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LFQBench / Orbitrap Astral

A × 3 + B × 3 · completed run · 5d12a532

Dataset history
Release
Not mappedCommit 5d12a532
Run date
2026-09-0700:59–06:28 · ClearML display
Elapsed time
5 h 29 minTask wall-clock time
Resource
c7i.8xlargeInstance tag, not host capacity

Run configuration

Recorded configuration · bion_lfq_astral.yaml

Library
Generated from FASTA
Enzyme
Trypsin/P
Missed cleavages
2
Match between runs
On
Peptide length
7–52 residues
Precursor charge
1–6
Maximum variable modifications
5
Random seed
42
Additional recorded settings

FASTA: napedro_3mixed_human_yeast_ecoli_20140403_iRT.fasta

Differential analysis enabled · condition-aware precursor correction on · quantity level: pg · output: parquet.

Only explicitly recorded settings are shown. FDR thresholds and release mapping have not been verified for this run.

Raw files

Six input files · protein column uses per-file protein_accessions

File nameConditionReplicatePrecursor IDsProtein accessions
20250206_OA_OP_LFQBench_A_R1.raw A 1 238,452 18,519
20250206_OA_OP_LFQBench_A_R2.raw A 2 238,003 18,481
20250206_OA_OP_LFQBench_A_R3.raw A 3 238,445 18,470
20250206_OA_OP_LFQBench_B_R1.raw B 1 238,198 18,462
20250206_OA_OP_LFQBench_B_R2.raw B 2 239,372 18,548
20250206_OA_OP_LFQBench_B_R3.raw B 3 239,578 18,561

Across the analysis: 252,078 distinct precursors; 19,671 reported total_proteins. These are not sums of the rows. Protein counting scopes differ. File sizes and acquisition durations have not been imported.

Expected and measured ratios

Precursor-level LFQ · Human 1×, Yeast 2×, E. coli 0.25× A/B

Dashed line: expected ratio. Dot: measured median. Band: middle 50% of measurements. A close median does not mean every measurement is close.

Human175,289 paired precursors
0.25× 0.5× 1× 2×
0.970×measured median A/B
Yeast49,859 paired precursors
0.25× 0.5× 1× 2×
1.900×measured median A/B
E. coli19,881 paired precursors
0.25× 0.5× 1× 2×
0.263×measured median A/B
Human175,289 paired precursors
0.71× Expected 1.41×
-3.0%median deviation
Yeast49,859 paired precursors
0.71× Expected 1.41×
-5.0%median deviation
E. coli19,881 paired precursors
0.71× Expected 1.41×
+5.1%median deviation

Ratio A/B on a log₂-spaced axis: equal distances mean equal fold changes. Bands are interquartile ranges, not confidence intervals. The outer 50% is not drawn.

Measured A/B divided by expected A/B, on a closer log₂-spaced axis (0.71×–1.41× expected). Bands are interquartile ranges, not confidence intervals. The outer 50% is not drawn.

How do I read the original LFQ scatter plot?

Each dot is a precursor with a usable quantity in both samples. Left to right is the amount measured in B; bottom to top is the A/B ratio.

The expected horizontal lines are 0 for Human, +1 for Yeast and −2 for E. coli on the log₂ scale. Those mean 1×, 2× and 0.25×. Dots near their species’ line recover the known mixture well.

The side histograms count measurements at each ratio. The final panel uses logarithmic counts to make rare, far-away measurements visible.

Source record

ClearML run at commit 5d12a532, checked on 7 September 2026. Date and time retain the source display; its timezone has not been established. Resource describes the recorded instance tag.

Ratios use mean quantity in A divided by mean quantity in B for each precursor with positive quantities in both conditions. Quartiles and medians below are transformed from logged log₂ ratios. One run does not establish performance on other datasets or a ranking against other tools.

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