diff --git a/R/data.R b/R/data.R index 8e56d4f..0d84857 100644 --- a/R/data.R +++ b/R/data.R @@ -2626,26 +2626,26 @@ ##' 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 @@ -2743,12 +2743,12 @@ ##' ##' - **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 @@ -2758,7 +2758,7 @@ ##' 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 diff --git a/man/petrosius2023_AstralAML.Rd b/man/petrosius2023_AstralAML.Rd index b3ccfd7..19b3d85 100644 --- a/man/petrosius2023_AstralAML.Rd +++ b/man/petrosius2023_AstralAML.Rd @@ -47,12 +47,12 @@ can be found in the source article (see \emph{References}). \itemize{ \item \strong{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. \item \strong{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. \item \strong{Liquid chromatography}: Chromatographic separation of peptides @@ -62,7 +62,7 @@ valves were configured to perform direct injections from a 384 well plate using a 25 uL injection loop on 11.8 min gradients. \item \strong{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 diff --git a/man/petrosius2023_mES.Rd b/man/petrosius2023_mES.Rd index 3bc5586..5150c53 100644 --- a/man/petrosius2023_mES.Rd +++ b/man/petrosius2023_mES.Rd @@ -46,26 +46,26 @@ The data were acquired using the following setup. More information can be found in the source article (see \code{References}). \itemize{ \item \strong{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. \item \strong{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). \item \strong{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. \item \strong{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