Systems and methods for aligning multiple point sets
Many biological data analysis problems require matching data points from different data sets. For example, high-throughput protein expression liquid chromatography and mass spectrometry (LC/MS) protocols developed generate 2-dimensional feature sets that require matching on a point-by-point basis. In these protocols, it can be useful to perform all data collection sequentially and analyze the data subsequent to lab work. This avoids the need to identify all of the components in a sample before comparing it to other samples, thus saving effort and avoiding the potential problem of missing an important component due to problems in the identification stage. Such methods can involve identifying, grouping and measuring sets of characteristic peaks in order to identify and quantify shared peptides. The present teachings provide, among other things, a method for comparing and associating multiple data sets. These methods, can be used, for example, for analyzing LC/MS runs, gel images etc.
1 . A method for matching features between a plurality of two-dimensional feature maps comprising,
receiving feature location information for features located in each of said plurality of feature maps,
receiving feature location error estimates of said feature locations,
performing a global optimization based on said feature location information and said feature location error estimates to match individual features related to the same feature across the maps, and
outputting the results.
2 . The method of claim 1 where the two-dimensional feature maps contain chromatographic and mass spectrometry data.
3 . The method of claim 1 where the two-dimensional feature maps contain data from two-dimensional electrophoresis gels.
4 . The method of claim 1 wherein the global optimization technique comprises,
defining rectangles based on the location of the features and the estimates of location error,
determining maximal cliques,
identifying ambiguous rectangles, and
assigning each ambiguous rectangles to a single clique.
5 . The method of claim 4 wherein assigning ambiguous rectangles to cliques comprises,
determining a score based on the average overlap of each ambiguous rectangle with the members of each clique to which it belongs, and
assigning each ambiguous rectangle to the clique that resulted in the highest score.
6 . A method of peptide analysis comprising,
analyzing a reference sample containing peptides of known composition on a liquid chromatography/mass spectrometry instrument,
analyzing a plurality of samples containing peptides of unknown composition on a liquid chromatography/mass spectrometry instrument,
receiving mass to charge ratio and retention time information for both the reference sample and plurality of samples,
estimating the error in the mass to change ratio and retention time information,
determining the identity of the unknown peptides by performing a global optimization technique and aligning the unknown peptides with the peptides in the reference sample, and
reporting the results.
7 . The method of claim 6 comprising,
performing relative quantitation between the peptides in the reference sample and the identified peptides in each of the samples of unknown composition.
8 . A system for matching features between a plurality of two-dimensional feature maps comprising,
a processor configured to execute program instructions, and
a memory containing program instructions for execution by the processor to;
receive feature location information for features located in each of said plurality of feature maps,
receive feature location error estimates of said feature locations,
perform a global optimization based on said feature location information and said feature location error estimates to match individual features related to the same feature across the maps, and
output the results.
9 . The system of claim 8 where the two-dimensional feature maps contain chromatographic and mass spectrometry data.
10 . The method of claim 8 where the two-dimensional feature maps contain data from two-dimensional electrophoresis gels.
11 . A computer readable medium containing instructions for controlling a computer system to perform a method for matching features between a plurality of two-dimensional feature maps comprising,
receiving feature location information for features located in each of said plurality of feature maps,
receiving feature location error estimates of said feature locations,
performing a global optimization based on said feature location information and said feature location error estimates to match individual features related to the same feature across the maps, and
outputting the results.
12 . The method of claim 11 where the two-dimensional feature maps contain chromatographic and mass spectrometry data.
13 . The method of claim 11 where the two-dimensional feature maps contain data from two-dimensional electrophoresis gels.