Sherpa: A Macintosh-based Expert System for the Interpretation of Electrospray Ionization LC/MS and MS/MS data from Protein Digests
✍ Scribed by J. Alex Taylor; Kenneth A. Walsh; Richard S. Johnson
- Publisher
- John Wiley and Sons
- Year
- 1996
- Tongue
- English
- Weight
- 1001 KB
- Volume
- 10
- Category
- Article
- ISSN
- 0951-4198
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✦ Synopsis
A computer program, Sherpa, has been implemented to aid in the elucidation of electrospray ionization liquid chromatography/mass spectrometry (LC/MS) and tandem mass spectrometry data from protein digests. The program differs from existing analyis software in its ability to search concurrently against multiple plotein sequences, to search and compare two LC/MS files concurrently, to search for glycosylated and phosphorylated peptides, and to give a simple evaluation of the quality of a match between the data and a prediction.
Details of the covalent structure of proteins are increasingly probed by using electrospray ionization mass spectrometry (ESI-MS)' to analyze their proteolytic digests. By directing the eluate from a high-performance, liquid chromatograph (HPLC) to an ESI mass spectrometer, the coupled technique, LC/MS,~-~ generates a very large amount of information from a single experiment in the form of hundreds of individual mass spectra. Although the LC/MS data can be collected in minutes, it may take many days to interpret them and correlate them to known sequences, depending on the complexity of the digest and the thoroughness of the investigation.
Tandem mass spectrometry (MS/MS)6*7 is a powerful aid to LC/MS interpretation, and can be used to test a hypothesis about the identity of a peptide ion by allowing the deduction of sequence information from an analysis of fragment ions. Typically, when acquiring LC/MS data, only a small portion of the sample flow is analyzed by the mass spectrometer, while the remainder is diverted to fraction collection for subsequent MS/MS or Edman analysis. Alternatively, with smaller amounts of material, a capillary column is used without splitting the post-column effluent, so that MSlMS is performed on-line on peptides eluted from the column (LCIMSIMS)? While MSlMS is invaluable in verifying and extending the interpretation of LC/MS data, it adds to the deluge of data that must be evaluated.
Currently there are several LC/MS or MS/MS data interpretation programs available for the analysis of protein data (e.g. Finnigan's BioWorks package,* and PE Sciex's BioToolbox9). The present communication describes a program which we call Sherpa (Yoaur guide to the peaks) and which is designed to aid in the interpretation of LClMS and MS/MS spectra from digests. This program offers several novel features, of which the most important are: the ability to search concurrently against multiple 0 the ability to search and compare two LC/MS files 0 search routines for glycosylated and phosphorylated 0 an evalualtion of the quality of a match between the protein sequences concurrently peptides data and a prediction.