Table III. The level of dependence of precision and robustness on the selection of manipulation chains assessed based on the benchmark dataset of the first study in Table I (23). These studied LFQs were collectively defined by five quantification tools and eight representative manipulation chains. As reported in original study (23), the log transformation together with median normalization were applied before any subsequent analysis, which defined the manipulation chain of that study as LOG-[NON-NON-MED]-NON (highlighted in gray background). The precision levels were defined by the PMAD values (superior: <0.14, good: 0.14∼0.3, fair: 0.3∼0.7, and poor: >0.7), and the robustness levels were assigned by the ranking of consistency scores (high: top 20%, medium: 20∼50%, and low: bottom 50%). Each manipulation method within an LFQ was abbreviated by a three-letter code that was systematically defined in Table I.
| Representative Chains for Data Manipulation | Precision: Reproducibility among technical replicates (PMAD) |
Robustness: Rank of manipulation chains by consistency scores |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| DecyderMS | MaxQuant | PEAKS | OpenMS | Sieve | DecyderMS | MaxQuant | PEAKS | OpenMS | Sieve | |
| LOG-[NON-NON-MED]-NON | 5.56E−01 (Fair) | 5.41E−01 (Fair) | 6.43E−01 (Fair) | 4.80E−01 (Fair) | 4.71E−01 (Fair) | 457 (High) | 358 (High) | 369 (High) | 313 (High) | 687 (Medium) |
| LOG-[MDC-RAN-EIG]-KNN | 1.31E−01 (Superior) | 1.40E−01 (Superior) | 1.33E−01 (Superior) | 1.33E−01 (Superior) | 1.20E−01 (Superior) | 176 (High) | 120 (High) | 104 (High) | 163 (High) | 122 (High) |
| LOG-[MEC-NON-EIG]-BAK | 6.45E−01 (Fair) | 7.41E−01 (Poor) | 7.85E−01 (Poor) | 8.04E−01 (Poor) | 4.06E−01 (Fair) | 193 (High) | 387 (High) | 1,421 (Low) | 936 (Medium) | 75 (High) |
| LOG-[MEC-RAN-PQN]-CEN | 1.64E−01 (Good) | 1.94E−01 (Good) | 2.64E−01 (Good) | 4.64E−01 (Fair) | 5.76E−02 (Superior) | 1,409 (Low) | 1,744 (Low) | 1,879 (Low) | 1,489 (Low) | 2,152 (Low) |
| LOG-[MEC-RAN-PQN]-BPC | 8.19E−02 (Superior) | 8.38E−02 (Superior) | 8.78E−02 (Superior) | 8.41E−02 (Superior) | 5.58E−02 (Superior) | 2,239 (Low) | 2,290 (Low) | 2,319 (Low) | 2,239 (Low) | 2,298 (Low) |
| BOX-[MDC-PAR-EIG]-ZER | 2.61E+00 (Poor) | 3.02E+00 (Poor) | 2.00E+00 (Poor) | 2.74E+00 (Poor) | 3.96E+00 (Poor) | 174 (High) | 138 (High) | 278 (High) | 228 (High) | 2 (High) |
| BOX-[MEC-RAN-NON]-KNN | 2.23E−01 (Good) | 2.29E−01 (Good) | 2.23E−01 (Good) | 2.25E−01 (Good) | 2.19E−01 (Good) | 474 (High) | 473 (High) | 379 (High) | 451 (High) | 332 (High) |
| BOX-[MEC-ATO-RLR]-BPC | 1.64E+00 (Poor) | 1.24E+00 (Poor) | 1.49E+00 (Poor) | 1.46E+00 (Poor) | 1.10E+00 (Poor) | 2,210 (Low) | 2,203 (Low) | 2,237 (Low) | 2,032 (Low) | 2,341 (Low) |