Advanced Research Facilities

Make:	Thermo Fisher
Model:	Q Exactive HF
Year of purchase:	2019
Funded by:	JNCASR
Location:	Biocon Building (SBS-C005)
Slot timings:
Contact:	massspecfacility@jncasr.ac.in, 080-2208-2957 suma@jncasr.ac.in, 080-2208-2866
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The mass spectrometer when coupled with analytical techniques for separation such as nano-LC (for proteomics) and UHPLC (for metabolomics, peptides, and proteins) will aid in the accurate and unambiguous detection and characterization of molecules with high resolution.
Advanced quadrupole technology which optimizes precursor ion selection and improves quantitation of low abundant ions in a complex sample mixture.
Resolution power up to 240,000 @ 200m/z.
High mass accuracy <3ppm
Maximum scan speed of 18Hz
m/z range 50-8000
polarity switching one full cycle in <1 sec (one full scan in positive mode and one full scan in negative mode at a resolution setting of 60,000)
Timed SIM (Single Ion Monitoring) for ions of interest
Intact protein mode and Native protein mode
MS full scan with selected ion fragmentation by HCD

Allowed Compounds: Peptides & Proteins (Enzyme digested peptides, intact proteins), Metabolites (Amino acids, nucleotides, sugars, lipids etc), Organic compounds (HPLC purified synthetic small molecules)
Prohibited Compounds: Non-volatile salts (NaCl, phosphate buffers), Strong acids/bases (HCl, NaOH), Inorganic compounds and metal complexes (Metal organic complexes), Polymers (PEG, plastics), Aggregation-prone proteins or samples likely to precipitate (Amyloid forming proteins), Surfactants (SDS, Triton-X-100)
Before preparing the samples: Contact us to discuss your sample preparation protocol and sample background, preferably with a reference publication. This helps ensure protection of instrument.
Plasticware and Consumables: 1. Use Axygen low-binding tubes and tips for all experimental steps, starting from sample generation. 2, · Avoid plasticware that may leach polymers (PEG, PPG, plasticizers), which contaminate the MS source and transfer optics.
Reagents and Solvents
· Use only LC-MS grade solvents and reagents.
· Ensure water is LC-MS grade (not Milli-Q).
· Strictly avoid TFA (trifluoroacetic acid) and TCA (trichloroacetic acid).
· If acidification is required, use Formic acid (e.g., 0.1% FA)
· Do not use non-volatile salts or buffers during sample preparation.
Avoid:
o All non-volatile salts
o Phosphate buffers
o Tris buffers
o HEPES
o Detergents (SDS, Triton, NP-40)
o Glycerol, DMSO, DMF
o PEG-containing reagents
o Aggregation-prone proteins (e.g., amyloids) or samples likely to precipitate
All samples must be:
· completely free of the above molecules
· Filtered (0.2 µm) or centrifuged
Sample submission Checklist
· Label all samples clearly and properly.
· Accurately mention the sample amount in each vial:
o Concentration for solubilized samples
o Quantity for lyophilized samples
· Provide complete and clear details for each sample in the ARF portal.
· For proteomics samples, include details of the enzyme used, source organism, relevant FASTA files, and any expected modifications if raw data analysis is required.

Sl. No. - Category	Fees ( in Rs/- ) + additional 18% GST
01. Other Academia for UHPLC-MS per 1 hour per sample	Rs. 600
06. Industry and others for UHPLC-MS per 1 hour per sample	Rs. 1200
04. Other Academia for Proteome Data analysis, per analysis	Rs. 2000
05. Other Academia for Proteome Repeat analysis, , per analysis	Rs. 1000
09. Industry and others for Proteome Data analysis, per analysis	Rs. 4000
10. Industry and others for Proteome Repeat analysis, , per analysis	Rs. 2000
03. Other Academia for Nano-LC-MS (Proteomics raw data only) per sample for 1 day	Rs. 4000
02. Other Academia for UHPLC-MS (Metabolomics raw data only), per sample for 3 hours	Rs. 2500
08. Industry and others for Nano-LC-MS (Proteomics raw data only) per sample for 1 day	Rs. 8000
07. Industry and others for UHPLC-MS (Metabolomics raw data only), per sample for 3 hours	Rs. 5000

Q Exactive HF Mass Spectrometer