Benchmark run 2026-06-04

LFQBench · Orbitrap Astral AWS g5.4xlarge 11.7 h

261,014 Precursors

18,330 Protein groups

6 Raw files analysed

Quantification accuracy was not recorded for this run — the LFQBench analysis was added to the pipeline later. See the run list for runs that include it.

Per-file Results

Each of the 6 raw files, analysed independently. Mass and retention-time errors indicate calibration quality.

File	Precursors	Proteins	MS1 error	MS2 error	RT error	FWHM (RT)
`A_R1`	242,745	19,636	0.4063	7.6055	11.282	2.6903
`A_R2`	241,463	19,623	0.4225	7.482	10.4647	2.6777
`A_R3`	244,330	19,724	0.4203	9.6079	12.0768	2.8364
`B_R1`	243,495	19,779	0.45	7.7419	11.2886	2.7051
`B_R2`	244,207	19,770	0.3851	9.7384	11.8904	2.8464
`B_R3`	244,326	19,774	0.4054	9.6217	11.8947	2.8398

How this was measured

LFQBench is a community-standard benchmark for label-free quantification. Because the mixing ratios are fixed when the samples are prepared, the correct answer is known independently of any software — which makes it possible to measure accuracy rather than merely report output volume.

Dataset

Orbitrap Astral — 6 raw files: conditions A and B, 3 replicates each.

Ground truth

Expected log₂ ratios — Human 0.0, E. coli -2.0, Yeast 1.0.

Environment

AWS g5.4xlarge, single run. Random seed fixed so the analysis is reproducible.

Scope

Measured on the main branch of the SynapSpec engine. Runtime reflects one run on shared infrastructure and will vary with hardware.

Benchmark run