MoWeD, a computer program to rapidly deconvolute low resolution electrospray liquid chromatography/mass spectrometry runs to determine component molecular weights.

A computer program is described that can rapidly process low-resolution electrospray liquid chromatography/mass spectrometry (LC/MS) for peptides and proteins and assign molecular weights for observed components. The program first analyzes individual scans using a deconvolution algorithm similar to that previously described by Zhang and Marshall. Results for the entire run are then sorted by mass and those values found in adjacent scans are grouped together. The list of found components can also be compared to a user defined list of target molecular weight values making it easy to compare the results from different analyses. The program also has the capability to process a rolling average of scans that improves the performance when analyzing high molecular weight components. Other program features facilitate closer examination of selected spectra or regions of the chromatogram to check the MoWeD mass assignments. The utility of the program was demonstrated by the analysis of LC/MS data derived from a complex mixture of proteins derived from a bacterial whole cell lysate that had previously been analyzed manually. The MoWeD analysis was 30 times faster and provided a more comprehensive list of the components present.

An expert virtual instrument approach to the automated, data dependent MS/MS and LC/MS/MS analysis of proteins.

Mass spectrometry has become an indispensable analytical tool for studies related to the structure and function of peptides and proteins. The variety of analytical methods, the range of instrument capabilities, and the complexity of the data obtained make it difficult for most laboratories to acquire the necessary expertise to make optimal use of their instrumentation.We describe an expert system approach to automating specific types of analyses in a way that makes it easier to transfer the capability to do specific experiments to other laboratories. Central to the approach is the creation of a computer program (ie, a virtual instrument) that controls the operation of physical components, analyzes incoming data, automatically adjusts instrument parameters to achieve the goal of the analysis, and reports the results. By interacting with the mass spectrometer through the computer operating system, it is possible to add useful functions to the system without altering any of the manufacturer-controlled data system software. The usefulness of this approach is illustrated by the automation of experiments to confirm the sequences of synthetic peptides and perform LC/MS/MS peak parking experiments and real-time database searches.