered calibrators and to assign calibrators to specific racks and
positions. The
rack assignment is necessary for calibrators that are used without
barcode identification.

5.4.6. Calibrating tests during operation

Calibration is usually performed at the beginning of routine operation
before sample processing begins. However, it can be done anytime during
routine operation as well.
The procedure for calibrating tests during operation is essentially the
same as the calibration at the beginning of routine operation:
To perform calibrations during operation
1 Request the recommended calibrations via the Calibration and QC
Selection button (highlighted yellow) on the System Overview
screen.
2 Print the Load List.

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3 Prepare the calibrator(s).

4 Place the calibrator rack(s) on the loader.
5 Start the calibration measurement

5.5. Quality control

5.8.1. QC concept
Regularly perform QC measurements to continually monitor the
instrument performance. After measurement of QC samples, data can
both be transferred to and evaluated on a Host or they can be
evaluated on the system.

5.8.2. QC Status screen

The following sections explain certain tasks associated with the QC >
Status screen.
Not all tasks are described, but the most important ones are discussed
here.
To display this screen choose QC > Status.

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Figure 23 : QC Status Screen

The QC > Status screen displays all installed controls with the
corresponding assigned and activated tests for each module and
measuring cell.
The test display can be sorted by module, test name (alphabetical order),
control name (alphabetical order), QC test selection, or QC cause. Tests
can be selected with the Select/Deselect button. Selected tests are
highlighted in green. A control test selection is made for the subsequent
control run. The control test selections of the status list are reset after the
control is measured.
An asterisk (*) in the first column of the QC > Status screen denotes which
control is used as automatic QC.

5.8.3. QC Run Status screen

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To display this screen choose QC > Run Status

Figure 24: QC status screen

Use the Run Status screen to get an overview of the last 500 quality
control (QC) measurements performed on the analyzer or to view the
most recent QC measurements for one particular test specified.
Use the Test box to select all tests or one specific test to be displayed
on the chart. Use the arrows at the top right of the chart to move the
focus from one result to the next.

5.8.4. QC Individual screen

To display this screen choose QC > Individual.

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Figure 25 : QC Individual Screen

The QC > Individual screen lists all non-accumulated QC results.

The list can be sorted by test name, module, and control name. The table
below explains the most important columns of the list.

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Figure 26 : most important column of QC list

On the QC > Individual screen, choose Chart to open the Individual QC Chart window.

Figure 27 : Individual QC Chart

This window displays all non-accumulated QC results for the selected test in a
Levey-Jennings chart. A Levey-Jennings chart provides a visual method of
monitoring trends in QC results. The result values are scaled to the standard
deviation (SD) of the respective test.
Up to three controls for one test can be selected (Select button) and displayed on
one chart.
5.8.5. Excluding an individual QC point or adding a
comment
Individual QC points on a QC chart can be excluded from QC
calculations if required. It is also possible to annotate individual
QC points.
1 Choose QC > Individual > Chart.
2 Select the QC point to be excluded from QC calculations.

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3 Choose Comment on the Individual QC Chart window to

display the Comment window.
4 If necessary type a comment (max. 20 characters) in the
Comment box.
5 Choose Exclude. The window is closed after confirmation.
This removes the point from statistics but continues to display
the information on the chart.

A comment is attached to this point

This point is excluded

Also results from a standby cobas e pack are shown as excluded without
a comment.

This point is excluded and a comment is attached

Excluded points cannot be included later.

6 Choose OK.

5.8.6. Accumulation of QC results

At the end of daily operation, QC measurement data should be accumulated. There
are two accumulation methods available: Mean-R and X-R. The choice for one or
the other method is made under Utility > System > QC Setting

Choose Utility > System > QC Setting to display the QC Setting window.

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Figure 27 : QC setting window

Accumulation Method
Select one of the two accumulation methods, Mean-R or X-R, from this box.

QC Calculation
If the accumulation method is Mean-R, select one of the two calculation
methods, DayToDay or Overall, from this box to specify how mean and SD
values are calculated in the cumulative QC.
This box is not available if X-R is selected in the Accumulation Method box.

5.8.7. Accumulating QC results

1 Select the data to be accumulated from the list on the QC > Individual
screen.
2 Choose Accumulate.
3 If Mean-R is set as accumulation method, go to step 4.

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If X-R is set as accumulation method, type the consecutive number of

the QC result to be used for the accumulation in the box or type 0 (zero)
to transfer the mean value; then choose OK.
4 In the confirmation window choose Yes to accumulate the selected
data.
After accumulation the corresponding data are deleted from the QC >
Individual screen and a new standard deviation (SD) and mean value is
calculated and displayed on QC > Cumulative. But if later new QC data
with this control is generated, the accumulated results will be displayed
again in the QC chart with the indication that they are already
accumulated.

5.8.8. QC Cumulative screen

To display this screen choose QC > Cumulative.

Figure 28 : QC Cumulative screen

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The QC > Cumulative screen lists all accumulated QC results.

The list can be sorted by test name, module, and control name. The table
below explains columns whose meaning is different from that on the QC >
Individual screen:

 N: Number of accumulations (max. 500)

 Mean: Accumulated mean for each test (using the
accumulation method selected on Utility > System > QC
Setting)

5.8. Maintenance

For most maintenance actions, either a module has to be in standby or the

analyzer has to be in shutdown status. This section explains what shutdown
status is, how to put the analyzer in shutdown status, how to restart the analyzer,
and how to release the analyzer in standby status after interlock function has
generated an error message.
Make sure to put the analyzer in shutdown status or in an appropriate
maintenance mode (for example, incubator bath cleaning mode) before replacing
parts.
Keep the top cover of the analytical module closed for maintenance carried out
with the system powered on. If a check or maintenance requires open covers, be
careful not to touch any other than the aimed-at parts.

5.9.1. Shutdown status

Shutdown status is the condition where analytical module(s) and control unit are
disconnected and the operation power switch is switched off. Power for keeping
the reagents cool, however, is still supplied.

System time approximately 3 minutes

 To shut down the analyzer

1 Choose Shut Down (global button) to display the Shut Down window.

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2 Select the Shut Down option, choose Execute and confirm the
shutdown.
3 Wait until the computer power supply turns off. Then, switch off the
power switch of the printer and monitor.
4 Switch off the operation power switch on the left of the rack sampler
unit.

 To switch on the analyzer

1 Switch on the analyzer’s operation power switch located on the left of
the rack sampler unit.
The system starts the initialization routine.
2 Switch on the computer of the control unit, the monitor, and the printer.
3 After initialization, the Logon screen displays. Enter your operator ID
and password to log on.
4 Choose OK to gain access to the software and begin system
operation.

5.8.1. Defining and editing maintenance types

To edit a maintenance type or define a new type
1 Choose Utility > System > Maintenance Setting.
2 If a new maintenance type is to be defined, select a free line from the
Maintenance Type list, choose Edit, and proceed with step 3. If an existing
maintenance type is to be edited, select the appropriate line from the
Maintenance Type list, choose Edit, and proceed with step 4.
3 Enter a name for the maintenance type in the text box at the top of the window.
4 Select an item from the Maintenance Items list box. This list includes both
maintenance items and user defined maintenance pipes.
5 Choose Parameter to display the Maintenance Parameter window for the
selected maintenance item, if available. Use this window to define parameters for
the selected maintenance item.

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6 For maintenance tracking, enter the frequency in the text box and select the time
period (Hour, Day and Month) from the Period list box.
7 Select a timer function from the Timer list box:
 Realtime: The actual time
 Power On: Cumulative power-on time of the analyzer (excluding sleep time)
 Operation: Cumulative operation time
Power on time and operation time are both listed on the Maintenance Report
(Print > Utility > Maintenance Report). If a frequency period is not required,
enter 0 in the field to cancel.
8 Enter the warning level (%) in the Warning Level text box. Example: If you define
a period of 10 hours in real time and a warning level of 90%, the analyzer will
remind you to perform the maintenance item after 9 hours.
9 Select the Comment check box to display the Comment field on the appropriate
maintenance item window and to print the comment on the Maintenance Report.
10 Choose Update to add the item to the Maintenance Items list.
11 Repeat steps 3 to 10 for all maintenance items for the maintenance type.
12 Choose OK to save the collection and its settings and close the Edit
Maintenance Type window.

Figure 29: Maintenance Setting Window

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Figure 30: Edit Maintenance Type Window

The following tables display the maintenance items and checks and indicate in which
operation mode they can be performed.

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5.9. Finalization

5.9.1. To perform Reagent Prime

1 Choose Utility > Maintenance.
2 Choose (8) Reagent Prime in the Maintenance Items list.
3 Choose Select to display the Reagent Prime window.
4 Deselect the c 501 module and select the e 601 module.
5 In the Elecsys area select Reagent from the e 601 list box. In the Prime
Cycles area enter 1 for the Reagent.

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6 Choose Execute to start reagent priming.

7 Wait until the reagent prime completes and the instrument enters standby, then
start finalization.

5.9.2. To perform Finalization

1 Choose Utility > Maintenance.
2 Choose (32) Finalization in the Maintenance Items list.
3 Choose Select to display the Finalization window.
4 Select the appropriate e 601 module and deselect all other modules and units.
Selected modules are highlighted in white. Channel 1+2 is activated.
5 Choose Execute to start finalization.
5 After the procedure has been completed, the system goes into
standby.

6. Appendices:
Cobas 6000 user manual

7. Signature Block:

Prepared by: Reviewed by: Approved by:

Head of Department Head of Quality Department General Manager

Dr Khalil Charafeddine Dr. Youssef Fares

Revised On

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