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LFQBench / Orbitrap Astral

Three archived reports, the same six input files. A and B each contain three replicate runs.

This is not a current-release ranking. Tool labels preserve source-folder labels; exact releases, execution dates, hardware and full search settings are not reconciled. Matching filenames do not establish identical search settings.
Precursor q-value < 0.01; decoys excluded. IDs are distinct modified-sequence and charge pairs across all six runs.
Tool / source label Precursor IDs Detected in all six Median CV: A Median CV: B
SynapSpec (v092 folder) 261,946 77.9%203,950 of 261,946 13.6%n = 221,891 12.6%n = 225,414
DIA-NN (archived) 289,626 78.7%228,010 of 289,626 9.8%n = 241,868 9.8%n = 242,484
Spectronaut (v21_0 folder) 300,293 88.9%266,933 of 300,293 13.8%n = 279,179 13.8%n = 280,697

CV uses sample standard deviation / mean within one condition, only for precursors with positive finite MS2 quantities in all three replicates. Each tool has its own eligible population. Missing observations are not imputed.

Accuracy vs. depth

Same layout as ProteoBench’s LFQ accuracy modules (proteobench.org): each point is one tool’s full run on these six files, not one point per precursor. Horizontal position is the median absolute error between measured and expected log₂ fold change across the three species (species-weighted, lower is more accurate); vertical position is how many precursor ions that run identified. Up and to the left is more precursors identified with less error — neither axis alone ranks a tool.

260k 280k 300k 320k 0.0 0.03 0.06 0.09 0.12 SynapSpec: 261946 precursors, median |error| 0.054 DIA-NN: 289626 precursors, median |error| 0.1065 Spectronaut: 300293 precursors, median |error| 0.0409 Median absolute log₂ fold-change error (species-weighted)
  • SynapSpec
  • DIA-NN
  • Spectronaut

Identification, repeatability and LFQ ratios

More IDs means broader coverage, not automatically better quantification. Lower CV means more consistent repeat measurements. For LFQ, a median closer to the dashed expected line and a narrower interquartile range indicate closer agreement and less spread.

LFQBench / Orbitrap Astral: three-tool precursor counts, six-run completeness, within-condition CV, and species-specific LFQ median and interquartile range. Exact values follow below. Download comparison PNG
Precursor MS2 log₂(mean A / mean B), using observed values; entities require positive means in both conditions. Mixed-species annotations are excluded. Intervals are quartiles, not confidence intervals.
ToolSpeciesExpectedMedian25–75%Precursors
SynapSpec (v092 folder) HUMAN 0.0 -0.054 -0.23 – 0.084 182,617
SynapSpec (v092 folder) ECOLI -2.0 -1.986 -2.254 – -1.673 19,869
SynapSpec (v092 folder) YEAS8 1.0 0.935 0.699 – 1.107 50,977
DIA-NN (archived) HUMAN 0.0 -0.053 -0.167 – 0.063 191,444
DIA-NN (archived) ECOLI -2.0 -1.858 -2.038 – -1.575 20,122
DIA-NN (archived) YEAS8 1.0 0.893 0.725 – 1.032 54,014
Spectronaut (v21_0 folder) HUMAN 0.0 -0.041 -0.197 – 0.11 211,296
Spectronaut (v21_0 folder) ECOLI -2.0 -2.05 -2.378 – -1.788 24,124
Spectronaut (v21_0 folder) YEAS8 1.0 0.997 0.802 – 1.237 62,139

Shared precursor IDs

Exact modified-sequence and charge matches, across all six runs; pairwise counts overlap and must not be added together.

  • synapspec / diann: 234,019
  • synapspec / spectronaut: 223,317
  • diann / spectronaut: 244,552
Input files and per-file IDs
Input stemSynapSpec (v092 folder)DIA-NN (archived)Spectronaut (v21_0 folder)
20250206_OA_OP_LFQBench_A_R1 241,256 260,389 290,562
20250206_OA_OP_LFQBench_A_R2 243,547 260,349 289,835
20250206_OA_OP_LFQBench_A_R3 241,698 259,813 290,981
20250206_OA_OP_LFQBench_B_R1 244,858 260,122 291,741
20250206_OA_OP_LFQBench_B_R2 244,390 260,030 291,212
20250206_OA_OP_LFQBench_B_R3 244,409 260,007 291,668
Limitations and reproducibility
  • No analysis engine was rerun. These are archived report extracts, imported on 2026-09-08.
  • Protein entities use tool-specific grouping definitions and are not presented as a cross-tool score.
  • Separate SynapSpec MBR files are not included. MBR settings in the base reports remain unverified.
  • Expected ratios follow the existing BION LFQ preset: human 1:1, yeast 2:1, E. coli 1:4 (A:B). Sample preparation records and full settings still need owner review.
  • Release, execution time, resource and analysis date: not verified. No metadata is borrowed from the September 7 run.
  • These internal LFQBench experiments are not labeled PXD028735; a provenance mapping is not established.