Spectrum data

Workflow of MALDI-Tof MS

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 What can you import?

Uncompressed
grayscale TIFF
images
8, 12 or 16 bit

Peak tables
BioNumerics®
- Fingerprint data module
- Dedicated experiment
Densitometric for spectral data
curves from
automated
sequencers

MALDI, HPLC,
LC/MS,…
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Several open file formats are supported

Text file mzML/mzXML

 No metadata  Metadata structured in xml
 Peaklists or entire tags
spectra as mass –  Peaklists or entire spectra
intensity points base 64 encoded

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Import is made easy using default import templates

Raw curve

After baseline
subtraction and
smoothing

Though for the geeks, high levels of

customisation are possible

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 Easily summarize technical of biological replicates

 Use levels or information fields to

quickly create summary spectra
from replicates
 Use predefined templates or develop
your own
 Add filters to exclude low quality
data

Cluster analysis consists of two steps

Data matrix
(set of banding patterns)

Coefficient

Similarity matrix

Clustering

Dendrogram/grouping

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 Similarity can be calculated using peaks or full curve

Peak based Curve based

…
…

… % similarity … % correlation
Takes into account
Only takes into account Exception: quantitative values of full
presence/absence of bands peak based curve
Pearson
correlation Pearson correlation, Cosine
Jaccard, Dice, Jeffrey’s x, Ochiai correlation
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Similarity can be calculated using peak

matching results

A B C D

Set of spectral profiles

global matching

Peak matching table

A B C D A B C D
A 100 1 1 1 1

B 68 100 1 1 1 0

C 77 96 100 1 1 1 1

D 97 85 72 100 1 0 0 1

Coefficient 0 1 1 0
1 0 0 1
Similarity matrix 1 0 1 1
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1 1 1 1

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 A dendrogram helps detect relationships

 Compare spectra of different samples using different similarity

coefficients
 Perform peak matching

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