SmartPeak validation experiments

[dmccloskey]

Description

In silico validation experiments required for publication of the new SmartPeak data processing algorithms

Objectives

1. MRMFeatureSelector validation experiments using LC-MS, HPLC, GC-MS, and CE-MS data
2. EMG fitting validation experiments on LC-MS calibrators and QCs
3. Example LC-MS and HPLC data set using AbsoluteQuantitation
4. Example LC-MS data using MRMFeatureFilter and MRMFeatureQC
5. Example LC-MS and GC-MS data set using the TargetedSpectrumExtractor workflow

[pcolaianni]

When proposing the targeted/untargeted methods PR to OpenMS, I made the following change in selectSpectra(): replaced unordered_map with map.

During the validation tests, we should check if such change provokes a performance regression.

The only advantage of using map is that users will have the extracted spectra sorted in the same order, no matter what platform (win, mac, linux) they work on.

[dmccloskey]

Notes on data collection for validation experiments:

MRMFeatureSelector validation experiments using LC-MS, HPLC, GC-MS, and CE-MS data

• [x] Dump manually integrated peak data from DB (LC-MS)
• [x] Ensure all raw data files have been converted to MzML (LC-MS)
• [ ] Clean up/organize example data for HPLC, GC-MS, and CE-MS
• [ ] Run LC-MS quantitation examples
• [ ] Run LC-MS fluxomic examples EMG fitting validation experiments on LC-MS calibrators and QCs
• [ ] Identify saturated compounds for calibrator example
• [ ] Identify cutoff compounds for QC example Example LC-MS and HPLC data set using AbsoluteQuantitation
• [x] Dump calibration curve fit statistics from DB (LC-MS) Example LC-MS data using MRMFeatureFilter and MRMFeatureQC
• [x] Figure of examples and scoring metric Example LC-MS and GC-MS data set using the TargetedSpectrumExtractor workflow
• [x] Dump manually processed isotopomer data from DB (LC-MS)
• [ ] NIST example
• [ ] LC-MS/MS DDA example?