The Center for Mass Spectrometry and Proteomics (CMSP) at the University of Minnesota provides mass spectrometry services to researchers. Over the past 3 years, CMSP has expanded its instrumentation, diversified its services, and improved its budget management. New mass spectrometers and staff were added, while older instruments were replaced. Services now include discovery and targeted proteomics and metabolomics. CMSP also paid down a $250,000 debt from prior instrument purchases.

1. CENTER
FOR
MASS
SPECTROMETRY
AND
PROTEOMICS
(CMSP):
EXECUTIVE
SUMMARY
(2013-­‐2016)
http://z.umn.edu/cmsp13to16
INTRODUCTION
The
CMSP
has
established
itself
as
an
essential
core
facility
serving
a
diverse
array
of
biological
mass
spectrometry
needs
of
researchers
at
the
University
of
Minnesota
as
well
as
regional
and
national
institutions
and
companies.
Advanced
instrumentation
coupled
with
deep
expertise
of
CMSP
staff
members
offers
researchers
services
for
characterizing
small
molecules
(e.g.
metabolites,
lipids,
signaling
molecules)
to
large
molecules
(peptides,
proteins
and
biopolymers).
The
CMSP
also
services
projects
of
all
scale
–
from
small
(e.g.
identification
of
a
purified
protein
or
molecular
weight
characterization
of
a
biochemical)
to
large
(high-­‐throughput
identification
of
all
proteins
or
metabolites
from
a
complex
sample
such
as
cells
or
tissues).
The
CMSP
staff
not
only
generates
data
for
users,
but
also
act
as
collaborators,
meeting
with
users
to
decide
on
the
best
choice
for
all
of
these
requirements
to
achieve
success.
Below
are
a
few
highlights
on
CMSP
progress
in
last
three
years.
• PERSONNEL
AND
INSTRUMENTATION:
Last
three
years
saw
a
good
turnaround
of
full
time
as
well
as
part-­‐time
personnel.
Ebbing,
Susan,
Jacob,
Adedolapo,
Jianji
joined
us
and
then
have
moved
on
to
take
newer
positions.
Candace,
Julie,
Tzu-­‐Yi,
Jean-­‐Paul
also
joined
the
team
in
last
three
years.
New
personnel
for
sample
preparation
have
been
hired
and
that
has
helped
greatly
in
having
the
sample
preparation
portion
of
the
workflow
being
handled
efficiently.
Along
with
the
Faculty
Director,
we
have
also
invested
in
purchase
of
new
instruments
(Q-­‐
Exactive,
MALDI-­‐TOF/TOF)
and
collaborating
with
new
faculty
(Parker
and
Chen)
to
have
their
instruments
(5600
and
Fusion)
co-­‐hosted
at
the
CMSP.
These
instruments
replaced
various
old
instruments
(LCQ,
Variant,
MALDI-­‐TOF,
Q-­‐Star,
4800
and
its
accessories).
Volume
of
usage
by
colleges
from
approximately
FY10-­‐FY16,
as
determined
by
fees
paid
to
the
CMSP.
PIs
using
the
CMSP
are
distributed
across
a
number
of
Colleges
and
Schools
at
the
UofM.

2. • BUDGET
MANAGEMENT
AND
RATE
CALCULATION:
One
major
task
that
was
taken
up
and
accomplished
in
early
2014
was
to
set
up
rates
based
on
the
volume
of
business
and
expenses.
The
service
rates
were
changed
last
in
2009
and
had
not
been
reviewed.
The
new
business
model
deviates
from
the
old
model
of
promoting
services
based
workshop
and
word-­‐of-­‐mouth;
keeping
expenses
low
and
narrow
range
of
services
(iTRAQ-­‐labeled
protein
quantitation,
targeted
metabolomics
and
NMR
service).
Since
2014,
budget
was
estimated
on
an
annual
basis.
The
service
rates
were
adjusted
rates
based
on
recommendations
from
the
ISO/
ESO
office
at
the
University.
Revenue
and
billing
and
‘in-­‐kind’
services
have
been
monitored
on
a
monthly
basis
(see
below).
The
services
have
diversified
now
into
including
discovery
metabolomics,
discovery
proteomics
(using
new
instruments),
targeted
metabolomics
and
proteomics
and
proteogenomics
and
metaproteomics.
In
2014,
The
CMSP
carried
a
debt
of
about
$250,000
to
the
UMN
Plant
fund.
This
debt
was
from
instrument
purchases
made
approximately
six
years
ago
in
an
effort
to
renew
and
refresh
instrumentation
and
technology
in
CMSP.
After
discussion
with
the
faculty
director
and
accounts
staff,
we
made
a
decision
to
pay
down
this
debt.
In
last
three
years,
we
have
paid
a
carryover
from
CMSP
budget
and
brought
down
the
debt
to
$129,000.
This
will
continue
to
be
the
practice
moving
forward.
As
a
result
of
instrument
and
computational
and
software
purchase;
instruments
being
down
for
service
repairs;
plant
fund
repayment
and
other
factors
–
last
two
years
have
seen
a
budget
deficit
when
internal
(UMN)
revenue
is
considered.
It
is
important
to
note
that
when
the
internal
and
external
revenue
is
taken
together,
the
total
revenue
has
not
resulted
in
a
deficit.
The
above
mentioned
factors
responsible
for
deficit
have
been
monitored
and
measures
have
been
taken
to
address
this
in
the
future.
• COMPUTATIONAL
INFRASTRUCTURE
AND
WORK
ENVIRONMENT:
In
last
three
years,
CMSP
has
moved
away
from
using
MSI
services
(TINT
and
MSI
software).
As
a
result,
computational
infrastructure
(on
both
campuses)
was
revamped
with
help
from
UMII
adding
more
software
and
computational
power
for
data
analysis.
Moreover,
Galaxy-­‐P
infrastructure
was

3. also
utilized
for
multiple
projects
I
the
emerging
areas
of
proteogenomics,
metaproteomics
and
for
large
scale
quantitative
data
analysis.
Support
instrumentation
(battery
backup,
etc.)
was
upgraded
to
improve
work
support
infrastructure.
New
chairs
(with
recommendations
from
ergonomic
department)
have
been
placed
at
the
St.
Paul
facility.
Older
instruments
have
been
handed
over
to
other
facilities
or
send
to
recycling
station
(during
spring
cleanup
–
2014
and
2015).
This
has
resulted
in
a
much
better
working
environment
at
the
St.
Paul
facility.
• PROJECT
MANAGEMENT
AND
DOCUMENTATION:
In
order
to
bring
in
an
open,
centralized
platform
for
project
management
-­‐
since
August
2014
-­‐
I
have
been
discussing
with
the
CMSP
Staff
about
project
management
platforms
from
multiple
vendors.
This
has
resulted
in
having
project
management
modules
and
documentation
using
Google
docs
infrastructure
in
place.
This
included
generating
service
quotes
for
all
customers
and
service
contracts
with
external
customers.
For
example,
we
have
a
process
in
place
for
Short-­‐term
and
long-­‐term
service
contracts
with
external
vendors
(as
suggested
by
the
ISO/ESO
organization)
so
that
we
are
legally
covered
for
any
of
the
services
offered.
Currently,
we
have
eight
service
contracts
with
external
clients
(as
compared
to
only
one
in
2013).
These
google
docs
document
steps
with
sufficient
details
so
that
instructions
can
be
followed
by
staff
or
new
manager.
Based
on
CMSP
staff
feedback
from
multiple
brainstorming
sessions
and
after
discussion
with
UMGC
and
UIC
facilities,
we
have
decided
to
extend
the
project
management
platform
using
FileMaker
Pro
15
(launched
recently
in
May
2016).
We
have
also
established
a
contract
with
a
professional
for
FileMaker
Pro
services.
I
anticipate
that
the
new
manager
will
carry
this
plan
forward
with
a
design
plan
and
discussing
with
FileMaker
Pro
expert
to
have
these
customized
workflows
in
place.
• DATA
ANALYSIS
STRATEGIES
IN
NEW
EMERGING
FIELDS:
Data
analysis
infrastructure
and
capabilities
were
added
in
the
field
of
label-­‐free
quantitation
(RIPPER
software),
proteogenomics,
metaproteomics
and
discovery
metabolomics
in
last
three
years.
In
2013,
data
analysis
and
dissemination
at
CMSP
was
performed
through
MSI
services
(using
TINT)
and
MSI
storage.
UMII
along
with
inputs
from
CMSP
Staff
has
resulted
in
a
structure
based
on
OIT
services.
We
also
invested
in
purchase
of
new
software
and
computers
so
as
to
satisfy
the
demand
for
data
analysis
from
newer
instruments
and
emerging
areas
of
research.
UMII
along
with
CMSP
provides
analytical
services
for
80%
of
standard
services
(iTRAQ
quantitation,
gel-­‐based
protein
identification,
label-­‐free
quantitation,
etc.).
Along
with
Tim
Griffin,
PI
on
Galaxy-­‐P
grant,
we
also
offered
Galaxy-­‐P
services
especially
in
the
emerging
areas
of
proteogenomics
and
metaproteomics
(and
soon
data-­‐independent
acquisition).
The
use
of
Galaxy-­‐
P
services
for
core
facility
data
has
resulted
in
multiple
publications
(z.umn.edu/galaxypreferences)
and
has
been
highlighted
in
oral
presentations,
posters
and
workshops
at
multiple
national
and
international
conferences.
• OPERATIONS
AND
STAFF
MANAGEMENT:
With
diversity
in
instrumentation
and
services
and
most
importantly
due
to
two
locations
in
which
staff
was
located
it
was
important
to
establish
a
centralized
communication
channel
for
regular
updates.
In
order
to
discuss
topics
and
open
them
up
for
discussion,
multiple
modes
such
as
one
to
one
meetings,
regular
quarterly
meetings
were
used.
A
CMSP
google
group
was
initiated
wherein
CMSP
staff
members
could
post
updates
/
discuss
topics
online.
Weekly
and
monthly
email
updates
and
important
announcements
are
also
communicated
through
this
google
group.
A

4. comprehensive
google
docs
based
project
communication
approach
was
also
discussed
in
details
–
but
staff
decided
to
explore
the
FileMaker
Pro
software
platform
further.
• CMSP
VISIBILITY
/
OUTREACH:
Traditionally,
promotion
of
CMSP
services
have
been
through
workshop,
website
and
word-­‐of-­‐mouth.
In
last
three
years,
the
focus
has
been
to
broadcast
services
to
the
UMN
research
community
through
multiple
avenues
such
as
its
website,
presentations,
newsletters,
workshops,
CBS
Connect,
twitter
and
handouts.
The
CMSP
website
was
revamped
to
offer
ease
of
navigation
and
access
to
most
requested
services
from
CMSP.
For
example,
based
on
inputs
from
Advisory
Committee,
‘example
projects’
were
added
onto
the
website
to
showcase
some
of
published
projects
from
the
facility.
Along
with
the
Faculty
Director,
I
have
given
overview
presentations
highlighting
services
offered
by
CMSP
in
a
variety
of
venues.
Recent
examples
include
presentations
at
the
Veterinary
Biomedical
Sciences
Faculty
Meeting
and
to
the
Molecular
Virology
training
program
faculty
and
students
and
the
CFANS
Research
Exhibition
Fair.
In
addition,
the
quarterly
workshop
was
restructured
in
March
2014
so
as
to
have
sample
preparation
on
the
first
day,
instrumentation
on
the
second
day
and
data
analysis
and
interpretation
on
the
third
day.
New
talks
and
speakers
were
added
to
the
schedule
and
tasks
were
distributed
so
that
organizing
and
conducting
workshop
became
an
easier
task
than
earlier.
Feedback
is
also
collected
electronically
and
changes
made
accordingly.
The
feedback
for
the
workshop
has
been
very
positive
for
last
ten
workshops.
Since
2015,
the
CMSP
has
published
a
semi-­‐annual
e-­‐newsletter.
This
newsletter
provides
updates
ongoing
activities
and
research
projects
in
CMSP.
A
UMN
faculty
member
is
invited
to
provide
a
short
write-­‐up
on
a
research
project
that
has
been
facilitated
by
CMSP
services.
The
CMSP
is
continuously
evaluating
new
avenues
for
promotion.
One
example
is
the
ScienceExchange
resource
(www.scienceexchange.com),
which
serves
as
a
portal
to
match
companies
and
institutions
with
core
facilities
and
services.
This
resource
is
currently
being
evaluated
as
an
option
to
further
promote
CMSP.
It
has
been
great
working
with
you
for
last
three
years
and
we
are
quite
confident
that
the
new
management
will
be
able
to
take
the
work
done
until
now
to
newer
heights.
With
Best
Regards,
Pratik
Jagtap,
Research
Assistant
Professor,
and
Managing
Director,
Center
for
Mass
Spectrometry
and
Proteomics,
43
Gortner
Laboratory,
1479
Gortner
Avenue,
St.
Paul,
MN
55108
pjagtap@umn.edu
http://cbs.umn.edu/cmsp/