Manuscript
Rudnick et al
A major unmet need in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS and peptide identification. Applied to datasets from replicate LC-MS/MS analyses, these metrics display consistent, reasonable responses to controlled perturbations. The metrics typically display variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications.
Associated Data
Rudnick et al - Click to launch Tranche download tool and begin downloading. Datasets are labeled chicken_egg_yolk and yeast_dilution_series within download subfolders.
Study 2
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Study 5
| File ID | Exp. ID | Alias | Size | Files | Links |
| 55 | 35 | LTQ-Orbitrap@86 | 9.9 GB | 42 |  More Info, Download |
| 53 | 40 | LTQ-OrbitrapW@56 | 6 GB | 20 | More Info, Download |
| 35 | 39 | LTQ-XL-OrbitrapP@65 | 4 GB | 43 | More Info, Download |
| 52 | 33 | LTQ2@95 | 1.5 GB | 49 | More Info, Download |
| 24 | 32 | LTQ@73 | 904.2 MB | 33 | More Info, Download |
| 37 | 37 | LTQc@65 | 2.4 GB | 55 | More Info, Download |
Study 6
| File ID | Exp. ID | Alias | Size | Files | Links |
| 64 | 104 | LTQ-Orbitrap@86 | 11.2 GB | 73 | More Info, Download |
| 85 | 116 | LTQ-OrbitrapO@65 | 21.4 GB | 56 | More Info, Download |
| 75 | 101 | LTQ-OrbitrapW@56 | 16.8 GB | 46 | More Info, Download |
| 70 | 106 | LTQ-XL-OrbitrapP@65 | 6.7 GB | 58 | More Info, Download |
| 86 | 110 | LTQ-XLx@65 | 2.5 GB | 57 | More Info, Download |
| 78 | 105 | LTQ2@95 | 2.2 GB | 50 | More Info, Download |
| 65 | 100 | LTQ@73 | 3 GB | 73 | More Info, Download |
