Notes 2024/11/12: MS1 retention time alignment in Comet

Comet’s real-time search interface has been extended to incorporate functionality to align an acquisition run against a reference run using MS1 scans.

Alignment is performed by scoring each query MS1 scan against the reference MS1 scans using a unit vector dot product (that’s also referred to as cosine similarity score). The range of reference MS1 scans is limited by those within the retentime time tolerance specified. Alignment of runs of different linear gradient lengths is supported although now that I’m writing this documentation, I think I may need to add another parameter to allow the user to specify the RTS query’s gradient length to support this. I guess I need to label this as an experimental feature until it can be tested in an real-time environment to identify whether or not any feature/parameters need to be implemented.

The best match reference MS1 scan, based on having the highest unit vector dot product score, is returned.

MS1 spectra are represented as spectral arrays in the same manner as Comet represents MS/MS spectra internally. These arrays are defined by the ms1_bin_tol and ms1_bin_offset parameters where 1.0005 and 0.4 is recommended for these two parameters, respectively. Smaller ms1_bin_tol values can be used for more sensitive matching (which I’ve found to be unnecessary) but at the expense of longer query times.

To mitigate local noise in the retention time alignment, Comet keeps a history of the 250 most recent retention time matches. A linear regresssion of the retention time matches is performed with outlier detection. See CometAlignment.cpp for details.

Real-time MS1 alignment queries can be performed alongside real-time MS/MS searches. The example C# program RealTimeSearch/SearchMS1MS2.cs gives an example of how these searches can be run by calling DoMS1SearchMultiResult() for MS1 scans and DoSingleSpectrumSearchMultiResult() for MS/MS scans in the CometWrapper interface.

MS1 alignment specific paramters

• retentiontime_tol
• ms1_bin_tol
• ms1_bin_offset
• ms1_mass_range

The graphs below show an example alignment between a 60 minute reference run and 60 minute query run.

The graph below shows an extreme example where a 180 minute run is aligned against a 60 minute run.