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fix more chars
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lgatto committed Apr 17, 2024
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26 changes: 13 additions & 13 deletions R/data.R
Original file line number Diff line number Diff line change
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##' can be found in the source article (see `References`).
##'
##' - **Sample isolation**: Cell sorting was done on a Sony MA900 cell sorter
##' using a 130 μm sorting chip. Cells were sorted at single-cell resolution,
##' into a 384-well Eppendorf LoBind PCR plate (Eppendorf AG) containing 1 μL
##' using a 130 microm sorting chip. Cells were sorted at single-cell resolution,
##' into a 384-well Eppendorf LoBind PCR plate (Eppendorf AG) containing 1 microL
##' of lysis buffer.
##' - **Sample preparation**: Single-cell protein lysates were digested with
##' 2 ng of Trypsin (Sigma cat. Nr. T6567) supplied in 1 μL of digestion
##' 2 ng of Trypsin (Sigma cat. Nr. T6567) supplied in 1 microL of digestion
##' buffer (100mM TEAB pH 8.5, 1:5000 (v/v) benzonase (Sigma cat. Nr. E1014)).
##' The digestion was carried out overnight at 37 °C, and subsequently
##' acidified by the addition of 1 μL 1% (v/v) trifluoroacetic acid (TFA).
##' acidified by the addition of 1 microL 1% (v/v) trifluoroacetic acid (TFA).
##' All liquid dispensing was done using an I-DOT One instrument (Dispendix).
##' - **Liquid chromatography**: The Evosep one liquid chromatography system was
##' used for DIA isolation window survey and HRMS1-DIA experiments.The standard
##' 31 min or 58min pre-defined Whisper gradients were used, where peptide
##' elution is carried out with 100 nl/min flow rate. A 15 cm × 75 μm
##' ID column (PepSep) with 1.9 μm C18 beads (Dr. Maisch, Germany) and a 10
##' μm ID silica electrospray emitter (PepSep) was used. Both LC systems were
##' elution is carried out with 100 nl/min flow rate. A 15 cm × 75 microm
##' ID column (PepSep) with 1.9 microm C18 beads (Dr. Maisch, Germany) and a 10
##' microm ID silica electrospray emitter (PepSep) was used. Both LC systems were
##' coupled online to an orbitrap Eclipse TribridMass Spectrometer
##' (ThermoFisher Scientific) via an EasySpray ion source connected to a
##' FAIMSPro device.
##' - **Mass spectrometry**: The mass spectrometer was operated in positive
##' mode with the FAIMSPro interface compensation voltage set to 45 V.
##' mode with the FAIMSPro interface compensation voltage set to -45 V.
##' MS1 scans were carried out at 120,000 resolution with an automatic gain
##' control (AGC) of 300% and maximum injection time set to auto. For the DIA
##' isolation window survey a scan range of 500–900 was used and 400–1000
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##'
##' - **Cell isolation**: Cell sorting was done on a FACS Aria III or
##' Aria II instrument, controlled by the DIVA software package and
##' operated with a 100 μm nozzle. Cells were sorted at single-cell
##' operated with a 100 microm nozzle. Cells were sorted at single-cell
##' resolution, into a 384-well Eppendorf LoBind PCR plate containing
##' 1 μL of lysis buffer.
##' 1 microL of lysis buffer.
##' - **Sample preparation** Single-cell protein lysates were digested
##' overnight at 37°C with 2 ng of Trypsin supplied in 1 μL of
##' digestion buffer. Digestion was stopped by the addition of 1 μL
##' overnight at 37°C with 2 ng of Trypsin supplied in 1 microL of
##' digestion buffer. Digestion was stopped by the addition of 1 microL
##' 1% (v/v) trifluoroacetic acid (TFA). All liquid dispensing was
##' done using an I-DOT One instrument.
##' - **Liquid chromatography**: Chromatographic separation of peptides
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##' well plate using a 25 uL injection loop on 11.8 min gradients.
##' - **Mass spectrometry**: Acquisition was conducted with an Orbitrap
##' Astral mass spectrometer operated in positive mode with the
##' FAIMSPro interface compensation voltage set to 45 V.
##' FAIMSPro interface compensation voltage set to -45 V.
##' MS1 scans were acquired with the Orbitrap at a resolution of
##' 120,000 and a scan range of 400 to 900 m/z with normalized
##' automatic gain control (AGC) target of 300 % and maximum
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10 changes: 5 additions & 5 deletions man/petrosius2023_AstralAML.Rd

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16 changes: 8 additions & 8 deletions man/petrosius2023_mES.Rd

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