mzPeakmzPeakexamples
↗ mzpeak.orgGitHub
mzpeak.org › examples › General MS Data

📈 General MS Data42 datasets · 68.5 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 22 dataset(s) > 50 MB · bars = mean, dots = runs.
MSV000084273MassIVE · Bruker micrOTOF II — secreted-proteins metabolomics, native vendor raw `.d` (BAF). Broad-vendor demonstrator (raw only; one representative run).9 files
raw 533.3 MB
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, mzPeak 1.0 GB (81%)
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, mzPeak 1.4 GB (87%)
MSV000096674MassIVE · Thermo Orbitrap Astral — DDA-TMT, native vendor raw `.raw`. Broad-vendor demonstrator (raw only; one representative run).2 files
raw 225.7 MB, mzPeak 88.8 MB (39%)
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, mzPeak 1.5 GB (100%)
MTBLS11742MetaboLights · Agilent 5977B MSD — flux GC-MS, native vendor raw `.D` (doi:10.1038/s41586-025-08635-6). Broad-vendor demonstrator (raw only).1 files
MTBLS243MetaboLights · Agilent 6490 Triple Quadrupole — dynamic-MRM metabolomics, native vendor raw `.d`. Broad-vendor demonstrator (raw only).1 files
MTBLS432MetaboLights · Shimadzu LCMS-IT-TOF — metabolome, native vendor raw `.lcd`. Broad-vendor demonstrator (raw only).1 files
MTBLS5861MetaboLights · Shimadzu LCMS-9030 Q-TOF — lipidomics (OAD), native vendor raw `.lcd`. Broad-vendor demonstrator (raw only; one representative run).2 files
mzPeak 30.1 MB
PXD018751PRIDE · Thermo LCQ Deca XP — IEF/SCX/RPLC proteomics, vendor raw `.raw` (zip). Broad-vendor demonstrator (raw only; one representative run).1 files
PXD022801PRIDE / iProX · SCIEX QTRAP 6500+ — MRM metabolome, vendor raw `.wiff`. Broad-vendor demonstrator (raw only).5 files
raw 1.4 MB, mzPeak 126.1 KB (9%)
PXD044023PRIDE · Bruker amaZon ETD — GeLC-MS, vendor raw `.d` (zip). Broad-vendor demonstrator (raw only; one representative run).1 files
PXD045201PRIDE · Thermo Orbitrap Eclipse — top-down, native vendor raw `.raw`. Broad-vendor demonstrator (raw only).2 files
raw 159.3 MB, mzPeak 11.5 MB (7%)
PXD053710PRIDE · SCIEX ZenoTOF 7600 — Zeno-SWATH exposome, vendor raw `.wiff`. Broad-vendor demonstrator (raw only).2 files
raw 656.8 MB
PXD057269PRIDE · Thermo TSQ Altis — SRM, vendor raw `.raw`. Broad-vendor demonstrator (raw only; one representative run).2 files
raw 112.0 MB, mzPeak 2.1 MB (2%)
PXD059353PRIDE · Waters Synapt G2-Si — HDX MSE, vendor raw `.raw`. Broad-vendor demonstrator (raw only).1 files
PXD065872PRIDE / jPOST · SCIEX TripleTOF 6600 — SWATH/DIA, vendor raw `.wiff`. Broad-vendor demonstrator (raw only).2 files
raw 3.2 GB
PXD073126PRIDE · Waters Synapt XS — HDDDA ion mobility, vendor raw `.raw`. Broad-vendor demonstrator (raw only).1 files
PXD076001PRIDE / iProX · Thermo Orbitrap Astral — DIA, native vendor raw `.raw`. Broad-vendor demonstrator (raw only).2 files
raw 2.5 GB, mzPeak 963.8 MB (38%)
PXD076861PRIDE · Bruker impact HD — native MS, vendor raw `.d`. Broad-vendor demonstrator (raw only).1 files
agilent-6490-triplequadMetaboLights MTBLS648 · Agilent 6490 triple-quad — native vendor `.d` (replaces PXD041762, which deposited no raw).41 files
raw 5.9 MB, mzPeak 303.3 KB (5%)
agilent-6560-dtims-imqtofZenodo 18481720 · Agilent 6560 IM-QTOF — drift-tube ion mobility (DTIMS), CE-MS standard mix.3 files
mzML 3.3 MB, mzPeak 313.9 KB (9%)
agilent-8890-gc-eiMetaboLights MTBLS11550 · Agilent 8890 GC / 7000D — electron-ionization GC-MS.3 files
mzML 15.9 MB, mzPeak 1.7 MB (11%)
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, mzPeak 191.2 MB (79%)
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, mzPeak 446.6 MB (59%)
bruker-microtof-q2MetaboLights MTBLS520 · Bruker micrOTOF-Q II ESI-QTOF (bryophyte seasonal metabolomics; Peters et al. 2018).3 files
mzML 56.6 MB, mzPeak 36.6 MB (65%)
bruker-timstof-proMassIVE MSV000101607 · Bruker timsTOF Pro — PASEF / TIMS ion mobility.55 files
raw 2.1 GB, mzML 1.4 GB, mzPeak 714.4 MB (34%/52%)
sciex-qtrap-6500MetaboLights MTBLS14853 · SCIEX QTRAP 6500 — native vendor `.wiff` (replaces PXD066465, which deposited no raw).4 files
raw 29.5 MB, mzPeak 4.3 MB (14%)
sciex-tripletof-6600Zenodo 17416537 · SCIEX TripleTOF 6600 — DIA / SWATH.3 files
mzML 243.1 MB, mzPeak 130.0 MB (53%)
sciex-zenotof-7600MassIVE MSV000095995 · SCIEX ZenoTOF 7600 — EAD / Zeno top-down (Searfoss et al. 2025).6 files
raw 73.4 MB, mzML 89.8 MB, mzPeak 48.4 MB (66%/54%)
shimadzu-lcms-9030-qtofMetaboLights MTBLS13204 · Shimadzu LCMS-9030 Q-TOF (seaweed metabolomics).4 files
mzML 36.2 MB, mzPeak 2.9 MB (8%)
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 148.4 MB (22%/25%)
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 5.4 MB (2%/18%)
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 109.5 MB (52%/26%)
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 52.3 MB (75%/30%)
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 107.6 MB (1%/36%)
thermo-orbitrap-astral-PXD0490284 files
raw 20.6 GB, mzML 224.5 MB, mzPeak 8.2 GB (40%/3730%)
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, mzPeak 70.5 MB (58%)
thermo-qexactive-plus-PXD0776193 files
mzML 457.7 MB, mzPeak 94.4 MB (21%)
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 (190–500 nm) + electromagnetic radiation (absorption) spectra. Demonstrates mzPeak's UV wavelength_spectra facet — the rare case of UV spectra carried inside the mzML.2 files
mzML 83.1 KB, mzPeak 157.0 KB (189%)
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.35 files
raw 1.0 GB
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
mzML 81.8 MB, mzPeak 46.7 MB (57%)