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Guidelines for Writing an SOP for
Mass Spectrometry
prepared by the Measurements & Standards Committee of the American Society for
Mass Spectrometry
1 September 1997
INTRODUCTION
The purpose of this document is to provide guidance and suggestions for writing Standard
Operating Procedures (SOPs) for mass spectrometer systems (MS.) The focus is on SOPs
for MS instrumentation that generates data in support of FDA filings. Other regulatory
agencies, such as the EPA, which may have different requirements, are not covered. An
overview of SOP formats and typical language is discussed. Several examples from SOPs
currently in place in laboratories in the community are included as appendices. These
guidelines are intended to provide a framework for implementing rational and useable MS
SOPs. The Society takes no position on the applicability of any specific suggestion in this
document or the examples shown for a specific laboratory operation. In fact, it is the
Society's view that a "boilerplate" or "fill-in-the-blank" SOP probably cannot be written. Each
laboratory situation is unique. Each laboratory needs to assess its current practices and in
consultation with its Quality Assurance Unit design SOPs that meet its particular needs.
Collaboration with the QAU is valuable as it represents the company's positions on GLP
issues and because it will likely be the first group to audit the laboratory. Furthermore, the
QAU may have an SOP that describes how laboratory SOPs should be written. In most
instances, SOPs should document a laboratory's current practices, not legislate new ones:
"write what you do and do what you write."
MS SOPs are only one part of an SOP package for mass spectrometry laboratories
generating data for registrational purposes. An entire suite of SOPs might include, but not be
limited to, assay validation procedures, study sample analysis procedures, personnel
training, sample tracking, archiving of data and change control.
The main Federal regulations pertaining to this topic are from CFR Part 58, "Good
Laboratory Practices for Nonclinical Laboratory Studies", Section 58.63 (reproduced here in
its entirety) (1,2):
§ 58.63 Maintenance and calibration of equipment
a. Equipment shall be adequately inspected, cleaned, and maintained. Equipment used
for the generation, measurement, or assessment of data shall be adequately tested,
calibrated and/or standardized.
b. The written standard operating procedures required under ' 58.81(b)(11) shall set
forth in sufficient detail the methods, materials, and schedules to be used in the
routine inspection, cleaning, maintenance, testing, calibration, and/or standardization
of equipment, and shall specify, when appropriate, remedial action to be taken in the
event of failure or malfunction of equipment. The written standard operating
procedures shall designate the person responsible for the performance of each
operation.
c. Written records shall be maintained of all inspection, maintenance, testing, calibrating
and/or standardizing operations. These records, containing the date of the operation,
shall describe whether the maintenance operations were routine and followed the
written standard operating procedures. Written records shall be kept of nonroutine
repairs performed on equipment as a result of failure and malfunction. Such records
shall document the nature of the defect, how and when the defect was discovered,
and any remedial action taken in response to the defect.
Note that the regulations in this part apply specifically to nonclincial studies used for
Investigational New Drug (IND) registration. Therefore, animal drug safety evaluation studies
are covered under these regulations, while clinical studies in humans are not. However, other
regulations in Chapter 48, Bioresearch Monitoring Human Drugs, require instrument SOPs
for bioavailability and bioequivalence studies (3.) Further, any work performed to support
Good Manufacturing Practices, GMP, must also be covered by instrument SOPs. Many
members of the ASMS community have taken the position that their laboratories will operate
under these regulations and use SOPs at all times. Nonetheless, if a mass spectrometry
laboratory never does any nonclinical GLP work for FDA filings, GMP or
bioavailability/bioequivalence testing, then that laboratory is not obligated to have MS SOPs.
But, if an instrument is used, even occasionally, for experiments that will support an FDA
filing, an SOP for that instrument should be developed and followed. See Boyd, et al. (4), for
an excellent report on the 1994 ASMS GLP workshop which includes a discussion on
"colloquial" vs. narrow interpretations of the term "GLP."
Note that neither the title nor the body of Section 58.63 includes the word "operation". The
MS SOPs should not be operator's manuals. The SOPs are meant to ensure that a particular
instrument is properly maintained and calibrated such that any data generated from it when
operating can be considered reliable. However, a laboratory may find it useful or important to
provide synoptic operations manuals or "Laboratory Operations Guides", that fall outside the
purview of SOP inspection criteria but provide critical information to instrument operators.
There are at least two general approaches to writing an MS SOP. The first might be termed a
"system-independent" document and the second a "system-specific document." In the first
case, the SOPs are written in a way general enough to cover the requirements of the
regulations while encompassing a wide variety of instrument models. Using this approach,
the laboratory might think it best to have separate SOPs for quadrupole and magnetic sector
instruments, while still not differentiating between specific models. The second approach is to
have SOPs for specific instrument models, e.g., one for a Finnigan TSQ 7000 and another
for a PE Sciex API 300. Again, the best approach for a particular laboratory can only be
determined by that laboratory after review and consideration of its current practices and in
consultation with its QAU, if appropriate.
It is also important to keep in mind that SOPs are "living documents." That is, they can and
should be modified on a regular basis as practices and procedures change. Further, it is
acceptable to deviate from current SOPs if valid scientific reasons exist for such a deviation
and the change is noted and supported in the appropriate study files and notebooks. Such a
deviation may be temporary for a particular problem or may represent an overall
improvement that should be included in the next SOP revision.
SOP FORMAT
An SOP document should consist of a title/information page and document body which
usually includes five topics or sections: Purpose, Scope, Introduction, Responsibilities and
Procedures. The first four of these sections provide the ground rules for the SOP, what it
encompasses, how it is to be applied, while the procedure section provides the details of
what needs to be done. This is not the only way to write an SOP, but this format provides
fairly clear delineation of the various aspects an SOP is expected to cover for the regulations.
It certainly seems possible, for example, that the first four sections might be contained within
a single section as an Introduction. In any event, the SOP should meet internal requirements
on formatting, writing and changing SOPs.
Title/information page
In addition to the title, the title page contains a procedure number incorporating some form of
version control, the author(s) name(s), approval name(s), signatures and dates of signatures
for all, an effective date for the procedure and total number of pages in the document. A title
might be "Maintenance and Calibration of Mass Spectrometer Systems" or "Maintenance and
Calibration of a Sciex API III Mass Spectrometer." A procedure number could be
"INST00006.01" where this is version 1 of the sixth in a series of instrument SOPs.
It's a good idea to include the author names as that provides a point of reference for those
with questions about the intent of certain language and it also provides a logical "volunteer"
for SOP re-evaluation and revision. Management sign-off indicates awareness of the
document, approval of its contents and assurance of enforcement.
Finally, dates, especially effective dates, are very important for historical control. These show
which SOP version was in force when a particular study was analyzed. It is important to keep
copies of old SOPs that are no longer in force for an auditor's review in case an audit is
directed at studies that were run under older versions of a particular SOP. Thus the study
can be audited based on the procedures in place at the time, not on current, perhaps
different procedures.
Purpose
This section simply describes the focus of the SOP, which, in this case, is to provide a
maintenance and calibration procedure for the instrument(s) defined in the title.
Scope
This section defines the applicability of the SOP, i.e., the work that will be subject to be the
provisions of the SOP. It could, for example, indicate whether only nonclinical GLP studies
are subject to the terms of SOP or all data generated to support registrational filings or
something in between.
Introduction
The SOP introduction provides background material for the procedure. A list of defined terms
can be included in this section. This is good place to define the mass spectrometer - is it just
the mass analyzer and supporting hardware, excluding data systems and inlet systems, or is
an LC/MS, for example, an all-inclusive system consisting of the HPLC, the MS and the DS?
The latter provides the advantage of the "black box" approach to instrument performance
verification,
Responsibilities
This section defines the person(s) who is going to be responsible for ensuring that the
procedure is implemented. This can be a single individual or it can be generic to state that
the person running the instrument to generate data covered by this SOP is the responsible
individual (RI).
Procedures
The procedures section will be the most detailed part of the SOP in which required
procedures for "maintenance and calibration" of the mass spectrometer(s) are itemized and
described. Before writing this section, it is very important to review and analyze current
laboratory procedures. It is likely that most of the everyday practices currently in place in a
particular laboratory are adequate, not only for good science, but also for the purposes of the
SOP. Thus all that is required is to formalize them by writing them down as an SOP,
including a procedure to document compliance. If deficiencies exist in maintenance and
calibration procedures, this may be good time to fix them, but the "wouldn't it nice if we did
this" syndrome should be avoided. Again "write what you do and do what you write." It is very
important to remember that the procedures listed in the SOP will form the basis of evaluation
for an audit. For example, if a procedure in the SOP specifies calibrating an instrument with
PFTBA everyday before use, then, to be in compliance, not only must the calibration be
performed daily (within the work scope of the SOP) but it must be documented in such a way
that an auditor can verify that it was in fact done (e.g., dated, signed copy of the PFTBA
spectrum, including a statement of acceptability.) If, in the best judgment of the laboratory,
daily calibration of an instrument with PFTBA is unnecessary, then such a procedure should
not be included in the SOP.
Maintenance items would include source cleaning and changing vacuum pump fluids, as well
as general inspections, such as checking vacuum levels and temperature-controlled zones.
Schedules for performing the maintenance items should be included in some form. For
example, source cleaning could be tied to an instrument performance criterion rather than to
the calendar. Formal preventive maintenance (PM), on the other hand, may be better put on
a calendar basis, but the time frame should be flexible enough to allow for scheduling delays.
For example, a PM might be specified for every 6-12 months or 12-18 months, as
appropriate to the particular equipment.
Calibration would most obviously include mass axis calibration, but in some instances might
include such things as voltage calibrations of power supplies, for example. Calibration
procedures should also include some acceptance guidelines, e.g., "determined m/z of
calibrant ion shall be within 0.1 amu of theoretical." Depending on the circumstance,
standard reference compounds, such as PFTBA or PEGs might be the preferred calibrant or
the analytes for a particular analysis might be a better choice. In either case, the calibrants
should be well-characterized reference materials. A laboratory performing qualitative analysis
or structural identification, would probably use standard reference materials. On the other
hand, a laboratory in the quantitative analysis business might find use of the actual analytes
as calibrants to be very useful. In either case, the SOP should be probably be written to allow
making either choice, or some combination, depending on the circumstance and at the
discretion of the scientist involved.
One approach used by some labs, is to have an SOP for general instrument maintenance
and calibration procedures and rely on specific analytical methods for actual operation and
sample analysis. Language in the SOP references analytical methods as the source for
operating details for a given analysis. This works particularly well for quantitative analysis,
where analytical methods include critical details on instrument parameters and special
calibrations which might be required for a particular analyte. Such methods might include
system suitability testing where the entire analytical system, chromatographic performance
as well as the sensitivity and resolution of the mass spectrometer for the compounds of
interest, would be examined prior to running a set of samples (a "black box" approach.) Thus,
system suitability testing might obviate the need for more general calibrations that might
otherwise be called for in an SOP.
Finally, the procedure should itemize how the specified practices will be documented. Some
instrument parameters might be best documented in a spreadsheet on the instrument's
computer. Service reports are probably most easily stored in a binder of some sort. The
regulations require that any instrument malfunction be documented with the nature of the
problem, who discovered it, and how it was corrected. Vendor service reports might suffice
for this purpose, if they include, or can be made to include, all required information, such as
the symptom of the problem, in sufficient detail. Further, system qualification after service
should be documented.
SUMMARY
This document hopes to provide approaches and suggestions for promulgation of Standard
Operating Procedures for mass spectrometers, which is only one of many SOPs required for
a laboratory supplying registrational data. While the main focus of this writing is to provide
guidelines for MS laboratories that need to be in regulatory compliance, the intent of SOPs
should also be to promote good science and to try to ensure high quality experimental
results. The regulations do not specify how to write SOPs or maintain and calibrate
instruments; those decisions fall to the laboratories and should reflect the sound scientific
and real-world practices of the individuals involved. The over-arching principle in generating
SOPs is always to document current practices, not legislate new ones. A corollary is that
SOPs are living documents: as practices and procedures evolve, so must SOPs.
REFERENCES
1. Code of Federal Regulations, Title 21, Food and Drugs; Office of the Federal
Register, National Archives and Records Administration: Washington, DC, 1994; Part
58. (Available from: New Orders, PO Box 371954, Pittsburgh, PA, 15250-7954.
2. FDA Compliance Program Guidance Manual. Chapter 48: Human Drugs Bioresearch
Monitoring. Program 7348.808, Good Laboratory Practice (Nonclinical Laboratory.)
1994.
3. FDA Compliance Program Guidance Manual. Chapter 48: Human Drugs Bioresearch
Monitoring. Program 7348.001, In Vivo Bioequilvalence. 1995.
4. Boyd, R.K., Henion, J.D., Alexander, M., Budde, W.L., Gilbert, J.D., Musser, S.M.,
Palmer, C. and Zurek, E.K. J. Am. Soc. Mass Spectrom. 1996, 7, 211- 218
ACKNOWLEDEMENTS
The Measurements and Standards Committee would like to thank the following individuals
for their thoughtful comments and suggestions which added significantly to the quality of this
document:
P.K. Bennett, K. Chan, R.W. Edom, R.L. Foltz, P.J. Gale, J.D. Henion, S.M. Musser, T.D.
Oglesby and T.V. Olah
SOP Example 1
Generic Format
Analytical Services Lab ABC
Standard Operating Procedure
Title: Maintenance and Calibration of Mass Spectrometer Systems.
Procedure No.: INST0009.01 (Original)
Prepared by: Date:
Approved by: Date:
Effective Date: July 1995
Number of Pages: 4
This procedure becomes effective when approved by the Executive Director or appropriate
Site Director. Approval of this page indicates approval of all pages in this procedure.
SOP INST0009.01
I. PURPOSE
The purpose of this document is to provide a standard operating procedure
(SOP) for the maintenance and calibration of mass spectrometer systems in
Analytical Services Lab ABC.
II. SCOPE AND IMPLEMENTATION
This SOP applies specifically to situations in which data obtained from a
particular mass spectrometer system are to be used for registrational filings.
III. DEFINITIONS
A. Mass Spectrometer (MS) System: For the purposes of this SOP an MS
system is defined as all components required to generate usable mass
spectral-based data for a given sample. This includes but is not limited to all
inlets (gas chromatograph, liquid chromatograph, solids probe, etc.), all
electronics (power supplies, amplifiers, digital to analog converters, etc.), all
hardware (lenses, mass analyzers, vacuum pumps, etc.) and all associated
data system hardware and software.
B. Operator: Person or persons responsible for generating MS system data for
a given sample or set of samples. C. Analytical method: Steps(s) to be
followed for a given analysis of a given compound(s) in a given matrix,
including an outline of specific operational parameters for an MS system used
in performing said analysis.
IV. RESPONSIBILITIES
A. It is the responsibility of the person(s) operating MS systems to follow this
procedure.
B. It is the responsibility of the Director, Analytical Services Lab, to interpret
this procedure.
V. PROCEDURES
A. Daily Procedures
MS settings appropriate for a given analysis of a given sample or sample set
will be found in the analytical method for a given assay. Assessment of proper
functioning of a given MS system in a given analytical run will be based on the
performance of standards and quality control samples in that run.
Prior to analyzing samples on a specific MS system, it is recommended that
the following items be checked. Critical parameters may be recorded in an
electronic log maintained in the system's computer, in the laboratory notebook
containing the data acquired or in the system's service log.
1. Vacuum system: pressures within normal range for that system.
2. Temperatures: temperature-controlled zones within normal range for the
given MS system and for the given analytical method.
3. Mass axis calibration and resolution: axis calibration and resolution may be
checked on an as-needed basis with either generic calibrants (PFTBA,
Ultramarks, PPGs, etc.) which generate ions of known m/z ratios or with the
compounds that are the subject(s) of the analysis. In all events, the calibrant
should bracket the mass range of interest for a given analysis. The mass axis
should be re-calibrated if the measured m/z of any of the calibrant ions in the
range of interest differ by more than 0.15 amu from their expected mass.
Resolution should be sufficient to discriminate all components of interest.
Peak widths greater than 1 amu (measured at half height) should be used with
caution. Special requirements for calibrants, mass range and resolution for a
given assay should 'be specified in the analytical method.
4. Chromatographic inlets should be checked for required quantity and quality
of carrier fluid and any leaks. Where found, deficiencies corrected prior to
sample analysis.
5. Inlet injector assemblies, ion source assemblies, lens assemblies, etc.
should be inspected and cleaned, if warranted by poor system performance,
as indicated by poor mass peak shape/resolution and/or low sensitivity of
calibrant or analyte.
6. If specified in the analytical method, a system suitability sample to test the
entire MS system may be run prior to analyzing registrational sample(s). An
appropriate system suitability sample might be, but is not limited to, a low level
standard from the analytical set to be run. In addition to whether sufficient
sensitivity is available for the analysis, chromatographic peak shape and
resolution (if appropriate) can be verified as well.
B. Annual Procedures
It is recommended that preventive maintenance be performed at 6-12 month
intervals (or according to manufacturer's recommendations.)
1. Preventive maintenance items might include, but are not limited to,
replacing vacuum pump fluids, changing gas adsorbers, cleaning mass
analyzer assemblies and electronics bins, etc. (to be determined based on the
manufacturer's recommendation for a given MS system.) Such maintenance is
to be performed by an authorized individual, either a manufacturer's
representative or another with suitable training or experience.
2. After completion of preventive maintenance, a test sample should be
analyzed to verify system performance. This may either be a generic
compound (PPGs, Ultramarks, etc.), or a specific compound whose
performance is known to the operator.
VI. MANUALS
Manuals, which detail the specific operation of a specific MS system, are to be
located where they are readily accessible to operators: either near the
appropriate system or in a centralized library.
VII. TRAINING
MS system operators are to be familiar with all SOPs and operating manuals
pertaining to the use of a given system.
VIII. DOCUMENTATION
A service log, maintained for each mass spectrometer system, will contain all
service reports. Records of mass axis calibrations and any system suitability
analyses will also be maintained, either in the service log or in the appropriate
laboratory notebook that contains the data acquired with those calibrations.
Archival storage of records shall follow SOP DOCU0009.02.
Example #2
Instrument Type Format
ANALYTICAL SERVICES LABORATORY DEF
STANDARD OPERATING PROCEDURE
Title: Use and Maintenance of a Tandem Triple
Quadrupole Mass Spectrometer
Procedure No.: INST0004.06
Supersedes
Procedure No.: INST0004.05
Prepared by: Date:
Approved by: Date:
Effective date: January 3, 1997
Number of pages: 6
Analytical Services Lab Standard Operating Procedure
SOP Number:
Title: Use and Maintenance of a Tandem Triple
INST0004.06
Quadrupole Mass Spectrometer
Page 2 of 6
Effective date:
Supersedes SOP No.:
January 3, 1997
INST0004.05
Author's Initials/Date:
Lab Director's Initials/Date:
I. PURPOSE
To provide general guidelines for conducting routine tandem triple quadrupole mass
spectrometer operation and maintenance.
II. SCOPE AND IMPLEMENTATION
Adherence to this SOP is required for all tandem triple quadrupole mass spectrometric
services offered by ABS that are subject to GLP guidelines.
III. INTRODUCTION AND DEFINITIONS
The mass spectrometer consists of a modern commercial quadrupole mass analyzing
system that may be interfaced via an appropriate interface to a solution delivery system such
as an infusion pump, a high performance liquid chromatograph or other condensed phase
separation system including capillary electrophoresis instrumentation. The mass
spectrometer is controlled by a data system that allows the operation of the mass
spectrometer in all the appropriate modes required for analyses.
The mass spectrometer system is a highly sophisticated analytical instrument. It may be
operated only by those who are conversant with the technique of mass spectrometry, have
been trained in its operation and maintenance, and deemed competent by the Laboratory
Director or designee. Routine operation of mass spectrometer systems are described in the
operator's manual provided by the manufacturer.
Calibration: The process of calibrating the mass axis. This is performed using a
representative mass spectrum of a suitable reference compound (e.g., PPGs) recorded
under experimental conditions appropriate for the analysis planned.
Tuning: The process of optimizing the mass spectrometer electronics (lens voltages
and resolution settings) for a particular compound(s).
IV. PROCEDURES
A. General Operation
The mass spectrometer system must be operated according to the procedures described in
the appropriate operator manuals and/or according to updated practices accepted and
demonstrated by this laboratory or by the manufacturer. The actual operation of the system
depends on the analysis being carried out and the nature of the sample.
Analytical Services Lab Standard Operating Procedure
SOP Number:
Title: Use and Maintenance of a Tandem Triple
INST0004.06
Quadrupole Mass Spectrometer
Page 3 of 6
Effective date:
Supersedes SOP No.:
January 3, 1997
INST0004.05
Author's Initials/Date:
Lab Director's Initials/Date:
B. Routine Mass Calibration
Mass axis calibration should be checked according to the procedures outlined below. This is
performed using a representative mass spectrum of a suitable reference compound (e.g.,
PPGs) recorded under experimental conditions comparable to those used for the analysis
planned for the study. Any deviations from expected mass assignments or sensitivity must be
corrected by appropriate methods described in the operator' s manual (i.e., recalibration). A
record of these data and the corresponding mass spectrometer conditions (e.g., lens
voltages, electron multiplier voltages, resolution settings) must be kept in the instrument
calibration log binder.
For mass spectrometers that require a defrost cycle (recycle), a mass axis calibration check
should be performed after a recycle, after maintenance that could affect calibration, prior to
the initiation of a new project, and prior to performing a different analytical method on an
instrument that has not been calibrated that day.
For mass spectrometers that do not require a recycle, a mass axis calibration check should
be performed when changing projects and if the instrument has not been calibrated that day
or after maintenance that could affect calibration. However, if a single method is being
performed over more than one day, the instrument does not require a calibration check.
C. Non-Routine Mass Calibration
A mass-axis calibration that brackets the mass range of interest should be performed
following non-routine maintenance by service engineers or by in-house trained operators. A
full mass range calibration should also be performed at least annually or as indicated
necessary by a performance check on a suitable reference mass standard (e.g., PPGs). The
results of mass calibrations must be maintained in chronological instrument calibration log
binders.
D. Data Collection
All data collection will be performed by the mass spectrometer's dedicated computer and
data handling system. The operation of this system will be performed as recommended by
the manufacturer as described in the instrument's operator manuals.
Analytical Services Lab Standard Operating Procedure
SOP Number:
Title: Use and Maintenance of a Tandem Triple
INST0004.06
Quadrupole Mass Spectrometer
Page 4 of 6
Effective date:
Supersedes SOP No.:
January 3, 1997
INST0004.05
Author's Initials/Date:
Lab Director's Initials/Date:
E. Data Handling and Storage
All data stored on magnetic media or printed copies are to be maintained and retained
according to SOP DOCU0003 and SOP COMP0005.
F. General Record Keeping
Periodic performance and maintenance records will be maintained in the mass spectrometer
Maintenance and Calibration log book. A sample copy of information to be kept is shown in
Appendix II.
G. Maintenance and Service
The mass spectrometer equipment will be maintained according to the procedures described
in the manufacturer's Operator's Manual(s). Basic consumable spare parts will be held in the
mass spectrometry laboratory. All spare parts may be obtained from the manufacturer or
suitable alternative sources.
Routine preventive maintenance will be performed by a trained operator of the mass
spectrometer system. When additional advice/expertise is required, the manufacturer's
service department should be contacted. All Customer Service Reports should be retained in
the Instrument Maintenance and Calibration log book.
In the event of malfunction or failure, non-routine maintenance may be performed. When
an instrument is found defective or out of specification, a notice shall be placed on it in clear
view indicating that the instrument is not to be used until serviced and re-calibrated and
found to be within specification. The notice shall indicate when service is expected. Records
of repair must be documented and should include the nature of the problem or defect, how
and when it was discovered and remedial action taken in response to the problem. This
information should be documented in the instrument log.
H. Training
All personnel using the tandem triple quadrupole mass spectrometer will be trained by a
qualified individual. Recurrency training will also be provided to ensure continued proper use
of the mass spectrometer. All training will be documented and maintained in training records.
SOP INST0004
Appendix A: Revision History
Section and page of Revision
revision
I, page 2
Revisor
II, page 2
Changed 'by which' to 'for conducting' J. Doe
Added 'tandem triple quadrupole mass
spectrometric'
III, page 2
Changed 'provides for' to 'allows'
IV.B, page 3
Renamed 'Routine Mass Calibration'
IV.C, page 3
changed 'Maintenance and Calibration log
book' to 'calibration log binder'
IV.E, page 4
(Section IV.C also).
IV.F, page 5
IV.G, page 5
Renamed 'Non-Routine Mass Calibration',
changed 'at least quarterly' to 'annually'.
IV.H, page 5
Last two sentences revised.
Revised entire section.
Date
5/5/95
Added
Added
IV.G, page 5
Added information on documentation of J. Doe
remedial action, placement of notice
12/4/95
III, page 2
Deleted 'as well as non-routine' in 2nd J. Doe
paragraph.
8/7/96
IV.A, page 3
IV.C, page 3
'Validated' changed to 'demonstrated' in
1st sentence
IV.E, page 4
Sentence 3 re-structured.
Appendix B, page 7
Added 'Quantitative' 1st sentence, deleted
'which covers this topic' 2nd paragraph.
Removed sentence 'When a...'
Updated form
III, page 2
Added definitions of calibration and tuning
IV.B, page 3
Defined requirements for recycled and
non-recycled instruments
J. Doe
12/16/96
IV.E, page 3
Revised section.
SOP INST0004
Appendix B
Mass Spectrometer Daily Performance Record
Operators
Compound(s)
PSI
He
PSI
Ar
Maintenance
Time
Temp
(K)
Vacuum
(torr)
Recycle
Status
Base
x10-5
Initiated?
Y/N
Start
am/pm
x10-5
am/pm
Finish
am/pm
x10-5
hrs./Auto
Vacuum
(torr)
Recycle
Status
Interface
(cyro)
Monday
Date
Operators
pg. ref.
Compound(s)
PSI
He
Interface
(cyro)
PSI
Ar
Maintenance
Time
Temp
(K)
Tuesday
Date
Operators
pg. ref.
Compound(s)
PSI
He
PSI
Ar
Base
x10-5
Initiated?
Y/N
Start
am/pm
x10-5
am/pm
Finish
am/pm
x10-5
hrs./Auto
Vacuum
(torr)
Recycle
Status
Base
x10-5
Initiated?
Y/N
Start
am/pm
x10-5
am/pm
Finish
am/pm
x10-5
hrs./Auto
Vacuum
(torr)
Recycle
Status
Base
x10-5
Initiated?
Y/N
Start
am/pm
x10-5
am/pm
Finish
am/pm
x10-5
hrs./Auto
Vacuum
(torr)
Recycle
Status
Base
x10-5
Initiated?
Y/N
Start
am/pm
x10-5
am/pm
Finish
am/pm
x10-5
hrs./Auto
Maintenance
Time
Temp
(K)
Interface
(cyro)
Wednesday
Date
Operators
pg. ref.
Compound(s)
PSI
He
PSI
Ar
Maintenance
Time
Temp
(K)
Interface
(cyro)
Thursday
Date
Operators
pg. ref.
Compound(s)
PSI
He
PSI
Ar
Maintenance
Time
Temp
(K)
Interface
(cyro)
Friday
Date
pg. ref.
SOP Example #3
Specific Instrument Format
STANDARD
Analytical Services Lab GHI
OPERATING PROCEDURES
10 Main St.
SOP
LABEQ002.01
Page 1 of 6
Analysisville, USA 1000
TSQ 700, USE AND MAINTENANCE
This SOP is designed to provide general guidelines by which analysis and maintenance are conducted on t
Mass Spectrometer for projects conducted in support of regulatory filings. The TSQ 700 Mass Spectrometer
with a DEC Station 5000/120 data system running Finnigan/MAT software. The TSQ 700 may be used with
optional equipment:
1. Finnigan API/Electrospray interface
2. Gas Chromatograph - Varian
3. High Performance Liquid Chromatograph - Waters, HP
4. Desorption Chemical Ionization (DCI) Probe
The TSQ 700 mass spectrometer is a highly sophisticated analytical instrument. It may be operated only b
are familiar with MS or MS/MS techniques and have been trained in its operation and maintenance.
General Operation: The MS is operated according to the procedures described in the appropriate Finniga
manuals and/or according to updated practices accepted by this laboratory or by Finnigan. The precise ope
MS depends on the analysis required and the nature of the sample. Although the operational procedures a
the scope and requirements of this SOP, the following general procedures apply at all times.
Routine Start-up:
Pressures:
The pressure of the manifold should be recorded on the daily TSQ log sheet. Normal operating pressures (w
but
without
CI
or
CID
gases)
should
< 2x10~ T. An increase in a half order of magnitude should be investigated for possible leaks. (If the sour
vented to atmosphere, it may take up to 4 days to reach ultimate vacuum pressures. However, the high vol
may be turned on when the manifold pressure is < 2x10-5 T
Check for sufficient gas tank pressures.
Check for appropriate pressure of CI reagent gas. Typical source pressure with ammonia reagent gas is abo
or set the pressure as indicated in the method SOP.
Temperatures: The manifold temperature is normally set at 750C and should be checked prior to use.
temperature should be set for the operation being performed.
Data System: Normally the data system is on. Change to the appropriate subdirectory for
collection of data.
Effective 6/5/96
STANDARD
Analytical Services Lab GHI
OPERATING PROCEDURES
10 Main St.
SOP
LABEQ002.01
Page 2 of 6
Analysisville, USA 1000
Calibration checks - Routine: On each day of analysis, the masses of interest of the analyte should be
ensure satisfactory calibration of the instrument. Alternatively, a spectrum of the tuning solution (i.e. pftba,
be collected if it covers the range of the masses being analyzed. Calibration checks should be documented
log as acceptable if within + 0.2 amu of the expected mass.
Instrument Use: At the beginning of an analytical batch, a clean ion volume is inserted as needed and the
tune is checked and/or adjusted. The tune is considered acceptable if sensitivity and specificity is adeq
assay. (Resolution should be a minimum of 2 amu for Q1 and 1.5 amu for Q3.) Analysis of a given sample
samples should only proceed as long as the performance of the TSQ 700 is suitable for analysis. (Refer to p
checks in SOP LABOP006 &/or specific method SOPs.)
Data Handling and Storage: Data is initially collected on the DEC Station hard disk. Hard copy printouts
pertinent information (chromatograms, quantitations). Computer data on the DEC hard disk is backed up on
storage tapes for archival.
Maintenance and Service: The equipment will be maintained according to the procedures described in the
TSQ 700 Operator's manual. Routine preventative maintenance and minor repairs can be performed b
operator. When additional advice/expertise is required, contact Finnigan Service. A11 Customer Service
retained. A schedule of routine maintenance procedures is found in Appendix A.
RF Adjustment & Coarse Mass Calibration - Non Routine: A mass calibration should be performed
engineers or by in-house trained operators according to the Finnigan Operator's Manual following
maintenance. A coarse mass calibration and RF adjustment should also be performed whenever the in
altered, i.e., if the source/quads are physically altered as in removal for cleaning or change in ionization tech
General Record Keeping: Instrument routine operation and maintenance, daily & weekly, will be logged b
operator (see example form 'MSMaintO1' in appendix B), kept in the "TSQ 700 Log Book". Other routine
maintenance and repair records will also be kept in the TSQ 700 log book, (see example form 'TSQ
Appendix C). Maintenance/repair of the associated turbo pump, rough pumps and data system are re
example maintenance form "GenO1", Appendix D). Calibration records are maintained in the calibra
chronological log of unexpected problems and corrective actions is also kept.
Effective 6/5/96
STANDARD
Analytical Services Lab GHI
OPERATING PROCEDURES
10 Main St.
SOP
LABEQ002.01
Page 3 of 6
Analysisville, USA 1000
Appendix A, TSQ 700 Routine, Preventative Maintenance
Daily*: Check pressures.
Check for air leaks
Check calibration
*Daily means each day of use
Monthly: Check RF tune
Quarterly: Change rough pump oil
Clean card cage fan filters
6-9 months: Change turbo pump oil
12-15 months: Clean Q1
Every 3 years or as needed: Clean Q3
As needed: Replace or clean ion volume. Generally at the start of an analytical batch.
Clean lens and source block
Replace filament
Tuning and calibration
Ballast (purge) rough pump. For example, it is needed when large amounts of volatile liquids are being
bubbles are seen in pump oil.
Effective 6/5/96
STANDARD
Analytical Services Lab GHI
OPERATING PROCEDURES
10 Main St.
SOP
LABEQ002.01
Page 4 of 6
Analysisville, USA 1000
Appendix B
Daily Log of Routine Maintenance and Checks
Instrument:
Month
Day
Init.
Ion
Type
Pressure
tuned
Manifold
(Torr)
pftba
calib ck
other,
specify
accept
y/n
cleaning
cmpd
ion
vol
API
spray
shield
heated
capillary
Effective 6/5/96
STANDARD
Analytical Services Lab GHI
OPERATING PROCEDURES
10 Main St.
SOP
LABEQ002.01
Page 5 of 6
Analysisville, USA 1000
Appendix C
Maintenance/Repair Log
Date
Filament
_
Lens
Cleaned,
as needed
Block
Cleaned, as
needed
Clean
Q1,
12-15 mo
Other Maintenance
Performed / Comme
Effective 6/5/96
STANDARD
Analytical Services Lab GHI
OPERATING PROCEDURES
10 Main St.
SOP
LABEQ002.01
Page 6 of 6
Analysisville, USA 1000
Appendix D
Maintenance / Repair Log
Equipment:
Location:
Serial# / ID:
Routine Maintenance:
Date
Routine
(Y/N)
Maintenance or Repair Performed
Comments
SOP Example #4
Instrument type format with separate method
specific instrument operation procedures
Standard Operating Procedure
Document# AI.001
Revision B
Title: Tuning and Calibration of Quadrupole Mass
Spectrometers
Preparation Date: 8/11/96
Effective Date: 8/17/96
Page 1 of 3
1.0 Purpose
The purpose of this SOP is to define generalized procedures
for tuning and calibration of quadrupole mass spectrometer
analytical systems.
2.0 Scope
This SOP pertains to tuning which is performed to establish
and/or verify proper calibration, resolution and ion transmission
of the instrument and defines when such activities are
warranted and required. More specific tuning and calibration
are method, instrument and interface dependent and are
included in Test Method SOPs. Tuning and calibration may be
performed only by trained persons who have demonstrated
proficiency in training module L4007.
3.0 Responsibilities:
The proper tuning and calibration of the instrument is the
responsibility of the user. For quantitative work, the user is the
operator who evaluates the system suitability criteria specified
in each Test Method before beginning an analytical sequence.
For qualitative work, the user is the qualified operator
performing the analyses and is identified in the System Log.
Prepared By Date
Management Date
Quality Assurance Date
AI.001.B Quadrupole Tuning and Calibration Page 2 of 3
4.0 Operation
4.1 Requirements for Tuning and Calibration
4.1.
1
Circ
ums
tanc
es
Tha
t
Req
uire
Tuni
ng
and
Cali
brati
on
of a
Vali
date
d
Qua
dru
pole
Mas
s
Spe
ctro
met
er
Syst
em
Before starting the validation of a
quantitative assay.
Before
starting
qualitative
analysis on a regulated study (as
indicated in the RFA).
When Test Method specific system suitability samples fail to meet the tolerances of analyzer
related criteria.
If the mass spectrometer is
vented and physical manipulation
of the ion optics is performed,
such as cleaning lenses or
removal and cleaning of the
quadrupole assemblies.
If the RF
modified.
parameters
are
If the electronic components that
effect calibration, resolution and
detection are changed. These
include DC Rod Driver, Phase
Lock Loop, RF Amplifier, and RF
Detector components.
4.1.
2
Circ
ums
tanc
es
Tha
t Do
Not
Req
uire
Tuni
ng
and
Cali
brati
on
If changing from ESI to APCI
(verify the system performance
using
a
system
suitability
standard).
If the system is vented to clean
the API skimmer, tube lens and
heated capillary, only (verify the
system performance using a
system suitability standard).
Changing the filament or ion
volume in EI/CI operation.
4.2 Application Specific Tuning
4.2.
1
Syst
em
Tuni
ng
and
Cali
brati
on
For
Elec
tron
Imp
act
(EI)
and
Posi
tive/
Neg
ativ
e
Che
mic
al
Ioni
zati
on
(CI)
Tuning
and
calibration
is
performed
on
the
generic
calibrant
FC-43
(perfluorotributylamine). For full
scan MS or MS/MS evaluation of
complex mixtures or molecular
determinations, the system is
tuned at unit resolution and
calibrated to the exact masses
listed below (1 0.05 amu). For
Test Methods using EI/CI, other
tuning requirements are outlined
in the specific SOP.
AI.001.B Quadrupole Tuning and Calibration Page 3 of 3
EI Tune and Calibration Masses
68.995,
130.992,
218.986,
413.978, 501.971, 613.965.
Positive Methane CI Tune and
Calibration Masses
68.995,
130.992,
218.986,
413.978, 501.971, 651.962.
Negative Methane CI Tune and
Calibration Masses
168.989,
282.985,
556.969, 632.963
413.978,
4.2.
2
Posi
tive/
Neg
ativ
e
Ion
Elec
tros
pray
(ESI
)
and
Atm
osp
heri
c
Pre
ssur
e
Ioni
zati
on
(AP
CI)
For
LC/
MS
and
Mol
ecul
ar
Wei
ght
Det
ermi
nati
ons
A tuning solution containing
Benzophenone, Adenosine and
Erythromycin, each at 100 ng/5L,
is infused and used to tune and
calibrate at the protonated
masses 183.081, 268.105, and
716.469, respectively (1 0.05
amu), at unit resolution.
For negative ion tuning, selected
parameters of the current positive
ion tune table are copied and/or
inverted to the negative ion tune
table. Tuning and calibration are
verified using a 100 ng/5L
solution of Estrone-3-sulfate,
molecular ion 349.111 (1 0.05
amu).
4.2.3 Electrospray Ionization
(ESI) of Peptides and Tryptic
Digests
For the analysis of tryptic digests
and peptides, refer to TM.064
(“Analysis of Peptide Digests”).
4.2.4 Electrospray Ionization
(ESI)
of
Proteins
and
Biomolecules
The instrument is tuned and
calibrated for single quadrupole
evaluation of proteins and
biomolecules using a solution
containing
5
pmol/5L
of
myoglobin and 20 pmol/5L MRFA
to the known average masses for
myoglobin
(848.5,
1060.4,
1211.8, 1413.5, 1696.0 ) and for
MRFA (262.6, 524.3). The
calibration is verified by acquiring
a 2 minute signal averaged
spectrum. The average spectrum
is deconvoluted and must be with
10.01% of 16,951 da.
4.3 Tuning and Calibration Documentation
Upon completion of tuning and calibration, the tune table is
stored to disk and documentation of the tune is entered in the
System Log.
Sections of a Specific Test Method pertaining to MS setup,
tuning and calibration
3.6 Mass Spectral Analyses
Mass spectra are acquired and recorded with a standard
Finnigan TSQ-700 (Finnigan Corp., San Jose, CA) equipped
with the standard ESI source manufactured and distributed by
Finnigan. The following are experimentally determined ranges
or specified settings. Final values within the ranges are
determined by the optimization of the ion current.
Electrospray Voltage: 4.5 kV
Heated Capillary Setting: 225 C
Nebulizing Gas Flow: 70-90psig
Auxiliary Gas Flow:
(flowmeter reading)
10-20
Argon Collision Gas Pressure:
Adjust manifold pressure to 2.5 2.7 x 10-5 Torr
Collision Energy: 27 eV
Conversion Dynode Voltage: -12
to -18 kV
Secondary Electron
Setting: 800-2000 V
Multiplier
Tuning and calibrating is done by infusing a solution of 10.0
5g/mL of XYZ-988 at 5 5L/min into the mobile phase stream
(80% B at 0.2 mL/min). The protonated parent ion mass for
XYZ-988 is 474.2. Correct calibration of 474.2 (1 0.1 amu) is
established in the profile mode for Q1 at unit resolution (FWHM
approximately 0.65 amu). Similarly, Q3 is calibrated at unit
resolution in the Daughter mode at product mass 290.1 (1 0.1
amu). The frequency of tuning and calibration is determined by
system suitability standards (see Section 4.0).
Analyses are performed in selected reaction monitoring (SRM)
mode using an ICL procedure "tm050" (see TM.050 test
method file). The precursor/product transitions used for each
SRM scan are shown below. The scanning quadrupole of the
mass spectrometer (Q3) scans a 0.3 amu window centered
around the product ion of interest. The scan time for each SRM
scan is set to 0.3 seconds resulting in a total cycle time of
approximately 0.6 seconds.
Component
Product Ion
XYZ-988 474.2 290.1
d5-XYZ-988 479.2 295.1
Precursor
Ion
Examples of chromatograms obtained from blank plasma, low,
and high calibrators are on file in the TM.050 test method file.
4.0 In-process Validation Criteria:
The system is normally prepared for an analytical run by
checking with a 1.00 ng/mL unextracted analytical standard
(system suitability standard). Upon injection, the sample must
yield the following results before proceeding with the analytical
run:
1) Chromatographic peak widths
< 10 seconds.
2) S/N on analyte > 15:1
3) Area ratio between 0.025 and
0.030 for xyz-988
4) Retention time between 4.6
and 4.8 min.
If the system fails to meet these criteria, appropriate action
(e.g. tuning) should be taken to rectify the deficiency and the
system suitability standard reanalyzed. Correct performance of
the system suitability standard is documented in the System
Log.