Peptide matching

Figure 7.3. The average number of peptides matching within various mass windows (ppm) as a function of the peptide mass (Da) for proteins from H. sapiens completely digested with trypsin. Note that there is negligible increase in the information value (no reduction in the number of matches) below 0.1 ppm.

Standard sequence similarity search including Peptide Match, Pattern Match, BLAST, FASTA, Pairwise Alignment, and Multiple Alignment... 

Step 2. Peptide matching It involves matching the parent mass of the intact peptide to the peptides in the database. Generally, the narrower parent mass constraint, the faster the search will proceed because fewer peptides will need to be correlated in the next step. 

Bastek etal also tested the ability of the identified affinity peptides to purify aj-PI from effluent 11 -i- 111, a process intermediate of the Cohn plasma fractionation process with eight major protein constituents. Several of the peptides achieved yields of 70-80% with purities ranging from 42% to 77%. Purification using these peptides matched or exceeded yields and purities reported in the literature using ion exchange chromatography. 

Peptide Search Number of peptides matched NCBlnr http //www.mann.embl- heidelberg.de/Services/PeptideSearch/ PeptideSearchIntro.html ... 

Peptldenl Number of peptides matched S w i ss Prot/TrEM B L http //www.expasy.ch/ Binz era/., 139... 

Rank Number of peptides matched Rank Number of peptides matched ... 

Proteins in the database are ranked in order of best correlation, usually with a significance threshold based on a minimum number of peptides matched. 

Recently, Koskinen et al. (2011) described the approach that seeks to present DB search results in a more logical format , that is, by creating a minimal set of proteins, grouped into families on the basis of shared peptide matches and by using hierarchical clustering with scores of non-shared peptide matches as a distance metric. This approach is very similar to that used by BacID/ABOid software (Dworzanski et al. 2006, 2010 Deshpande et al. 2011) for presenting DB search results of unknown microbial strains represented as pseudo-poly proteins. Unfortunately,... 

Under these circumstances the highest scoring strain, LVS, was correctly identified because among all unique peptides, the matches to other closely related strains were lower than 0.2%. However, in case of ATCC 25015 strain matches to other strains were substantially higher because 37 (2.6%) of unique peptides matched Francisella noatunensis subsp. orientalis str. Toba 04 and 30 (2%) matched the Francisella sp. TX077308 strain. This indicates minor sequence differences between strains ATCC 25015 and ATCC 25017, and proves that LC-MS/MS can potentially discriminate isolates from the subspecies philomiragia. 

Fig. 5.8 Peptide matches per Helicobacter strains for the H. pylori J99 sample, compared to whole-genome analyses using TETRA and ANI. The peptide matches per strain are shown as bars accompanied by the FSPs values, and the TETRA (multiplied by 100) and ANI indices are depicted by lines connected by symbols as indicated by the legend box. (Reprinted with permission from Karlsson et al. (2012, pp. 2710-2720). Copyright 2012 American Chemical Society)...

Tryptic peptides matched by BioWorks (version 3.2) to the Na" /K -transporting ATPase a-subunit in the 98-120 kDa SDS-PAGE band of the rat synaptic plasma-membrane fraction (BioWorks version 3.2) after in-gel digestion and data-dependent LC/ESI-MS/MS... 

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