General MS Data — mzPeak examples

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 11 dataset(s) > 50 MB · bars = mean, dots = runs.

agilent-6490-triplequadPRIDE PXD041762 · Agilent 6490 triple-quad, SRM/dMRM (COVID-19 plasma).3 files
Raw n.a., mzML 5.3 MB, mzPeak 955.6 KB (n.a./18%)

mdREADME.md992 B
mzmlREC-2349_P2_F1.mzML5.3 MB
mzpeakREC-2349_P2_F1.mzpeak▶ Explorer955.6 KB

agilent-6560-dtims-imqtofZenodo 18481720 · Agilent 6560 IM-QTOF — drift-tube ion mobility (DTIMS), CE-MS standard mix.3 files
Raw n.a., mzML 3.3 MB, mzPeak 307.6 KB (n.a./9%)

mzmlCEMS_10ppm.mzML3.3 MB
mzpeakCEMS_10ppm.mzpeak▶ Explorer307.6 KB
mdREADME.md1.1 KB

agilent-8890-gc-eiMetaboLights MTBLS11550 · Agilent 8890 GC / 7000D — electron-ionization GC-MS.3 files
Raw n.a., mzML 15.9 MB, mzPeak 1.6 MB (n.a./10%)

mzmlEFWS-1.mzML15.9 MB
mzpeakEFWS-1.mzpeak▶ Explorer1.6 MB
mdREADME.md980 B

agilent-qtofZenodo 18502866 · Agilent 6490 triple-quad dMRM standard mix (chromatogram-only). Note: directory name is legacy; the instrument is a QqQ, not a Q-TOF.3 files
Raw n.a., mzML 2.3 MB, mzPeak 811.9 KB (n.a./35%)

mzmlMRM-standmix-5.mzML2.3 MB
mzpeakMRM-standmix-5.mzpeak▶ Explorer811.9 KB
mdREADME.md652 B

bruker-impact-ii-qtofMetaboLights MTBLS12824 · Bruker impact II UHR-QTOF.3 files
Raw n.a., mzML 31.3 MB, mzPeak 20.4 MB (n.a./65%)

mzml21P0055_Tissue_Georges_NEG_N_01_17471.mzML31.3 MB
mzpeak21P0055_Tissue_Georges_NEG_N_01_17471.mzpeak▶ Explorer20.4 MB
mdREADME.md1.2 KB

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 36.0 MB (n.a./64%)

mdREADME.md540 B
mzmlneg_01_Fistax_1-A,2_01_5715.mzML56.6 MB
mzpeakneg_01_Fistax_1-A,2_01_5715.mzpeak▶ Explorer36.0 MB

bruker-timstof-proMassIVE MSV000101607 · Bruker timsTOF Pro — PASEF / TIMS ion mobility.55 files
raw 2.1 GB, mzML 1.4 GB, mzPeak 677.2 MB (32%/49%)

sciex-qtrap-6500PRIDE PXD066465 · SCIEX QTRAP 6500 — scout-triggered MRM (host-cell proteins).3 files
Raw n.a., mzML 3.0 MB, mzPeak 259.5 KB (n.a./8%)

mzmlDrug_substance_3_scheduled_MRM.mzML3.0 MB
mzpeakDrug_substance_3_scheduled_MRM.mzpeak▶ Explorer259.5 KB
mdREADME.md1004 B

sciex-tripletof-6600Zenodo 17416537 · SCIEX TripleTOF 6600 — DIA / SWATH.3 files
Raw n.a., mzML 243.1 MB, mzPeak 138.1 MB (n.a./57%)

mzml12_80.mzML243.1 MB
mzpeak12_80.mzpeak▶ Explorer138.1 MB
mdREADME.md453 B

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 50.9 MB (69%/57%)

mzml20240826_RNAseB_Reduced_50ngul_1ul_MRM_03.mzML89.8 MB
mzpeak20240826_RNAseB_Reduced_50ngul_1ul_MRM_03.mzpeak▶ Explorer50.9 MB
raw20240826_RNAseB_Reduced_50ngul_1ul_MRM_03.wiff2.1 MB
scan20240826_RNAseB_Reduced_50ngul_1ul_MRM_03.wiff.scan69.0 MB
wiff220240826_RNAseB_Reduced_50ngul_1ul_MRM_03.wiff22.4 MB
mdREADME.md1.1 KB

shimadzu-lcms-9030-qtofMetaboLights MTBLS13204 · Shimadzu LCMS-9030 Q-TOF (seaweed metabolomics).3 files
Raw n.a., mzML 36.2 MB, mzPeak 2.4 MB (n.a./7%)

mzmlBlind_P1_pos_012.mzML36.2 MB
mzpeakBlind_P1_pos_012.mzpeak▶ Explorer2.4 MB
mdREADME.md850 B

thermo-fusion-lumosPRIDE PXD008952 · Thermo Orbitrap Fusion Lumos — CPTAC NCI-7 TMT (Clark et al. 2018).4 files
raw 659.4 MB, mzML 1.3 GB, mzPeak 348.9 MB (53%/25%)

mzml01_CPTAC_TMTS1-NCI7_P_JHUZ_20170509_LUMOS.mzML1.3 GB
mzpeak01_CPTAC_TMTS1-NCI7_P_JHUZ_20170509_LUMOS.mzpeak▶ Explorer348.9 MB
raw01_CPTAC_TMTS1-NCI7_P_JHUZ_20170509_LUMOS.raw659.4 MB
mdREADME.md575 B

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 460.6 MB, mzPeak 90.8 MB (41%/20%)

mdREADME.md966 B
rawmtab_BIOS_CRAM1620_1_072617_34.RAW221.1 MB
mzmlmtab_BIOS_CRAM1620_1_072617_34.mzML460.6 MB
mzpeakmtab_BIOS_CRAM1620_1_072617_34.mzpeak▶ Explorer90.8 MB

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 568.6 MB, mzPeak 133.9 MB (64%/24%)

mdREADME.md639 B
rawTMT_Erwinia_01.raw210.3 MB
mzmlTMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML568.6 MB
mzpeakTMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzpeak▶ Explorer133.9 MB

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 55.6 MB (80%/32%)

mzml2013_30_Amrutha_050713_1.mzML173.5 MB
mzpeak2013_30_Amrutha_050713_1.mzpeak▶ Explorer55.6 MB
raw2013_30_Amrutha_050713_1.raw69.7 MB
mdREADME.md942 B

thermo-orbitrap-astralMassIVE MSV000100943 · Thermo Orbitrap Astral — high-throughput DIA plasma proteomics (Coon lab 2025).4 files
raw 8.4 GB, mzML 7.3 GB, mzPeak 3.5 GB (41%/48%)

mzml20240912_WFB_exp01_magnet_5_0.mzML7.3 GB
mzpeak20240912_WFB_exp01_magnet_5_0.mzpeak▶ Explorer3.5 GB
raw20240912_WFB_exp01_magnet_5_0.raw8.4 GB
mdREADME.md783 B

thermo-qexactive-plusZenodo 17549994 · Thermo Q Exactive Plus (IBDMDB teaching re-deposit).3 files
Raw n.a., mzML 242.1 MB, mzPeak 98.4 MB (n.a./41%)

mzml160920_SM-AKTWT_509.mzML242.1 MB
mzpeak160920_SM-AKTWT_509.mzpeak▶ Explorer98.4 MB
mdREADME.md520 B

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 44.8 MB (n.a./55%)

mzmlQC01.mzML81.8 MB
mzpeakQC01.mzpeak▶ Explorer44.8 MB
mdREADME.md484 B

📈 General MS Data18 datasets · 28.8 GB