Proteomics > Our instruments

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Instrument Reservation

Instrument reservations can only be made by employees. If you would like to make a reservation of an instrument, please check the availability of the corresponding instrument on the FGCZ Instrument Reservation System (IRS). If you find a slot which suits your plans, please contact your project coach or the person responsible for the corresponding instrument.

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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)

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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)

MS Instruments

Name	Detailed informations by clicking on the instrument *	Schema *	Mass analyzer	Fragmentation	Max resolution @ m/z 200 & Max scan rate	Operation Modes*	Instruments at FGCZ - Service/user lab access
QExactive			Hybrid quadrupole, Orbitrap	HCD	140,000 & 12 Hz @ 17,500 resolution	DDA, Full MS, SIM, DIA, PRM	Service QEXACTIVE_1 and User QEXACTIVE_2
QExactive HF			Hybrid quadrupole, Orbitrap	HCD	240,000 & 18 Hz @ 15,000 resolution	DDA, Full MS, SIM, PRM, DIA, AIF, In-source fragmentation, Positive/negative ion switching, timed SIM	User QEXACTIVEHF_2
Fusion			Tribrid™ combines quadrupole, Orbitrap, and linear ion trap	CID/HCD/ETD detected by the Ion Trap or Orbitrap at any level of MSn	450,000 &18 Hz @ 15,000 resolution	DDA, Full MS, SIM, PRM, DIA, AIF, In-source fragmentation, Positive/negative ion switching, timed SIM, SPS-MS3, FAIMS	User FUSION_2
Fusion Lumos			Tribrid™ combines quadrupole, Orbitrap, and linear ion trap	CID/HCD/ETD detected by the Ion Trap or Orbitrap at any level of MSn	450,000 &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 Quant	User LUMOS_1 and Service LUMOS_2
Exploris 480			Hybrid quadrupole, Orbitrap	HCD	480,000 & 40 Hz @ 7,500 resolution	DDA, Full MS, SIM, PRM, DIA, AIF, In-source fragmentation, Positive/negative ion switching, timed SIM, APD, FAIMS, Sure Quant	User EXPLORIS_1
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), diaPASEF	User TIMSTOF_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 HDMS			Q-TOF, T-Wave IMS	CID	Up to 60,000	DDA, Full MS, DIA	Service G2HD_2
Q-​TOF SYNAPT G2-​Si			Waters Synapt G2-SI 8k with ETD	CID and ETD	Up to 60,000	DDA, Full MS, DIA	Service 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

Name	Detailed informations by clicking on the instrument *	Schema *	Description	Operation 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 Plus	Service QDA_1
ACQUITY FLR Detector			Fluorescence (FLR) Detector	The 2475 FLR Detector helps achieve high-sensitivity, low-dispersion methods with unsurpassed accuracy, maximum uptime, and complete confidence in the analysis. Integrated in Acquity	Service Characterization_Nlinked_glycans

Other MS sources

Name	Detailed informations by clicking on the instrument *	Description	Operation Modes*	Instruments at FGCZ - Service/user lab access
NanoMate Source		Nanoelectrospray ionization technology. Chip-based electrospray ionization technology from Advion. It combines the benefits of liquid chromatography, mass spectrometry, chip-based infusion, fraction collection, and direct surface analysis into one integrated ion source platform.	Can be used with FUSION_2	NanoMate

Other equipment for MS workflow

Sample preparation

Name	Detailed informations by clicking *	Principle *	Description	Remarks	Coupled to	Instruments at FGCZ
Barocycler NEP2320 Enhanced			Pressure Cycling Technology (PCT). Sample Preparation System - Process up to 16 samples simultaneously	Pressure 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.	NA	Barocycler (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.	NA	GEML - Covaris LE220
KingFisher™ Flex			Automated sample preparation system Process up to 96 samples simultaneously	Prepare samples efficiently from a variety of materials with the Thermo Scientific™ KingFisher™ Flex Purification System, which offers highly versatile, automated magnetic-particle processing for DNA/RNA, protein or cell purification from virtually any source. Using revolutionary magnetic particle separation technology, this system provides excellent reproduciblity and quality. Protocol Automated Magnetic Separations for Proteomics	NA	KingFisher 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 formation	NA	HTX M5 sprayer

Sample fractionation

Name	Detailed informations by clicking *	Principle *	Description	Remarks	Coupled to	Instruments at FGCZ
Agilent HPLC offline			Analytical-Scale LC Purification System for offline prefractionation	Analytical-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 allows versatile application within a wide range of analytical-scale purification workflows. Collection of up to 4 x 96 fractions in microtiter plates, or up to 216 fractions in glass tubes with 4 outer diameters of tubes available collector	NA	LC1100 and LC1200
FAIMS Pro online			Post-ionization gasphase fractionation based on differential ion mobility - space seperation	The FAIMS Pro interface reduces chemical noise and matrix interferences, resulting in improved assay robustness and increased sensitivity. The FAIMS Pro interface offers separation based on a combination of factors, such as charge state, shape, conformation, and size of gas phase ions. It also improves dynamic range and peak capacity, which are particularly beneficial in some proteomics applications. Details FAIMS Pro & FAIMS-MS2 for TMT QuantificationShotgun ProteomicsFAIMS Exploris 480	EXPLORIS_1	NA

High-throughput chromatography

Name	Detailed informations by clicking *	Principle *	Description	Remarks	Coupled to	Instruments at FGCZ
EVOSEP ONE			High-throughput nanoUPLC system	Evosep makes clinical proteomics 100 times more robust and 10 times faster. Short gradients (i.e. 300 samples/day with 4.8 min) for throughput. Samples are loaded on evotips and eluted directly from tips. Robust solutions for clinical and large-scale proteomics. Application	TIMSTOF_1 and QEXACTIVE_2	EVOSEP_1

Commercial softwares for data analysis

Name	Detailed Informations *	Use	Need help? Contact person at FGCZ	Software access at FGCZ
Progenesis QI for Proteomics		Proteomics software for LC-MS data	Jonas	ProgenesisQI_Proteomics@170 or 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. ProteinPilot Software is compatible with all proteomics MS/MS systems via the.*mgf format.	Jonas	ProteinPilot V4
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
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
Byonic™		Commercial software with top-down and bottom-up search capabilities.	Chia-wei	Byonic @ FGCZ-h-076
IntactMass™		Commercial software for mass spectra of intact (undigested) proteins.	Serge	IntactMass @ FGCZ-h-078

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