1088 LCGC NORTH AMERICA VOLUME 24 NUMBER 10 OCTOBER 2006
com
MS – THE PRACTICAL ART
How to Build a GLP
Adam Brockman and
Bioanalytical Lab
Jing-Tao Wu
In the words of this
month’s guest
contributors, “Good
laboratory practices work
represents the public and
repeatable foundation for
a new drug entity’s safety
margin.”
T his month’s “MS — The Practi-
cal Art” will interest those start-
ing a new good laboratory prac-
tices (GLP) bioanalytical laboratory,
reassessing an existing laboratory, or
revamping a “spirit-of-GLP” laboratory
to full GLP status. Historically, mass
spectrometers have been used largely in
drug discovery owing to their qualitative
capabilities and have escaped rigorous
regulation. This is clearly no longer the
case. Mass spectrometers are used
increasingly as primary detectors in all
facets of operations, which led to a col-
umn in 2004 exploring the changing
nature of validation: “Taming the Regu-
latory Beast: Regulation Versus Function-
alism” (1).
Many firms conducting internal
accounting analyses find that performing
GLP bioanalyses internally (as opposed
to outsourcing them to contract labora-
tories) saves time and money. This eco-
nomic efficiency is particularly true for
large-sample-number studies because
pricing tends to be based upon a per-
sample method.
The principle rarely extends to con-
tract laboratories performing small-sam-
ple-number studies, however, because
smaller numbers of samples often lack
profit potential. Consequently, those lab-
oratories sometimes delay a sponsor’s
small-sample-number studies or assign
Michael P. Balogh them a lower priority. This frustrates
MS — The Practical Art Editor pharmaceutical sponsors because early
www.chromatographyonline.
studies, no matter how small, can be
time-critical, as in the case of toxicology
studies.
Compared with a contract laboratory,
internal resources are held accountable
more easily for timeliness and compli-
ance. A sponsor can always outsource,
but a contract laboratory cannot always
subcontract. Moreover, an internal
resource that is active in performing GLP
bioanalysis knows the latest trends in
compliance and cost effectiveness. For
that reason, such a resource is well-suited
to managing external resources, expecting
them to implement those trends.
This column presents the key steps
necessary to start up a new GLP bioana-
lytical laboratory. Many of the examples
derive from the contributors experience
starting up the GLP bioanalytical facility
at Millennium Pharmaceuticals, Inc.
(Cambridge, Massachusetts). A recent
FDA audit of Millennium and a sup-
ported investigational new drug (IND)
application succeeded without issue or
official action.
We recommend treating a spirit-of-
GLP laboratory as you would a non-
GLP laboratory to convert it to full GLP
status. To begin constructing a new GLP
facility, we suggest you first put into
effect a master plan (Sidebar I). The mas-
ter plan should address these major cate-
gories of work, with each category
assigned its own manager and allocated
its own resources:
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• Standard operating procedures effective for the laboratory. This advan-

• Installation, operational, and perform-
ance qualification (IQ, OQ, and PQ,
respectively) of facilities, instrumenta-
tion, and software
• Personnel selection, staffing, and train-
ing
• Quality control (QC) procedures and
staffing
• Quality assurance
• Procedures and staffing
• Documentation and archival process
• Final gap analysis.
The SOPs
The standard operating procedure (SOP)
is a good starting point for discussing
each of the master plan’s components.
Sponsors hold an advantage over the
contract laboratory with respect to their
ability to clearly define a philosophy for
the group. In contrast, contract research
organizations (CROs) must accommo-
date the competing philosophies of a
diverse customer base at minimal cost.
So sponsors find themselves at a compet-
itive advantage because they can adopt a
specific strategy to pursue the approach
they regard as the most compliant and
tage should manifest itself in the SOPs.
We advocate a strongly minimalist phi-
losophy and a core team of GLP-sea-
soned individuals to write the SOPs. We
viewed the SOPs as a layered pyramid
with each layer providing a foundation
for the higher-level SOPs (Figure 1). In
the bioanalytical laboratory, the actual
work products are method validations
and sample analyses. The highest level
SOPs that detail oversight of all the
processes are the documentation and
quality control SOPs.
A desire to keep the SOPs as simple as
possible, and all nonregulatory detail
restricted to business practice rather than
legislation, characterizes the minimalist
philosophy. Absent a scientific basis,
guidance, FDA Form 483, regulatory
code, or other (regulatory) reason for a
procedure, business practice, not SOPs,
should govern work procedures. The
SOPs should be unequivocal documents
written for simplicity and easy remem-
bering. That said, the minimalist philos-
ophy should be tempered by a desire to
eliminate all possible errors while being
able to attack issues in a thorough,

Quality control

Documentation

Production:
validation and sample analysis

Chain of custody, critical and noncritical reagents

Critical and noncritical equipment

Figure 1: SOP pyramid.

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or work area when building or rebuilding

Sidebar I: Seven major
categories of work for the
validation master plan
1. SOPs
2. IQ/OQ/PQ of facilities/software
3. Personnel selection, staffing, and
training
4. Quality control
5. Quality assurance
6. Documentation and archival process
7. Gap analysis
reconstructable manner. Sidebar II lists
and describes briefly the SOPs we recom-
mend addressing immediately.
IQ/OQ/PQ: Separate Facilities are
Best for New Labs
We cannot overstate our recommenda-
tion for a physically separate laboratory
a GLP bioanalytical laboratory. A sepa-
rate facility obviates the often unneces-
sary requirement to validate a discovery
infrastructure and the additional over-
head of establishing GLP procedures,
such as strict labeling, for discovery
work. By adopting this approach, we
were able to minimize the scope of the
initial IQ/OQ/PQ validation work to
only two instrumentation systems and
three freezers in our initial rollout of the
GLP facility.
Hire external partners: At a reason-
able cost, you can purchase audit-proven
protocols and processes from external
consultants. We hired external consult-
ants for significant portions of our
IQ/OQ/PQ. These partners provided a
draft protocol and on-site assistance for
the IQ/OQ/PQ execution, which our
staff performed.

Sidebar II: List of recommended starting SOPs

1. SOP on SOPs: Describe the process of enacting SOPs, archiving them, and training
personnel in them.
2. Validations : State that the guidance will be followed, or detail the in-house valida-
tion procedure.
3. Sample analysis : State that the guidance will be followed, or detail the in-house
procedure. (Reassay decision trees and PK repeats require special attention.)
4. Quality control: The quality assurance unit (QAU) delegates the performance of
detailed audits to the quality control department. The QAU should therefore review
and approve the QC SOP and checklists to ensure that acceptable work practices are
followed. The QAU should do this even when the manager does not sign QC depart-
ment SOPs. QC peer reviewers should perform all aspects of all reviews. The reviewers
should be accountable for the completeness and accuracy of those reviews.
5. Documentation Procedures: An overview of acceptable acronyms and abbreviations.
Also, other details of the documentation process like binders, notebooks, packets of
worksheets, electronic, or hybrids of those systems.
6. Noncritical equipment: Noncritical equipment is equipment that does not affect the
regression curves. Its use, care, and maintenance should be described.
7. Mass spectrometry: As critical equipment, mass spectrometers are usually afforded a
detailed SOP.
8. HPLC systems, balances, and pipettes: Such equipment is usually considered critical.
Each of these items is usually afforded a detailed SOP.
9. Reference standards: Describe the storage, handling, and purity analysis require-
ments (certificate of analysis requirements and so forth) in this SOP.
10. Reagents: Expiration dates, storage, tracking and any definition of critical and
noncritical reagents should be detailed. Decisions regarding whether to centralize the
preparation, documentation, and storage of these reagents must be made.
11. Freezers: Temperature tracking, emergency procedures, and general use and main-
tenance should be described.
12. Chain of custody: Extensive tracking of sample chain of custody must be planned
and described.
13. LIMS: The use and maintenance of any LIMS system must be described.
14. Acquisition software: The use and maintenance of software and archival of e-data
must be planned and described.
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Personnel Management and
Recruiting
GLP work represents the public and
repeatable foundation for a new drug
entity’s safety margin. The validated
exposures of a drug in an animal model
establish the threshold of highest tolera-
ble dose. The difference in this exposure
and the dose anticipated to demonstrate
efficacy is the basis of the safety margin,
the therapeutic index. The work of per-
sonnel who perform GLP bioanalyses
represents a critical component of the
entire organization’s assessment of safety
margin. That work must be unassailable.
If necessary, it must be able to withstand
scrutiny in a court of law. Training docu-
mentation for analysts must emphasize
the importance of this work and specifi-
cally warn against any sort of fraud,
back-dating, or reporting false quality-
control (QC) results. This might seem
obvious, but you must anticipate and
plan for preventing the weakest of
defenses: “I wasn’t trained,” “I was
rushed,” or “I didn’t have proper
resources.” On a more positive note, an
analyst’s ability to perform GLP-quality
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work is a mark of distinction. It provides
breadth to a résumé and proves the ana-
lyst able to give a remarkable degree of
attention to details and quality. It also
offers him or her significant professional
satisfaction: the ability to produce a
highly refined bioanalytical method, as
opposed to the fast, generic methods
seen in the discovery phase of drug
design. You should seek analysts who
understand the accountability associated
with GLP work, its intrinsic importance,
and the personal opportunities it affords.
QC: Accountability Pyramid
In the accountability pyramid (Figure 2),
Each step is 100% accountable for any
errors or omissions determined by the
subsequent step. However, each subse-
quent step is responsible for providing
oversight to ensure that reasonable proce-
dures are utilized by the proceeding step.
A management team retains overreaching
accountability for each step.
We found that even for a relatively
small facility, true 100% QC combined
with metrics tracking, outsourcing man-
agement, SOP training, and SOP revi-
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Sidebar III: Systems
requiring IQ/OQ/PQ
1. Freezers and refrigerators
2. Mass spectrometers
3. HPLC systems
4. Autosamplers
5. LIMS system
6. Acquisition software
sions justifies the services of a full-time
employee. We adopted a model in which
a QC scientist, wherever possible, main-
tains a checklist system approved by a
quality assurance unit (QAU) and other
procedures to maintain documentation,
chromatograms, electronic archival
resources, and all other QC mechanisms
for the work. We highly recommend you
do the same, creating a dedicated
resource for this function and staffing it
with an experienced GLP bioanalyst
whose sense of the urgency and necessity
of performing unassailable bioanalytical
work is fully developed. Management is
responsible for ensuring adequate staffing
for proper surveillance of the work, as
stated in the preamble to the 1987 GLP
regulations. If the QAU is able to deliver
100% QC service by retaining an experi-
enced analyst whose time is fully dedi-
cated to QC activities (as perhaps origi-
nally envisioned in the preamble and
code), then doing so would suffice. Nev-
ertheless, to maintain a connection to the
process we recommend the QC scientist
perform some amount of bench work in
addition to his or her QC responsibili-
ties. Further recommendations for qual-
ity control measures are delineated in the
following section
Electronic Records
We recommend you develop a strict file
nomenclature and include this task as a
line item in a QC checklist to follow
when reconstructing electronic data.
Accepted and rejected runs should be
indexed in the paper data, and any rein-
jections also should be indexed and
explained.
While many well-characterized chro-
matographic software systems have
evolved to a highly “validatable” state this
is not always true of software developed
to control mass spectrometers and other
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instruments in the laboratory that pro-

duce GLP-defined raw data. Electronic
raw data also require specific archival
procedures that are somewhat less estab-
lished. For example, you might consider
FDA
this approach:
• Creating a new subdirectory for each
run
Management
• Acquiring the data team
• Transferring the entire subdirectory into
a validated, write-once, read-only, share
drive
Quality assurance unit
• Verifying and documenting that the
data are retrievable and viewable.
With such a system, you can protect
the data against hard-drive crashes and Quality control scientist
define a final version of the integrated
data. Also, because the data are read-
only, they are protected against corrup-
tion. We recommend this system or a Lead bioanalyst
similar one that relies on indelible media
such as CD-ROM storage. An article
appearing in this column on “The High- Technical support (extraction assistance,
Speed State of Information and Data glassware, facilities, informatics)
Management” (2) is worth a look on this
topic because there are numerous deci-
sions to be made depending upon such Figure 2: Accountability pyramid.
things as archival needs (how long must

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1098 LCGC NORTH AMERICA VOLUME 24 NUMBER 10 OCTOBER 2006
data be maintained) and at what level of
access.
Chromatogram Review
Acceptance of chromatographic quality
remains a subjective assessment. The
director of the facility should approve a
detailed guidance on chromatographic
quality, and QC scientists should be pre-
pared to implement this subjective
guidance.
Integration Parameters
Current acquisition software makes it
clear to an auditor whether different
integration methods are applied during
the course of a run. Whether it is prefer-
able to improve baselines via individual
integrations or objectively draw them
using the same integration methods for
all samples is a matter for legitimate
debate. We adopted the latter approach
(automated baselines only) and recom-
mend it as more objective and unassail-
able than a subjective system and less
open to abuse. We also recommend that
chromatograms using manual or altered
parameters are printed both ways and
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approved by the functional manager, Quality Assurance
who is usually the facility director. Rely- All GLP work requires a protocol, a
ing on archived, secured, electronic, raw study director, and a QAU. Without a
data facilitates the QC review and audit- QAU, a GLP group cannot exist. When
ing of integration parameters. drafting the master plan to build a GLP
bioanalytical laboratory, the need to ade-
quately staff the quality assurance unit is
Whether it is sometimes underestimated. The firm
contemplating building or rebuilding the
preferable to laboratory often tries to combine this
improve baselines new work function with its existing in-
life GLP or good manufacturing prac-
via individual tices (GMPs) regulatory groups. We do
integrations or not support this approach. GLP bio-
analysis requires complex and highly
objectively draw cross-referenced documentation, and its
them using the regulatory environment is fast evolving.
Form 483s and guidances are highly
same integration technical and require a focused effort to
methods for all capture in an applied audit. If resources
are limited, alternatives to hiring a new
samples is a matter auditor exist, but we do not recommend
for legitimate avoiding the hire by appointing a GMP
or in-life GLP auditor in an “overtime”
debate. scenario.
In the 1987 GLP preamble, the FDA
makes two important statements. The
first is that the QAU auditor can be any
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scientist not involved in the study, and
the second is that audits must be made
in a timely fashion so that correction can
be made. We interpret this to indicate
that the agency recognizes that some
firms lack sufficient resources to recruit
new employees for the QAU position.
You might therefore staff QAU positions
with existing employees, provided those
employees are not involved in a current
study. This is a far cry from the level of
separation often called for by QAU
groups. As applied today, the industry
trend calls for the QAU to report directly
to the senior council rather than the
department head. This minimizes con-
flicts-of-interest, insulates the auditor
from the work, and provides each audi-
tor with an enhanced career opportunity
to audit multiple areas of work: GMP,
GLP in-life, GMP dose formulations,
GLP Bioanalysis. However, it limits the
specialization of the auditor in highly
complex and increasingly specialized
technical applications. We are not against
centralized QAU groups or generalist
models per se. Yet we strongly recom-
mend that the QAU be adequately
staffed to enable satisfactory specializa-
tion and turnaround time to support a
new lab, requirements that might super-
sede a few additional layers of independ-
ence or auditor career track.
Audit turnaround time, a critical issue
for all organizations, is particularly criti-
cal for a new laboratory. An audit of sev-
eral months’ delay could catastrophically
affect a new group. If the QAU group
takes several months to return its audit of
a single study while a new group contin-
ues to produce several studies’ worth of
data, the QAU would, in so doing, place
the entire organization at risk of regula-
tory noncompliance. For lack of feed-
back, the resultant safety margin data for
the several studies produced would all
potentially contain the same flaws as the
first study. Millennium’s QAU commit-
ted from the beginning to achieve very
short turnaround times for each compo-
nent of the work it audited for the new
group, including a run-to-run data
review. We believe speedy turnarounds
are becoming standard for contract
research organizations (CROs) and
throughout the industry. Indeed, the
1987 preamble to the GLPs states that
audits “must be conducted in a timely
OCTOBER 2006 LCGC NORTH AMERICA VOLUME 24 NUMBER 10 1099
Sidebar IV: Documentation for archiving
1. Protocols: Protocol supersedes SOP as a study-specific procedure.
2. Binders, forms, or bound notebooks: Various possibilities for documentation sys-
tems exist. Characteristics of a good system include:
• That it be designed to evolve rapidly
• That centralized vs. study-specific raw data systems are considered
• That the system directs the analyst to capture all necessary information
3. Electronic records: With the advent of the FDA’s Part 11 Compliance effort, you can
now use electronic, rather than paper, raw data. We adopted LC–MS acquisition soft-
ware and a LIMS system as our primary electronic raw data tools. We believe that the
audit trail and signature functionalities on these systems are compliant, and we vali-
dated them utilizing the same protocols that met with auditor approval elsewhere.
4. Delineate raw data: We believe that it is critical for the management team to delin-
eate for the group what the official raw data are: paper records, electronic records,
some combination of paper and electronic records.
We recommend electronic data as raw data and that they be audited as secured, read-
only, electronic raw data. This gives the auditor full access to all the data including the
integration methods, which are emphasized in the FDA guidance on method develop-
ment and validation.
5. Strict file nomenclature: We strongly recommend that a strict file nomenclature be
developed and followed to facilitate reconstruction of the electronic data. The
accepted and rejected runs should be indexed in the paper data. Any reinjections
should also be indexed and explained.
6. Archival: Paper-data archival systems are relatively well established throughout the
industry and include temperature and climate control, document custody tracking,
fireproofing, and other controls and procedures. Electronic raw data, on the other
hand, require archival procedures that are somewhat less established. We archive our
electronic acquisition data is as follows:
• Create a new subdirectory for each run
• Acquire the data
• Transfer the entire subdirectory into a validated write-once, read-only
shared access file
• Verify and document that the data are retrievable and viewable
With this system, we can protect the data against hard-drive crashes and define a final
version of the integrated data. Because the data are read-only, they are also protected
against corruption. We highly recommend this system or a similar one that would rely
on other indelible media such as CD-ROM storage.
fashion so that corrections can be made.” quality assurance. Many CROs see inter-
As the accepted time for the making of nal laboratories as competitors or cus-
corrections becomes shorter, the need for tomers and so, either way, have a conflict
fast audits becomes more pressing. To of interest in performing the gap analy-
fulfill this need when internal resources sis. Other useful information can be
are unavailable, you can outsource the found in government publications (3,4).
work to one of the many organizations
that provide auditing services. Alterna- Documentation and Archival
tively, as allowed for in the 1987 pream- Processes
ble, you can adopt a peer audit model Sidebar IV offers a summary of key con-
whose participants are not involved in siderations for the documentation sys-
the study. tem. We used a three-ring binder system
Before rolling out a new group, we to file the approved, official, tracked
recommend that you engage an external forms issued by our documentation
auditor to perform a full gap analysis. group. In addition, we added an SOP for
For this, you should choose an individual a rigorous file nomenclature and archival
consultant or firm specializing only in system to facilitate the use of electronic
1100 LCGC NORTH AMERICA VOLUME 24 NUMBER 10 OCTOBER 2006
raw data. We elected to use protocols to
drive our validation, and a portion of the
validation report constitutes a bioanalyti-
cal procedure used during sample
analysis.
Conclusion
We have presented here for discussion
within the community the high-level
details of a master plan that we followed
to build and roll out a GLP facility at
Millennium Pharmaceuticals. We believe
these recommendations should serve as a
useful tool to facilitate building a quality
facility for performing this important
work.
References
(1) M.P. Balogh, LCGC 22(9), 890–894 (2004).
(2) M.P. Balogh, LCGC 23(6), 576–584 (2005).
(3) 21 CFR Part 58, OECD Principals of Good
Laboratory Practice.
(4) Guidance for Industry: Bioanalytical Method
Validation, U.S. Department of Health and
Human Services, FDA, CDER, CVM, May
2001.
Acknowledgments
The authors would like to thank the
other members of the team that built the
Millennium Pharmaceuticals GLP facil-
ity with them, particularly Cheryl Riel,
Ann Chernosky, John Brown, Eyal Wulz,
and Becca Greenberg, and the manage-
ment team, Gerald Miwa and Peter
Smith.
Adam Brockman began his industrial career
as a scientist at Covance Laboratories in
their GLP LC-MS/MS facility in Madison Wis-
consin. Following this initiation into G(X)P
bioanalysis, Dr. Brockman joined Pfizer Gro-
ton to head a high throughput ADME
screening laboratory where, in addition to
his contributions there, he subsequently
helped to rebuild a GLP bioanalytical facil-
ity. He then brought the benefits of both of
those experiences to Millennium Pharma-
ceuticals, where he built both new GLP and
HT-ADME facilities. Now at Merck Boston,
he is working in a generalist DMPK group
supporting the broad needs of Discovery
project teams.
Jing-Tao Wu received the Ph.D. degree in
Analytical Chemistry from the University of
Michigan. He is the Director and the head
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of the bioanalytical group in the Drug
Metabolism and Pharmacokinetics Depart-
ment of Millennium Pharmaceuticals, Inc. In
this role, he leads the bioanalytical group
to provide mass spectrometry based bioana-
lytical support for all discovery and devel-
opment projects. Before joining Millen-
nium, Jing-Tao worked in the DMPK
Department of DuPont Pharmaceuticals as a
Senior Research Scientist. He has published
nearly 40 papers in peer reviewed journals
in the field of bioanalytical mass
spectrometry.
Michael P.
Balogh
“MS — The Practi-
cal Art” Editor
Michael P. Balogh
is principal scien-
tist, LC–MS tech-
nology develop-
ment, at Waters
Corp. (Milford,
Massachusetts); an
adjunct professor
and visiting scien-
tist at Roger Williams University (Bristol,
Rhode Island); and a member of LCGC’s edi-
torial advisory board.