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📈 General MS Data35 datasets · 46.0 GB

Non-imaging LC-/GC-MS instrument-vendor examples (Thermo, Bruker, SCIEX, Agilent, Shimadzu, Waters) — published mzML converted to mzPeak.

Provenance. Openly published runs from PRIDE, MetaboLights, MassIVE and Zenodo spanning 6 vendors and the major analyzer classes — Orbitrap, Q-TOF / UHR-QTOF, FT-ICR, pure ion trap, triple-quad (SRM/MRM), QqLIT, TIMS & DTIMS ion mobility, DIA, and GC electron-ionization. Each dataset below names its accession and source publication.

Raw / mzML / mzPeak sizes for General MS Data
Size vs vendor RAW (=100%) across 24 dataset(s) > 50 MB · bars = mean, dots = runs.
MSV000090203MassIVE · Agilent 6560 Q-TOF — lipidomics, native vendor raw `.d` (MassHunter). Broad-vendor demonstrator (raw only; one representative run).36 files
raw 1.3 GB, mzML n.a., mzPeak 1.0 GB (81%/n.a.)
MSV000092457MassIVE · Bruker timsTOF Pro 2 — metabolome, native vendor raw `.d` (TDF). Broad-vendor demonstrator (raw only; one representative run).14 files
raw 1.6 GB, mzML n.a., mzPeak 1.6 GB (99%/n.a.)
MSV000096674MassIVE · Thermo Orbitrap Astral — DDA-TMT, native vendor raw `.raw`. Broad-vendor demonstrator (raw only; one representative run).2 files
raw 225.7 MB, mzML n.a., mzPeak 101.6 MB (45%/n.a.)
MSV000099123MassIVE · Bruker timsTOF Pro 2 — proteomics, native vendor raw `.d` (PASEF TDF). Broad-vendor demonstrator (raw only; one representative run).38 files
raw 1.5 GB, mzML n.a., mzPeak 1.4 GB (94%/n.a.)
MTBLS11742MetaboLights · Agilent 5977B MSD — flux GC-MS, native vendor raw `.D` (doi:10.1038/s41586-025-08635-6). Broad-vendor demonstrator (raw only).2 files
raw 1.4 MB, mzML n.a., mzPeak 968.5 KB (68%/n.a.)
MTBLS243MetaboLights · Agilent 6490 Triple Quadrupole — dynamic-MRM metabolomics, native vendor raw `.d`. Broad-vendor demonstrator (raw only).2 files
raw 1.2 MB, mzML n.a., mzPeak 433.3 KB (36%/n.a.)
MTBLS5861MetaboLights · Shimadzu LCMS-9030 Q-TOF — lipidomics (OAD), native vendor raw `.lcd`. Broad-vendor demonstrator (raw only; one representative run).2 files
Raw n.a., mzML n.a., mzPeak 22.9 MB (n.a./n.a.)
PXD018751PRIDE · Thermo LCQ Deca XP — IEF/SCX/RPLC proteomics, vendor raw `.raw` (zip). Broad-vendor demonstrator (raw only; one representative run).2 files
Raw n.a., mzML n.a., mzPeak 3.9 MB (n.a./n.a.)
PXD022801PRIDE / iProX · SCIEX QTRAP 6500+ — MRM metabolome, vendor raw `.wiff`. Broad-vendor demonstrator (raw only).6 files
raw 1.4 MB, mzML n.a., mzPeak 531.3 KB (38%/n.a.)
PXD045201PRIDE · Thermo Orbitrap Eclipse — top-down, native vendor raw `.raw`. Broad-vendor demonstrator (raw only).2 files
raw 159.3 MB, mzML n.a., mzPeak 11.0 MB (7%/n.a.)
PXD053710PRIDE · SCIEX ZenoTOF 7600 — Zeno-SWATH exposome, vendor raw `.wiff`. Broad-vendor demonstrator (raw only).3 files
raw 656.8 MB, mzML n.a., mzPeak 575.7 MB (88%/n.a.)
PXD057269PRIDE · Thermo TSQ Altis — SRM, vendor raw `.raw`. Broad-vendor demonstrator (raw only; one representative run).2 files
raw 112.0 MB, mzML n.a., mzPeak 2.1 MB (2%/n.a.)
PXD059353PRIDE · Waters Synapt G2-Si — HDX MSE, vendor raw `.raw`. Broad-vendor demonstrator (raw only).2 files
Raw n.a., mzML n.a., mzPeak 43.8 MB (n.a./n.a.)
PXD065872PRIDE / jPOST · SCIEX TripleTOF 6600 — SWATH/DIA, vendor raw `.wiff`. Broad-vendor demonstrator (raw only).3 files
raw 3.2 GB, mzML n.a., mzPeak 2.0 GB (63%/n.a.)
PXD073126PRIDE · Waters Synapt XS — HDDDA ion mobility, vendor raw `.raw`. Broad-vendor demonstrator (raw only).2 files
raw 1.1 GB, mzML n.a., mzPeak 359.9 MB (31%/n.a.)
PXD076001PRIDE / iProX · Thermo Orbitrap Astral — DIA, native vendor raw `.raw`. Broad-vendor demonstrator (raw only).2 files
raw 2.5 GB, mzML n.a., mzPeak 1.0 GB (41%/n.a.)
PXD076861PRIDE · Bruker impact HD — native MS, vendor raw `.d`. Broad-vendor demonstrator (raw only).2 files
raw 216.0 MB, mzML n.a., mzPeak 28.6 MB (13%/n.a.)
agilent-6490-triplequadMetaboLights MTBLS648 · Agilent 6490 triple-quad — native vendor `.d` (replaces PXD041762, which deposited no raw).41 files
raw 5.9 MB, mzML n.a., mzPeak 728.6 KB (12%/n.a.)
agilent-8890-gc-eiMetaboLights MTBLS11550 · Agilent 8890 GC / 7000D — electron-ionization GC-MS.3 files
Raw n.a., mzML 15.9 MB, mzPeak 1.5 MB (n.a./9%)
agilent-qtofMetaboLights MTBLS14741 · Agilent LC-QTOF — C18 isoflavone, native vendor `.d` (replaces Zenodo 18502866, a mislabeled QqQ chromatogram-only mzML with no raw).39 files
raw 241.6 MB, mzML n.a., mzPeak 191.1 MB (79%/n.a.)
bruker-impact-ii-qtofMetaboLights MTBLS14574 · Bruker impact II UHR-QTOF — native vendor `.d` (BAF) (replaces MTBLS12824, which deposited no raw).38 files
raw 762.4 MB, mzML n.a., mzPeak 103.7 MB (14%/n.a.)
bruker-microtof-q2MetaboLights MTBLS520 · Bruker micrOTOF-Q II ESI-QTOF (bryophyte seasonal metabolomics; Peters et al. 2018).3 files
Raw n.a., mzML 56.6 MB, mzPeak 20.6 MB (n.a./36%)
bruker-timstof-proMassIVE MSV000101607 · Bruker timsTOF Pro 2 — TIMS-PASEF proteomics (SBA415); native TDF .d.55 files
raw 2.1 GB, mzML 1.4 GB, mzPeak 2.0 GB (97%/148%)
sciex-qtrap-6500MetaboLights MTBLS14853 · SCIEX QTRAP 6500 — native vendor `.wiff` (replaces PXD066465, which deposited no raw).4 files
raw 29.5 MB, mzML n.a., mzPeak 4.4 MB (15%/n.a.)
sciex-tripletof-6600SCIEX TripleTOF 6600 — DIA/SWATH acquisition; broad-vendor demonstrator for the SCIEX QTOF family, converted through the native Clearcore2 reader. Zenodo 17416537.3 files
Raw n.a., mzML 243.1 MB, mzPeak 135.3 MB (n.a./56%)
shimadzu-lcms-9030-qtofMetaboLights MTBLS13204 · Shimadzu LCMS-9030 Q-TOF (seaweed metabolomics).4 files
Raw n.a., mzML 36.2 MB, mzPeak 3.8 MB (n.a./10%)
thermo-fusion-lumosPRIDE PXD008952 · Thermo Orbitrap Fusion Lumos — CPTAC NCI-7 TMT (Clark et al. 2018).4 files
raw 659.4 MB, mzML 588.6 MB, mzPeak 354.4 MB (54%/60%)
thermo-ltq-ft-ultra-fticrMetaboLights MTBLS3512 · Thermo LTQ FT Ultra — FT-ICR (marine dissolved organic matter; Liu et al. 2020).4 files
raw 221.1 MB, mzML 30.2 MB, mzPeak 85.2 MB (39%/283%)
thermo-ltq-orbitrap-velosPRIDE PXD000001 · Thermo LTQ Orbitrap Velos — TMT “Erwinia” spike-in, the first ProteomeXchange dataset (Gatto & Christoforou 2013).4 files
raw 210.3 MB, mzML 429.2 MB, mzPeak 126.0 MB (60%/29%)
thermo-ltq-xl-iontrapPRIDE PXD059878 · Thermo LTQ XL — pure linear ion trap (PC4 acetylation; Agrawal et al. 2025).4 files
raw 69.7 MB, mzML 173.5 MB, mzPeak 61.8 MB (89%/36%)
thermo-orbitrap-astralMassIVE MSV000100943 · Thermo Orbitrap Astral — high-throughput DIA plasma proteomics (Coon lab 2025).4 files
raw 8.4 GB, mzML 299.9 MB, mzPeak 3.3 GB (39%/1125%)
thermo-qexactive-plusMetaboLights MTBLS14885 · Thermo Q Exactive Plus — native vendor `.raw` (replaces Zenodo 17549994, an mzML-only re-deposit with no raw).3 files
raw 121.0 MB, mzML n.a., mzPeak 67.3 MB (56%/n.a.)
waters-pda-uvProteoWizard Waters vendor-reader test data · Waters ACQUITY UPLC PDA — the corpus's UV / photodiode-array exemplar: ProteoWizard read the PDA function from a MassLynx .raw and wrote wavelength array (210–400 nm) + electromagnetic radiation (absorption) spectra. Demonstrates mzPeak's UV wavelength_spectra facet — the rare case of UV spectra carried inside the mzML.2 files
Raw n.a., mzML 83.1 KB, mzPeak 212.1 KB (n.a./255%)
waters-synapt-g2si-hdmseMetaboLights MTBLS812 · Waters SYNAPT G2-Si HDMS — HDMSe traveling-wave ion mobility (TWIMS); LC-IMS-MS metabolomics of pancreatic-cancer cell lines (Drabik et al.). Per-spectrum drift time (MS:1002476) — the corpus's Waters ion-mobility exemplar, alongside Agilent DTIMS and Bruker timsTOF PASEF.36 files
raw 1.0 GB, mzML n.a., mzPeak 158.0 MB (15%/n.a.)
waters-xevo-g2s-qtofMetaboLights MTBLS1129 · Waters Xevo G2-XS QTof — label-free metabolomics (colon cancer; Cai et al. 2020); also our SDRF fixture.3 files
Raw n.a., mzML 81.8 MB, mzPeak 48.5 MB (n.a./59%)