Westermeier R., Naven T., H?pker H.-R. Proteomics in Practice: A Guide to Successful Experimental Design

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Symptom Cause Remedy

Poor crystallization,

presence of salt/buffer.

Microscale purification

to remove contaminants.

Poor crystallization,

presence of nonvolatile

contaminants.

Eliminate nonvolatile

components from sam-

ple before analysis. Do

not use nonvolatile com-

ponents to solubilize

sample.

Poor crystallization,

presence of visualization

agent, i.e. CBB.

Destain gel plug prior to

digestion.

Laser power below re-

quired threshold.

Increase laser power.

Old matrix. Prepare fresh matrix.

Unsuitable matrix. See Table 3.1 for correct

matrix selection.

Known contaminants,

keratin, dominate and

suppress analyte signal.

Address sample hand-

ling prior to digestion.

See Step 8, page 179 ff.

Poor digestion and

extraction efficiency.

Improve digestion and

extraction procedure.

Poor resolution across

mass range of interest.

Pulse time and voltage

not optimized for mass

range of interest.

See manufacturer’s

recommendations.

Laser poor far above

threshold level.

Reduce laser power to

optimal point.

Incorrect reflectron volt-

age.

See manufacturer’s

recommendations.

Poor mass accuracy

across mass range of

interest.

Poor resolution, unable

to select

C peak of the

isotopic envelope.

Improve resolution, see

above.

Unable to calibrate, one

or both internal cali-

brants absent.

Perform external calibra-

tion. In worst case sce-

nario, respot sample

with calibrants added to

the mixture.

Incorrectly calibrated. Check internal calibrants

and their masses.

430 Trouble Shooting

Symptom Cause Remedy

Unsuccessful or ambigu-

ous protein ID from

PMF.

Insufficient peptides. Acquire more specific

information; combine

PMF with composition

or partial sequence.

Acquire actual sequence.

Protein does not exist in

the database or low

homology with other

proteins.

Acquire sequence data

from product ion MS/

MS or PSD experiments.

Sample is a mixture. Acquire more specific

information.

Error tolerance too high

due to poor mass accu-

racy.

Constrain the database

search by improving

mass accuracy.

Keratin contamination. Remove known keratin

peaks from mass list (see

Step 8) and repeat

search.

Incorrect database

search settings.

Check settings: enzyme,

error tolerance, fixed and

potential modifications,

taxonomy, charge state

and mono-isotopic or

average masses.

C isotope not selected

from mass list.

Non-quantitative deriva-

tization CAF.

Reagent not freshly pre-

pared.

Always prepare reagent

freshly and use immedi-

ately.

Residual ammonium

bicarbonate.

Perform a micro-scale

purification.

Incorrect ratio of reagent

to sample.

Ensure reaction condi-

tions.

Reaction pH not opti-

mal.

Ensure correct reaction

conditions.

Reaction pH not opti-

mal.

Ensure correct reaction

conditions.

4312 Mass Spectrometry

433

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Proteomics in Practice. A Guide to Successful Experimental Design 2

Ed.

Reiner Westermeier, Tom Naven, and Hans-Rudolf Hçpker

ISBN: 978-3-527-31941-1

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