MASCOT program

The mass spectra analysis of peptides was performed on an Ultraflex-TOF-TOF instrument (Bruker Daltonics, Germany) with a MALDI source equipped with UV laser (337 run) operated with positive ion detection m/z 700-2,000) and in reflection mode. The spectra were processed using Flex Analysis 2.4 software. A SwisProt database search was performed using the MASCOT program package (Matrix Science, UK). The exact monoisotope masses and... 

To perform a comparison of the untreated and treated samples, both are loaded on the MALDI sample plate and analysed (Figure 2). The spectrum of the unmodified digest is used for a primary protein identification using PMF (Table 2). The modified material is also analysed by MALDI, and masses of the modified peptides are used for protein identification using PMF with the Mascot program (see section 3.1.2.). In this case, esterified carboxylic groups are considered as permanent modifications like chemical modifications of cysteines, e.g. carboxymethylation. 

Mascot www.matrix-science.com/cgi/ index.nl nage=/h ome.html peptide mass and fragment ion search programs... 

The development and use of various protein sequence databases for automated search routines (Eng et al., 1994 Clauser et al., 1999) are an essential component of protein analysis that uses mass spectrometry techniques. These programs (i.e., SEQUEST, MASCOT) require only a few peptides for matching therefore, the absence of a match for a particular peptide does not affect the search performance. Using protein database searches provides an efficient way of confirming a putative sequence from corresponding full-scan mass spectrometry and MS/MS data. 

Mascot is another popular database-searching program that emphasizes the quality of the match using a probability-based approach to peptide identification. In contrast to... 

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