A method for assessing and maintaining the reproducibility of mass spectrometric analyses of complex samples

Abstract

Direct injection mass spectrometric analysis of biological samples is potentially an attractive approach to the discovery of diagnostic patterns for specific pathophysiological conditions because of its speed and simplicity. Despite the possible benefits offered by such a method, its extensive application has been limited so far by several factors, including the inadequate reproducibility of the analytical results. We describe a method for monitoring and optimizing the performance of mass spectrometers used for biomarker discovery studies, based on the analysis of patterns of standardized spectral features. The method was successfully applied to maintaining spectral reproducibility during a multi-day analysis of hundreds of serum samples despite an ion source failure, which necessitated minor maintenance. The monitoring method allowed the early detection of that failure and the restoration of the spectral profiles after the system was restarted.

Some possibilities of an analysis of complex samples by a mass spectrometry with a sample pretreatment by an offline coupled preparative capillary isotachophoresis

“…Direct infusion MS analysis of biological samples may provide a possibility to discover a diagnostic pattern for specific physiological conditions due to the speed, simplicity and increasing signal-to-noise ratio [55]. In addition, MS/MS analyses can confirm the presence of the analytes of interest, e.g.…”

What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows

“…Furthermore, the samples would cluster by the day they were run, as has been shown via performing a principal component analysis [78]. This is in contrast to the oft-quoted idea that the same sample, even when run multiple times, will significantly cluster together [79,80].…”

A method for monitoring and controlling reproducibility of intensity data in complex electrospray mass spectra: A thermometer ion-based strategy

“…One useful way of presenting these data is by defining a reference point in a multi-dimensional space based on the intensity of various ions in a reference mixture [50]. For example, using a mixture of three species, one could define a reference point in a three-dimensional space, with the intensity of each molecular ion representing one coordinate in that space.…”

“…In principal, such measurements could be made with any mixture of reference compounds [50]; however, repeated preparations of the reference mixture and differential chemical stability of it constituents would create their own variability in the analysis. Alternatively, by using thermometer ions that fragment internally, the data from each individual thermometer ion species can be expressed as a survival yield (S1, S2, S3,.…”

“…This behavior may afford a means for retuning an instrument to compensate for drift over time as the front end of the source becomes contaminated by repeated sample analyses. We recently demonstrated [50] that a mixture of compounds can be used to retune an instrument to yield comparable spectral data from serum after a variety of routine maintenance procedures.…”