Proteomics > Our instruments

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Instrument Reservation

Instrument reservations can only be made by employees.
If you have a running User Lab project and you would like to reserve an instrument, please check its availability on the FGCZ Instrument Reservation System (IRS), and submit a request for the desired time-slot. Your project coach, or the person responsible for the instrument, will contact you as soon as possible.

Proteomics equipment available at FGCZ

Default ESI and nLC setup

Ion source

For electrospray ionization (ESI), nearly all MS instruments are by default equipped with Digital PicoView nanospray sources (DPV)


Liquid chromatography

For sentitive, high peak capacity chromatography, our MS instruments are coupled to waters nanoACQUITY UPLC systems or ACQUITY UPLC M-Class systems.


The standard chromatographic separation is done with trapped elution prior the analytical elution in nano-flow mode. Separation is based on reversed-phase chromatography with C18.
Following trap and analytical columns are installed:
  • nanoEase M/Z Symmetry C18 100 A, 5um, 1/PK 180 um x 20 mm (Trap column)
  • nanoEase M/Z HSS C18 T3 Col 100 A, 1.8 um, 1 P/K 75 um x 250 mm (Analytical column)

High-throughput chromatography

For large batches of samples, or in specific cases (e.g., very low-input material), the Evosep One platform is used for integrated purification and chromatographic separation. Evosep is particular suited for clinical proteomics (robust and fast).

NameDetailed informations by clicking * ideaPrinciple * ideaDescriptionRemarksCoupled toInstruments at FGCZ
EVOSEP ONE High-throughput nanoUPLC systemShort gradients (i.e. 30-200 samples/day) for throughput. Samples are loaded on evotips and eluted directly from tips. ApplicationTIMSTOF_1,EXPLORIS_2, or LUMOS_2 EVOSEP_1 and EVOSEP_2

MS Instruments

NameDetailed informations by clicking on the instrument * ideaSchema * ideaMass analyzerFragmentationMax resolution @ m/z 200 & Max scan rateOperation Modes*Instruments at FGCZ - Service/user lab access
Orbitrap Fusion Lumos Tribrid™ combines quadrupole, Orbitrap, and linear ion trap CID/HCD/ETD detected by the Ion Trap or Orbitrap at any level of MSn450,000 &30 Hz @ 7,500 resolution DDA, Full MS, SIM, PRM, DIA, AIF, In-source fragmentation, Positive/negative ion switching, timed SIM, SPS-MS3, APD, FAIMS, Sure QuantUser LUMOS_1 and Service LUMOS_2
Exploris 480 Hybrid quadrupole, Orbitrap HCD480,000 & 40 Hz @ 7,500 resolution DDA, Full MS, SIM, PRM, DIA, AIF, In-source fragmentation, Positive/negative ion switching, timed SIM, APD, FAIMS, Sure QuantUser EXPLORIS_1
Q Exactive Hybrid quadrupole, OrbitrapHCD140,000 & 12 Hz @ 17,500 resolutionDDA, Full MS, SIM, DIA, PRMService QEXACTIVE_1 and "test instrument" QEXACTIVE_2 (shared with metabolomics)
Orbitrap Fusion Tribrid™ combines quadrupole, Orbitrap, and linear ion trapCID/HCD/ETD detected by the Ion Trap or Orbitrap at any level of MSn450,000 &18 Hz @ 15,000 resolution DDA, Full MS, SIM, PRM, DIA, AIF, In-source fragmentation, Positive/negative ion switching, timed SIM, SPS-MS3, FAIMSUser FUSION_2
timsTOF Pro https://doi.org/10.1074/mcp.TIR118.000900 dual Trapped ion mobility (TIMS), quadrupole, time-of-flight (TOF)CID >200 for resolution of ion mobility, >100 Hz for PASEF Parallel Accumulation Serial Fragmentation (PASEF), diaPASEFUser TIMSTOF_1
timsTOF Flex MALDI-2 See details hereMALDI-2 post-ionization, dual Trapped ion mobility (TIMS), quadrupole, time-of-flight (TOF)CID >200 for resolution of ion mobility, >150 Hz for PASEF From 4D-Omics to molecular imaging without stopping, changing, modifying or compromises (learn more), diaPASEFService timsTOF_Flex_1
RapiFlex MALDI TOF-TOF Matrix Assisted Laser Desorption Ionization — Time of Flight Mass Spectrometry (MALDI-TOF-TOF) high energy collision dissociation MS/MS techniques and in-source decay in the reflector mode of the mass analyzer (reISD) as a pseudo-MS/MS technique ≥ 50,000 for Somatostatin 28 (m/z 3,147.5) FWHM MS in liner or reflectron mode, HCD-MS/MS, Imagining (Imaging Pixel shape Squared pixel for best tissue coverage with variable pixel size of 20 μm to 100 μm; Imaging Speed Up to 40 pixel / sec.Service RapiFlex_1
Q-​TOF SYNAPT G2-​Si Waters Synapt G2-SI 8k with ETD, or 4k with IMS CID and ETD Up to 60,000 DDA, Full MS, DIA Service G2SI_1 and G2SI_2
* • Full MS with high-resolution accurate mass detection • Selected Ion Monitoring (SIM) with high-resolution accurate-mass detection • Parallel Reaction Monitoring (PRM) for improved screening and quantitative confidence • Data-Independent Acquisition (DIA) for unbiased identification and quantitative analysis • All-Ion Fragmentation (AIF) in the HCD collision cell with high-resolution accurate-mass detection • In-source fragmentation of all ions • Positive/negative ion switching on chromatographic timescale • On-the-fly data-dependent decision making ddMS2 > data dependent acqusition (DDA) • Timed SIM for scheduled data acquisition of the targets of interest • synchronous precursor selection (SPS)-based MS3 • advanced peak determination (APD) algorithm • High-Field Asymmetric waveform ion mobility (FAIMS) • laser-induced dissociation (LID)

Other detectors

NameDetailed informations by clicking on the instrument * ideaSchema * ideaDescriptionOperation Modes*Instruments at FGCZ - Service/user lab access
ACQUITY QDa Mass Detector Single Quadrupole Mass Detection ACQUITY QDa is as intuitive as an optical detector. Integrated in Acquity UPLC H-Class PlusService QDA_1
2475 Fluorescence (FLR) Detector The detector helps achieve high-sensitivity and low-dispersion methods. Integrated in AcquityService Characterization_Nlinked_glycans

Other equipment for MS workflow

Sample preparation

NameDetailed informations by clicking * ideaPrinciple * ideaDescriptionRemarksCoupled toInstruments at FGCZ
KingFisher™ Flex Automated sample preparation system. Process up to 96 samples simultaneouslyPrepare samples efficiently from a variety of materials. It offers highly versatile, automated magnetic-particle processing for DNA/RNA, protein or cell purification from virtually any source. Protocol Automated Magnetic Separations for Proteomics NAKingFisher Flex
HTX M5 Sprayer Te HTX M5 Sprayer™ is an easy-to-use, versatile spraying system that provides automated process for Sample Preparation in Mass Spectrometry Imaging. Proprietary technology providing very small matrix droplets ( <5 microns), High fow rate and fast sample prep (2 to 18 minutes per slide), Highly consistent matrix deposition across entire sample area (+/- 3% by weight), Unique use of temperature and nitrogen flow to control evaporation rate and matrix crystal formationNAHTX M5 sprayer
Barocycler NEP2320 Enhanced Pressure Cycling Technology (PCT). Sample Preparation System - Process up to 16 samples simultaneouslyPressure Cycling Technology (PCT) is a unique, patented technology platform based onrepeated cyclesof hydrostaticpressure betweenambient (14.7 psi) andultra-high levels (up to 45,000psi). The PCT platform allows for a high degree of safety, speed, reproducibility, and convenience in modern sample preparation protocols. NABarocycler (PCT)
Covaris LE220 Ultrasonicator for DNA shearing and tissue lysis 1 to 8 tubes at a time parallel processing; 96 tube capacity Accurate, reproducible, and robust sample preparation powered by Adaptive Focused Acoustics® (AFA®) technology.NAGEML - Covaris LE220

Sample fractionation

NameDetailed informations by clicking * ideaPrinciple * ideaDescriptionRemarksCoupled toInstruments at FGCZ
Agilent HPLC offline Analytical-Scale LC Purification System for offline prefractionationAnalytical-scale purification LC system ideal for purification of multi-milligram quantities of materials. Dynamic flow range up to 10 mL/min at maximum 600 bar. Collection of up to 4 x 96 fractions in microtiter plates NALC1100 and LC1200
FAIMS Pro online Post-ionization gas phase fractionation based on differential ion mobility - space separation. It offers separation based on a combination of factors, such as charge state, shape, conformation, and size of gas phase ions. The FAIMS Pro interface reduces chemical noise and matrix interferences, resulting in improved assay robustness and increased sensitivity. It can be particularly beneficial in some proteomics applications.Details FAIMS Pro & FAIMS-MS2 for TMT QuantificationShotgun ProteomicsFAIMS Exploris 480EXPLORIS_1 NA

Commercial softwares for data analysis

NameDetailed Informations *ideaUseNeed help? Contact person at FGCZSoftware access at FGCZ
Proteome discoverer PD commercial software offers a full suite of analysis tools with the flexibility to address multiple research workflows, and an easy-to-use, wizard·driven interface. Supporting multiple database search algorithms (SEQUEST HT, Mascot, Byonic, MS Amanda, and ProSightPD) and multiple dissociation techniques (CID, HCD, ETD, and EThcD) wiki pd @ fgcz-rds-2
Spectronaut Commercial discovery proteomics software for the targeted analysis of DIA measurements from various MS platforms.wiki or Jonas Spectronaut
SpectroDive Commercial Targeted proteomics software for the analysis of PRM and MRM measurements from various MS platforms Jonas SpectroDive
Byonic™ Commercial software with top-down and bottom-up search capabilities. Chia-wei Byonic @ FGCZ-h-076
ScaffoldPTM Visualize and Quantitate Site Localized PTMs from various search engines Jonas ScaffoldPTM
ScaffoldQ+S Visualize and Quantitate iTRAQ/TMT/SILAC from various search engines Jonas ScaffoldQ+S
IntactMass™ Commercial software for mass spectra of intact (undigested) proteins.Serge INTERNAL USE ONLY - IntactMass @ FGCZ-h-078
Progenesis QI for Proteomics Proteomics software for LC-MS dataJonas ProgenesisQI_Proteomics@170 or DISCONTINUED - used only in special cases ProgenesisQI for Proteomics on 166
ProteinPilot™ ProteinPilot™ Software is a paradigm shift in protein identification and relative protein expression analysis for protein research. Combining sophisticated algorithms with an intuitive interface, you can now confidently identify more proteins and search large numbers of post translational modifications, without increasing search time or false positives.Jonas DISCONTINUED - ProteinPilot V4

Created by spfammatter. Last Modification: 2023-10-28 20:09 by paolo.