Benchmark run 2026-03-31

LFQBench · Orbitrap Astral AWS c7i.8xlarge 18.82 h

191,366 Precursors

15,006 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`	165,314	14,425	0.6412	6.9699	162.367	2.9026
`A_R2`	180,761	14,667	0.4228	9.7932	205.2631	3.0107
`A_R3`	165,889	14,447	5.5254	7.1778	197.4352	2.8371
`B_R1`	167,242	14,610	0.5732	9.5586	329.1115	3.183
`B_R2`	181,743	14,728	0.841	12.2549	142.5877	3.1357
`B_R3`	163,606	14,623	0.3517	10.8027	343.9853	3.185

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 c7i.8xlarge, 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