TOF/IMS — mzPeak

Provenance. Two families share this grid structure. Ion mobility — openly published runs across the major IMS technologies: Agilent 6560 drift-tube (DTIMS), Bruker timsTOF trapped-ion mobility (PASEF), and further PRIDE deposits, converted to mzPeak with the mobility axis preserved per spectrum/peak. SCIEX TOF grid-profile — TripleTOF / ZenoTOF runs (SWATH/DIA and MRM-HR) read with the native SCIEX reader, which recovers each run's flight-time grid from the vendor calibration, from PRIDE (PXD071869 · PXD011326) and MassIVE (MSV000090684 · MSV000093587 · MSV000095995). Each dataset names its accession and source.

Raw / mzML / mzPeak sizes for TOF/IMS — Size vs vendor RAW (=100%) across 13 dataset(s) > 50 MB · bars = mean, dots = runs.

PXD052561Waters SELECT SERIES Cyclic IMS (+ Xevo G2-XS ToF) — top-down proteoform analysis of forest cobra (Naja melanoleuca) venom with ECD/CID fragmentation. Read natively through MassLynx; the tile's cyclic-ion-mobility reference. PRIDE PXD052561.2 files
raw 1.1 GB, mzML n.a., mzPeak 177.9 MB (16%/n.a.)

mzpeak20231129_NM4_Xevo_MSe.mzpeak▶ View177.9 MB
zip20231129_NM4_Xevo_MSe.raw.zip573.3 MB

PXD059079Bruker timsTOF HT (TIMS/PASEF) with a companion Orbitrap Ascend FAIMS run — single-cell DIA proteomics of drug-resistant prostate-cancer cells (Homo sapiens). One representative timsTOF run of the 27 in the 19.7 GB deposit is published, with its vendor .d. PRIDE PXD059079.23 files
raw 137.1 MB, mzML n.a., mzPeak 112.6 MB (82%/n.a.)

PXD076703Bruker timsTOF HT (TIMS/PASEF) — DIA affinity purification (anti-FLAG co-IP) of FLAG-HA-tagged FAM98A/B/C from human HEK Flp-In T-REx 293 cells. The largest archive in this tile. PRIDE PXD076703.2 files
raw 9.6 GB, mzML n.a., mzPeak 8.5 GB (88%/n.a.)

PXD077098Waters Synapt — travelling-wave ion mobility (TWIMS), DIA proteomics of the maize (Zea mays) seed-borne microbiome under DNA hypomethylation. Since 0.11.3 the mzPeak stores every drift bin of every scan as an ion-mobility frame with its zero flanks (the 2.0 GB archive of earlier releases held drift-summed scans). PRIDE PXD077098.2 files
raw 14.3 GB, mzML n.a., mzPeak 6.6 GB (46%/n.a.)

mzpeak2024_08_15_Clicia_Milho_A1_B.mzpeak▶ View6.6 GB
zip2024_08_15_Clicia_Milho_A1_B.raw.zip9.7 GB

PXD078573Bruker timsTOF SCP (TIMS/PASEF) — chemical cross-linking MS (XL-MS) resolving the U1 snRNP–RNA-polymerase-II interaction via Prp40 in Saccharomyces cerevisiae. PRIDE PXD078573.2 files
raw 1.5 GB, mzML n.a., mzPeak 1.3 GB (86%/n.a.)

mzpeak20250305_AI_Rui_Xlink_F19_Slot1-28_1_9629.mzpeak▶ View1.3 GB
zip20250305_AI_Rui_Xlink_F19_Slot1-28_1_9629.d.zip1.4 GB

PXD079072Thermo Orbitrap Fusion Lumos with a FAIMS interface — field-asymmetric ion mobility, bottom-up LC-MS/MS of hemimethylated-CG-guided histone ubiquitylation in Xenopus laevis. PRIDE PXD079072.2 files
raw 1.2 GB, mzML 3.0 GB, mzPeak 774.8 MB (64%/26%)

mzpeakXinyi3.mzpeak▶ View774.8 MB
rawXinyi3.raw1.2 GB

PXD079300Bruker timsTOF Pro (TIMS/PASEF) — DIA and DDA proteomics of boar (Sus scrofa domesticus) seminal-plasma extracellular vesicles. PRIDE PXD079300.2 files
raw 2.5 GB, mzML n.a., mzPeak 2.2 GB (86%/n.a.)

mzpeak25NP03340023_RD8_1_27806.mzpeak▶ View2.2 GB
zip25NP03340023_RD8_1_27806.d.zip2.4 GB

PXD079445Thermo Orbitrap Exploris 480 with a FAIMS interface (compensation-voltage stepping) — DIA proteomics of extracellular vesicles from primary-tumour, recurrence and metastasis sarcoma patient-derived cultures (Homo sapiens). PRIDE PXD079445.2 files
raw 1.3 GB, mzML 1.6 GB, mzPeak 499.8 MB (38%/31%)

mzpeak240617_SAR186_A1_EVs.mzpeak▶ View499.8 MB
raw240617_SAR186_A1_EVs.raw1.3 GB

agilent-6560-dtims-imqtofAgilent 6560 IM-QTOF — drift-tube ion mobility (DTIMS) of a CE-MS standard mix; the tile's DTIMS reference, 0.3 MB mzPeak. Zenodo 18481720.2 files
Raw n.a., mzML 3.3 MB, mzPeak 280.5 KB (n.a./8%)

mzpeakCEMS_10ppm.mzpeak▶ View280.5 KB
mzmlCEMS_10ppm.mzML3.3 MB

MSV000090684SCIEX TripleTOF 6600 — SWATH/DIA BioID proximity-labelling map of nuclear bodies in human cells (Dyakov et al. 2023); one run of a 334-sample deposit. Filename records the instrument (TOF6600). MassIVE MSV000090684.3 files
raw 1.0 GB, mzML n.a., mzPeak 704.2 MB (66%/n.a.)

mzpeak9611_NSMF_CBF_BR1_BioID_20180119_TOF6600_AS13_SWATH.mzpeak▶ View704.2 MB
raw9611_NSMF_CBF_BR1_BioID_20180119_TOF6600_AS13_SWATH.wiff5.6 MB
scan9611_NSMF_CBF_BR1_BioID_20180119_TOF6600_AS13_SWATH.wiff.scan1.0 GB

MSV000093587SCIEX QTOF (model not stated in the deposit) — SWATH/DIA lung proteome of CD-1 mouse offspring after developmental PFAS exposure (PFOS/PFOA/PFHxS mixture). MassIVE MSV000093587.3 files
raw 1.0 GB, mzML n.a., mzPeak 780.2 MB (74%/n.a.)

MSV000095995SCIEX ZenoTOF 7600 — top-down proteomics platform with electron-activated dissociation (EAD), reduced RNase B measured in MRM-HR; the native SCIEX reader recovers the uniform-m/z flight-time grid. MassIVE MSV000095995.4 files
raw 73.4 MB, mzML n.a., mzPeak 46.7 MB (64%/n.a.)

mzpeak20240826_RNAseB_Reduced_50ngul_1ul_MRM_03.mzpeak▶ View46.7 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

PXD011326SCIEX TripleTOF 6600 — SWATH/DIA proteomics of an iPSC model of early-onset Parkinson's disease (Homo sapiens). Filename records the instrument (SWATH_6600). PRIDE PXD011326.3 files
raw 1.6 GB, mzML n.a., mzPeak 1.0 GB (63%/n.a.)

mzpeakVD_170826_SWATH_6600_PD_01.mzpeak▶ View1.0 GB
rawVD_170826_SWATH_6600_PD_01.wiff12.5 MB
scanVD_170826_SWATH_6600_PD_01.wiff.scan1.6 GB

PXD071869SCIEX ZenoTOF 7600 — SWATH/DIA benchmarking of biomanufacturing pipelines in Halomonas bluephagenesis and E. coli; the study compares five DIA platforms and this is its SCIEX arm. PRIDE PXD071869.4 files
raw 2.2 GB, mzML n.a., mzPeak 1.8 GB (80%/n.a.)

🌀 TOF/IMS14 datasets · 56.7 GB