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lipids > lipidomics > Flashcards

lipidomics Flashcards

1
Q

what does “ome” mean

A

is a suffix that refers to the
collective objects of study within a field
– “ome” was derived from the Greek “ομα”,
which itself is not a Greek suffix

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2
Q

what does genome mean

A

the complete collection of
genes within a species

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3
Q

what is genomics

A

the study of
genomes within a species

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4
Q

what are some of the other omic subfields of genomics

A

– Cognitive genomics
– Comparative genomics
– Functional genomics
– Transcriptomics
– Epigenomics
– Nutrigenomics

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5
Q

proteome

A

the complete collection of
proteins and modified proteins produced
by a species

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6
Q

peoteomics

A

the study of proteomes within
a species
* Proteomics typically requires the use of
mass spectrometry methods

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7
Q

what are the subfield omics of proteomics

A

– Structural proteomics
– Nutriproteomics
– Immunoproteomics

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8
Q

lipidome

A

the complete collection of lipids
and modified lipids within a species

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9
Q

lipidomics

A

the study of lipidomes within a
species
Advances in mass spectrometry (in 1991)
allowed for its use to detect different
classes of lipids

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10
Q

emergence of lipidomics

A

Lipidomics first emerged in 2003 whereby
differing multiple species and classes of
lipids from animal models of various
metabolic disorders could be quantified
simultaneously within minutes

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11
Q

why care about the lipidome

A

understanding cellular functions
deciphering metabolic changes
identifying markers of sudden physiological events
food: are you really getting what you think you are purhcasing

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12
Q

understanding cellular function

A

identifying the specific lipid species that
modify protein functions, membrane
localization of lipid species, specific lipid
species involved in intracellular signalling

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13
Q

deciphering metabolic changes

A

specific
changes to the lipidome can reflect
specific metabolic disorders associated
with lipid metabolism

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14
Q

identifying markers of sudden physiological events

A

levels of specific
species of lipids can abruptly change in
the bloodstream or in sections of tissues in response to a pending event or already
occurred event

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15
Q

what are the basic steps prior to lipidomics analases

A

tissue or cells

homogenization and membrane fractionation

//optional: addition of antioxidants

lipid extraction

//optional: addition of internal standards

storage/ concentration of lipid extracts

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16
Q

basic steps for lipidomics analyses

A

storage concentration of lipid extracts

direct infusion or front end separation

(branches into two sections)

1- survey scan

provide information on molecule ion mass

  1. tandem mass spectrometry/ product ion scan/ precursor ion scan/ neutral ion scan

provide information on polar headgroups and fatty acyl constituents

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17
Q

how many primary mass spectrometry
methods are typically used for identifying
and quantifying lipids and what are they

A

three

– Gas chromatography mass spectrometry
(GC-MS)
– Electrospray ionization mass spectrometry
(ESI-MS)
– Matrix assisted laser desorption ionization
mass spectrometry (MALDI-MS)

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18
Q

what does mass spectrometry involve

A

Mass spectrometry involves the charging
of a particle which then passes through a
magnetic field to deflect the charged
particle along a circular path on a radius
that is proportional to the ratio of mass to
charge (or m/z)

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19
Q

mass spectrometry steps

A

sample goes into ion source then into mass analyzer then to a detector and finally we analyze the data

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20
Q

what does EI-MS produce

A

it is the simplest mass spectrometry method and produces cations
that undergo fragmentatio

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21
Q

EI-MS is considered

A

a ‘hard ionization’
method because radical-mediated
fragmentation of a molecule continues
until a stable fragment is achieve

22
Q

what is CI-MS

A

method of mass spectrometry
that introduces a gas to act as a reagent
for ion generation at a lower voltage

23
Q

what is the voltage used for CI-MS

A

20-40 eV

24
Q

what is the voltage used for EI-MS

A

70 eV

25
Q

what does the ion generated in CI-MS do

A

The ion generated can react with the
compounds injected into the mass
spectrometer, and in turn the ion transfers
its charge to the compounds

26
Q

charged compounds of CI-MS

A

The charged compounds exhibit little
fragmentation (‘soft ionization’)

27
Q

Ion production in CI-MS using methane as the reagent gas

A

The CH 5+ and C 2H5+ ions collide with the
compound M to form the following ions:

28
Q

what is GC-MS

A

GC-MS combines the chromatographic
separation of gas vapours based on time
and sample temperature, together with
either EI-MS or CI-MS

29
Q

Why is GC-MS useful

A

GC-MS is useful for the detection of fatty
acids, fatty alcohols, and cholesterol

30
Q

generated ions in GC-MS

A

Generated ions are up to m/z of 400

31
Q

how can we detect lipids in GC-MS

A

The lipids cannot normally be detected by
GC-MS because they do not vaporize due
to their associated –OH groups
– However, the –OH group on lipids can be
esterified with other molecules to make them
capable of vaporizing

32
Q

What does PFB-Br stand for

A

Pentafluorobenzyl bromide

33
Q

why is Pentafluorobenzyl bromide useful in GC-MS

A

Pentafluorobenzyl bromide (PFB-Br) can
readily esterify with the –OH group of most
lipids
* PFB esters readily vaporize in a GC-MS

34
Q

PFB in GC-MS

A

In the MS, PFB readily dissociates from
the lipid through ‘neutral loss’
– during detection, you would look for the lipid of interest at an m/z corresponding to [M-H] - (ie. MW palmitate is 256… m/z will be 255)
– detection will be using ‘negative ion mode’ for anions (which is unlike ‘positive ion mode’ for detecting cations generated by EI or CI)

35
Q

positive ion mode

A

a detection mode that
identifies only positively charged ions

36
Q

negative ion mode

A

a detection mode that
identifies only negatively charged ions

37
Q

neutral loss

A

(NL): the loss of an
uncharged fragment of an ion during MS

38
Q

collision induced dissociation

A

CID

the
fragmentation of an ion via inert gas (i.e.,
argon) bombardment

39
Q

NL scan

A

the filtering for all ions that
exhibit a specific NL

40
Q

survey scanning (also seen as MS, MS1,
and Q1MS):

A

a scan of all ions detected
without any filtering

41
Q

precursor ion

A

charged ion that is
derived from an ion during fragmentation

42
Q

precursor ion scanning

A

the filtering for all
ions that produce a specific precursor ion

43
Q

ESI-MS generates what

A

ESI-MS generates charged molecules
from a liquid stream (provided by direct
infusion/injection or from chromatographic
separation)

44
Q

what voltage is used for ESI-MS

A

2000-6000 V

45
Q

What temperature is used for ESI-MS

A

200-500 °C

46
Q

what happens to molecules in ESI-MS

A

In the presence of voltage (2000-6000 V)
and temperature (200-500 °C), the
molecules in the stream ionize; during this
process, an extremely fine spray of
droplets is formed

47
Q

what happens to the electrospray in ESI-MS

A

The ‘electrospray’ loses solvent, and the
ions enter the quadrupoles - (region with
four sets of magnets)

48
Q

what m/z ions can be detected in ESI-MS

A

Ions with m/z between 50-3000 can be
detected

49
Q

what lipids can ESI-MS detect

A

ESI-MS can be used to detect all classes
of lipids without chemical modification,
except cholesterol (which poorly ionizes
with this method)

50
Q
A

lipids (13 decks)

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