Chapter 14: Multiple Choice Questions

Question 1

Which of these is the most important aspect of planning and designing a good
proteomics experiment?

a) Effective data analysis

b) Appropriate choice of samples and controls
c) Robust sample preparation methods
d) All of the above
Feedback:
It is important for an experiment to be carried out successfully that the right samples must
be selected to answer the question being posed, that these samples are prepared and
analyzed in a robust fashion to allow gathering of data pertinent to the biological question
(and not related to experimental error or variation), and to be able to analyze these data
properly. There is no point designing and executing a good experiment if you can't analyze
the data. Likewise if the data quality is poor, or if you have not performed the right
comparisons, there is no point analyzing the data in the first place. These experiments must
be viewed in totality, rather than as a series of small experiments (sample preparation, data
acquisition, data analysis), and it is critical that the total experiments works well.

Question 2

Which of these is an advantage of difference in-gel electrophoresis (DiGE) compared to

gel-free approaches?

a) More sensitive
b) Intact proteins allow detection of changes in protein modification
c) Allows a greater range of proteins to be analyzed
d) Proteins are identified as part of the quantification
Difference in-gel electrophoresis (DiGE) is distinct from gel free approaches in that the
quantification is performed on whole proteins, therefore a change in protein post-
translational modification (provided that it alters the mass or pI of the protein by a sufficient
amount) can be seen as a 'shift' in spot position. In gel based approaches, because proteins
are digested into peptides, changes in modification can only be detected either by
 serendipitous identification of a modified peptide, or by enriching for peptides which carry a
specific (known, pre-defined) modification, intimating that only one type of modification can
be analyzed per experiment. The trade-off for DiGE is that while changes in any type of
modification can potentially be detected, there is still the need to identify the nature of that
modification, usually by MS-based approaches.

Question 3

A good way to increase total proteome penetration by gel-free LC-MS/MS methods is to:

a) Use two, orthogonal types of chromatography

b) Enrich for phosphopeptides only
c) Analyze whole proteins
d) Label the proteins with a chemical tag

Feedback:
A good way to increase coverage, without requiring more sample, is the use of multiple
modes of chromatography where peptides are separated by two different properties. This
effectively 'spreads out' the peptides over a greater area, so more can be seen. Enriching
for a particular peptide type may reduce the overall peptides in the sample, but only
selected protein will be seen. Analysis of whole proteins currently lacks sensitivity compared
to analysis of protein digests, and chemical tagging approaches, while allowing protein
quantification, do not increase the sensitivity of an analysis.

Question 4

If your quantitative proteomics experiment contains a large number of samples, which

of these would be a good method to chose?

a) iTRAQ
b) SILAC
c) Label-free quantification
d) Western blotting

Feedback:
 Choice of method can be key, and all of the below could be used in this case, with the
exception of Western blotting (presuming that the aim of the experiment is the quantification
of more than one or a handful of proteins). However the limited nature in terms of sample
numbers for SILAC and iTRAQ, and the ratiometric nature of their quantitation, mean that
these methods would need all samples to be compared to an internal reference, introducing
additional measurement error into the experiment. With iTRAQ, this would be compounded
since quantification occurs in the MS/MS spectrum, and as such the only proteins which can
be quantified in all samples will be those identified in all analyses, limiting the total number
of quantified peptides.

Question 5

Isobaric tags are:

a) Molecules of equal charge

b) Molecules of equal mass
c) Fluorescent labels for proteins
d) Used in selected reaction monitoring
Feedback:
Isobaric means 'equal weight or pressure'.

Question 6

Proteins from clinical samples can be labelled with stable isotopes by which of the
following?

a) SILAC
b) Cy dyes
c) iTRAQ
d) 18O water
Neither Cy dyes, which are fluorescent labels for proteins in DiGE experiments, nor iTRAQ
are stable isotope labels. Although ITRAQ tags do contain stable isotopes each tag has the
 same number per tag (their distribution round the molecule is different). SILAC and 18O
water are both stable isotope-containing labels for peptides, but for clinical samples,
only 18O water can be used. SILAC labelling requires the sample to be fed nutrients
containing heavy-isotope containing amino acids, and as such this is primarily used for the
labelling of cells in culture. 18O water is used to replace 'normal' 16O with 18O during enzyme
(usually trypsin) digestion of protein.
Question 7

If you require a complex sample preparation workflow to enrich a particular population

of proteins from cultured cells, an appropriate method of quantification would be what?

a) DiGE
b) SILAC
c) Selected Reaction Monitoring
d) Label-free methods
Feedback:
While each of these methods could be used, in this example where the method is on
cultured cells, SILAC would be the method of choice. In both DiGE and label-free
quantification methods, samples would need to be processed in parallel and, since each
step in a complex preparative workflow would introduce some technical variation, this would
need to be carefully assessed and minimised for the full experiment to be successful. The
same applies to selected reaction monitoring. In addition this would also be unsuitable if the
aim of the experiment was to quantify a large number of proteins also. SILAC allows
samples for comparison to be pooled immediately, and as such proteins from each sample
are enriched in the tube simultaneously, minimising the effect of technical variation on
comparing samples inherent to a multi-step procedure, i.e. each sample is subjected to
exactly the same errors.

Question 8

Selected reaction monitoring is useful for which of the following?

a) Comparing the levels of hundreds or thousands of proteins

b) Comparing the levels of a specific protein
 c) Identifying a protein in a gel band/spot
d) Identifying the position of an unknown post-translational modification

Feedback:
Selected reaction monitoring is a very sensitive method for mass spectrometric detection
and quantification of specific peptides, meaning that only peptides which are known are
analysed, i.e. it is a targeted method. In that case, it is unsuitable for the comparison of
hundreds of proteins, nor is it suitable for discovering 'unknowns' such as what protein is in
a gel band (unless the experimental question is focussed i.e. does my gel band contain
protein X?) or to determine a post-translational modification of unknown nature (although it
can be used to ask specific questions i.e. 'is this peptide phosphorylated at a specific
position?').

Question 9

What is a 'proteotypic' peptide?

a) A post-translationally modified peptide

b) A stable isotope-containing peptide
c) A peptide which is unique to a specific protein
d) A peptide which is typical of all other peptides
Feedback:
A 'proteotypic' peptides is one which is typical of, and exclusive to, a specific protein. Such
peptides can be used as surrogates in selected reaction monitoring experiments to infer
levels of the parent protein.

Question 10

When quantifying proteins from an MS experiment, how do you work out what level a
change is likely to be due to biology, and not experimental or technical variation?

a) Use 2-fold as a generic cut-off

b) Use pathway analysis software
 c) Look in the literature to see what other people use
d) Analyze replicates to measure experimental noise

Feedback:
While all of these methods have been used(!), the correct method would be to assess the
level of technical and/or experimental variation by analysing (biological) replicates of the
same sample. This allows you to determine what the magnitude of changes that can be
introduced by change is, and as such all changes of greater magnitude between
experimental samples are likely to be due to genuine differences between samples. In most
cases, using a 2-fold cut-off will yield 'real' differences (unless there is large variation
introduced during sample prep, including culturing cells), but may miss other real
differences which fall below this threshold. Using the literature is inappropriate as methods
will vary between labs. Use of pathway analysis software could lead to erroneous
conclusion being drawn if a pathway is affected by some technical variable.