New Statistical Algorithms for the Analysis of Mass - FU Berlin, FB MI ...

156CHAPTER 6. PROTEOMICS.NET - PRODUCT-ORIENTED CASE STUDIES
the platform, get the worker status information and display it can be written
in less than 20 lines as the following listing 6.1 shows:
Listing 6.1: Minimal code for using the “get current worker()” web-service in Java.
1 import org . apache . a x i s . c l i e n t . C a l l ;
2 import org . apache . a x i s . c l i e n t . S e r v i c e ;
3 import javax . xml . namespace .QName;
4 import de . f u b e r l i n . mi . proteomics . p r o t e o m i c s n e t w e b s e r v i c e s . � ;
5
6 public class c l i e n t j a v a {
7 public s t a t i c void main ( S t r i n g [ ] a r g s ) {
8 try
9 {
10 S e r v i c e s i n f o L o c a t o r l o c = new S e r v i c e s i n f o L o c a t o r ( ) ;
11 S e r v i c e s i n f o S o a p port = l o c . g e t s e r v i c e s i n f o S o a p ( ) ;
12 System . out . p r i n t l n ( port . g e t c u r r e n t w o r k e r ( ) ) ;
13 }
14 catch ( Exception e )
15 {System . out . p r i n t l n ( e . getMessage ( ) ) ; }
16 }
17 }
The actual (synchronous) call to the web-service happens in line 12. This
line could also contain far more complex calls, for example including objects
as input and output parameters. Thanks to the transformation services (e.g.
within the WSDL2Java tool) parameters send to and received from the webservice
are mapped to Java data types.
6.2.3 Integrating External Web Services on the Example of
Protein Identification
Background
One key issue in proteomics is to identify proteins and characterize their expressions
in cells. In mass-spectrometry based proteomics this is done by
either peptide mass fingerprinting (PMF) of MS 1 spectra or by further fragmenting
single peptides producing MS 2 spectra where (ideally) the amino acid
sequence can be derived from.
The PMF approach (also known as protein fingerprinting) is an analytical
technique for protein identification developed in the early 1990s. The
basic idea is to digest an unknown protein of interest by a sequence specific
protease (such as Trypsin). The set of resulting peptides (fragments) build a
unique identifier (fingerprint) of the unknown protein based on this protease
and subsequently compared to databases containing known fragmentation patterns
for this protease. Obviously, the mass accuracy to which the peptides
are measured plays a crucial role (Green et al., 1999).
In MS 2 spectra analysis peptides of interest - identified during a MS 1
run - are fragmented further in a collision cell to produce tandem (MS/MS,
MS 2 ) mass spectra. Since fragmentation (usually) happens at the backbone
peptide bonds, by putting together matching pieces (that result in the full
peptide) and analyzing the point of rupture (in principle) determination of
the amino acids gets possible. This approach is called De Novo sequencing
(see e.g. (Ma et al., 2003; Halligan et al., 2005) and references therein). The
second large class of algorithms for the identification problem is based on
comparing the experimental spectrum against a database of theoretical spectra
determined by in silico digestion and fragmentation of known proteins.