Peptidomics is the study of endogenous peptides in biological samples. It analyzes peptides on a larger scale than proteomics due to peptides' lower molecular weight and higher numbers produced through proteolytic processing. Peptidomics can detect markers not accessible by proteomics as peptides reflect protease activity. The process involves fractionating samples, analyzing peptides by mass spectrometry, and correlating peptide signals to variables like disease markers. Key factors for successful peptidomics studies include design, quality control, technology integration, and a holistic biological and technical approach.

1. PXBioVisioN
Peptidomics -
Analysis of Native Peptides by Offline-LC-MS
Harald Tammen , CMO

3. Peptidomics
- - +
Genomics
Cumulative Information
DNA
Genetic Code
Number of Entities
Molecular Weight
splicing
x 104
Transcriptomics
x 106
mRNA
Expression Levels
post-trans.
Proteomics
x 105 modifications x 10 5
Proteins / Modifications Protein
proteolytic
Peptidomics x 106 processing x 105
Processing
Peptide
+ + -
3

4. NCBI-PubMed Search
Proteomics Genomics
0.700
0.525
% of Publications [normalized]
0.350
0.175
0
1980 1986 1992 1998 2004 2010
4

5. Proteomics vs. Peptidomics
Proteomics is the large-scale study of proteins,
particularly their structures and functions.
Peptidomics is defined as the systematic, comprehensive,
qualitative and quantitative multiplex analysis of endogenous
peptides in a biological sample at a defined time point and
location
Main difference: Molecular Weight and Degree
of Proteolytic Processing

6. Proteomics vs. Peptidomics
Number of Publications in PubMed
30000
23938
22500
15000
7500
1011
231
0
Proteomics SELDI Peptidomics
6

7. Peptides Mirror Protease Activity
COAGULATION FIBRINOLYSIS
Thrombin Plasmin
Fibrinogen 20-866 Protein
20-35 582-602 603-620 Peptides
Peptides are suitable to encode conditions diametrically opposed to
each other (Coagulation versus Fibrinolysis), which are not accessible
by classical Proteomics methods (e.g. after Tryptic Digestion)
7

8. Plasma Concentration of Peptides
Postulated Markers
Classical
(SELDI) Plasma Peptides Tumormarkers
LOD

9. Peptidomics Process

10. Process Pipeline

11. Peptide Display CSF
Molecular Weight
Chromatographic Fraction
www.spectromania.com

12. Correlation Analysis
m/z
Each datapoint (1-3 Mill./Display) is [INS_human 57-87]
correlated to a corresponding
variable (e.g. plasma level insulin).
Fraction
[INS_human 25-54]
By applying a threshold value only
correlating datapoints are shown.
In contrast to „conventional“
methods no export of signals is
required:
The full information content of each
mass spectrum is used for analysis.

13. Keys
Peptides are generated by proteases from larger
precursor proteins and therefore are surrogates for
protease activities
Peptides exhibit better permeability between tissue
compartments due to their relatively low molecular
weight facilitating the peripheral detection
Identification and management of key factors of success
(e.g. study design, quality control, technology) and a holistic
approach (biological and technical integration) is of utmost
importance to successfully conduct Peptidomics studies

14. Contact
PXBioVisioN GmbH
Feodor-Lynen-Str. 5
30625 Hannover
Germany
PX
Dr. Harald Tammen
CMO
info@pxbiovision.com