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Smith"],"technology_type":["Mass Spectrometry","Top-down proteomics","Data-independent acquisition"],"software":[""],"submitter_keywords":["Host cell proteins","Mab based therapeutics","Mass spectrometry","Orbitrap astral ms"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD067004"],"sample_protocol":["To illustrate the capabilities of the Orbitrap Astral MS, NISTmAb was prepared for native digestion, using NISTmAb reference material standard RM8671. Duplicate digestions were performed and for each digest 1 mg (100 μL of 10 mg/mL mAb) was supplemented with 90 μL of ultra-purified water and 5 μL of 1 M Tris-HCl, pH 8. Tryptic digestion was performed overnight at 37 °C using a 1:400 trypsin/protein ratio. After digestion, 1.5 μL of 303 mM DTT were added with subsequent incubation for 10 min at 90 °C to perform disulfide bond reduction. Centrifugation at 13,000 × g for 2 min was performed to pellet the reduced mAb and the supernatant was transferred to a fresh tube where it was acidified with 0.5 μL of FA. Samples were subsequently dried down using a speed-vac until ready for analysis. Prior to LC-MS analysis, samples were reconstituted in 2% acetonitrile and 0.1% FA to obtain a final concentration of 1 μg/μL. SP3 digest of NISTmAb was performed to evaluate differences between native digestion and the SP3 digestion utilised for the analysis of the protein biotherapeutics in this study. SP3 digestion was performed in duplicate following the procedure described below for the other mAb products analysed.   For each protein biotherapeutic, a volume corresponding to 50 µg of protein biotherapeutic was brought to a final volume of 95 µL with 50 mM ammonium bicarbonate before reduction (incubating at 56 °C while shaking at 700 rpm for 20 min) and alkylation (incubating at RT in the dark without shaking for 15 min) with 0.2 M dithiothreitol (DTT; 2.5 µL) and 0.4 M iodoacetamide (2.5 µL), respectively. Samples were bound to a 1:1 mixture of hydrophilic (5 µL) and hydrophobic (5 µL) Sera-Mag SpeedBeads Carboxyl Magnetic Beads and washed with 80% ethanol using a KingFisher Duo Prime purification system under the control of Thermo Scientific BindIt software, version 4.0. Samples still bound to the beads were then transferred to clean low-bind 1.5 mL tubes where 1 µg of trypsin was added to each sample, for a 1:50 trypsin to protein biotherapeutic ratio. Samples then underwent 4-hour tryptic digestion at 37 °C using a Thermomixer shaking at 700 rpm. After 4 hours the samples were removed from the Thermomixer. Trifluoroacetic acid was added to each sample at a final concentration of 0.1% and samples rested at RT for 5 min to quench the tryptic digestion. Samples were subsequently centrifuged for 5 min at 14,000 rpm to pellet any residual magnetic beads and then were transferred to clean low-bind 1.5 mL tubes. Finally, samples were dried down in a speed vac and stored at -20 °C until ready for LC-MS analysis. For each sample, triplicate digestions were performed.  Prior to LC-MS analysis, each digested sample was reconstituted in 50 µL of 0.1% formic acid (FA) in water for a concentration of 1 µg/µL of digested protein biotherapeutic. 5 µg of sample was transferred to a 0.2 mL SureSTART screw vial where 500 fmol of Hi3 E. coli peptide standard, previously reconstituted in 0.1% FA in water, were added. The sample in the vial was then brought to a final volume of 50 µL using 0.1% FA in water, resulting in protein biotherapeutic and Hi3 E. coli peptide concentrations of 100 ng/µL and 10 fmol/uL respectively.  All analyses were performed using a Thermo Scientific Vanquish Neo UHPLC system, operated in Trap & Elute mode, coupled to an Orbitrap Astral MS with a Thermo Scientific Easy-spray source, operated in data-independent acquisition (DIA) mode. Two 500 ng (5 µL) injections of protein biotherapeutic were performed for each digest, totalling 6 injections per protein biotherapeutic product. Separations were performed on an EASY-Spray PepMap RSLC C18 column (2 µm, 100 Å, 150 µm x 15 cm) heated to 50°C using a 60 SPD method (21 min gradient, 24 min total) at a flow rate of 800 nL/min. Mobile phase A was 0.1% FA in water and mobile phase B was 0.1% FA in 80% acetonitrile.    DIA-MS analysis was performed in positive ion mode using a spray voltage of 1,900 V, an ion transfer tube temperature set to 290°C, and an expected peak width of 10 s. Peptide application mode with standard pressure mode settings were used. MS1 scans were acquired in the Orbitrap at a resolution setting of 240,000 (at m/z 200) every 0.6 s between a scan range of 380 - 980 m/z. The maximum injection time was 5 ms and the number of microscans was 1. The normalized AGC target and RF lens settings were 500% and 40% respectively. MS/MS (MS2) spectra were acquired in the Astral analyser across a scan range of 150 – 2,000 m/z, where the precursor mass range was set the same as the MS1 scan range. The isolation window and maximum injection time used were m/z 4.9 and 10 ms respectively. The normalized HCD collision energy was set to 25%. The number of microscans, normalized AGC target, and RF lens settings were the same as those used for MS1 scans."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Raw DIA data were processed with Thermo Scientific Proteome Discoverer software version 3.1 (PD 3.1), utilising the CHIMERYS intelligent search algorithm and INFERYS 3.0.0 fragment intensity prediction model. Search criteria allowed a maximum of two missed cleavages, a peptide length of 7 - 30 residues, a peptide charge state range of 1-4, and a fragment ion mass tolerance of 10 ppm. Carbamidomethylation of cysteines was applied as a static modification while oxidation of methionine set as a variable modification. The FDR for PSMs during processing was 1% while peptides and proteins were validated using a confidence threshold target FDR of 1% as well. For each protein biotherapeutic, the data files generated during the analysis of the digests were processed together using the “One Job for All Files” processing mode. The search databases comprised of the respective protein biotherapeutic sequences, the Cricetulus griseus (CHO) Uniprot reference proteome database (Downloaded August 22, 2024), and the sequence of the Hi3 E. coli standard (provided by Waters). Additionally, the common Repository of Adventitious Proteins (cRAP) and MaxQuant contaminant databases were searched and utilised to identify and filter out potential protein-based contaminants introduced during sample preparation."],"omics_type":["Proteomics"],"labhead":["Dr. Jonathan Bones"],"instrument_platform":[""],"labhead_affiliation":["National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland, A94 X099  School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland, D04 V1W8."],"submission_type":["COMPLETE"],"species":["Cricetulus Griseus (chinese Hamster) (cricetulus Barabensis Griseus)","Mus Musculus (mouse)"],"submitter_mail":["josh.smith@nibrt.ie"],"publication":["10.1021/JASMS.5C00272"],"submitter_affiliation":["NIBRT"],"submitter_country":["Ireland"],"doi":["10.6019/PXD067004"],"additional_accession":[]},"is_claimable":false,"name":"Quantitative Host Cell Protein Analysis across Innovator Monoclonal Antibody-Based Protein Therapeutics using the Orbitrap Astral Mass Spectrometer","description":"Protein biotherapeutics such as monoclonal antibodies (mAbs) are generally produced using cell-based production systems that generate endogenous proteins, commonly referred to as host cell proteins (HCPs), along with the desired drug products. A critical challenge is the removal of HCPs from the final drug product as they can be detrimental to product efficacy and patient safety, even at low levels. HCP clearance is monitored during process optimisation and assessed before product release. Tandem liquid chromatography-mass spectrometry (LC-MS/MS) is increasingly utilized as an orthogonal method to enzyme-linked immunosorbent assays (ELISA) for HCP monitoring during downstream processing due to its untargeted nature and ability to determine total HCP concentrations. The dynamic range of the recombinant proteins makes detection of low-level HCPs difficult. However, the recently developed Orbitrap Astral MS has the potential to overcome such challenges, having previously demonstrated significant improvements in protein identifications in complex sample matrices while simultaneously reducing analysis times. Here we utilise the Orbitrap Astral MS to perform HCP analysis on a cohort of 37 protein biotherapeutics. Its speed and sensitivity enable the use of a short 60 samples-per-day (SPD; 24-minute injection to injection) separation method, dramatically reducing analysis time compared to standard LC-MS methods without sacrificing HCP identifications 544 HCPs were detected across the cohort and 63.60% of those found to be quantifiable in at least one product using Hi3 quantitation. Over 80% of quantifiable HCPs were detected at concentrations below 10 ppm, including approximately 9% below concentrations of 1 ppm. These included HCPs considered as “high-risk” by the Biophorum Development Group. Excluding an outlier, on average 20 HCPs were identified per product. Overall, this study shows how the Orbitrap Astral MS can improve detection of low-level HCPs while significantly reducing analysis times, allowing for a rapid and more informed understanding of a products HCP 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