--- title: "make-data" author: - name: Christian Panse affiliation: Functional Genomics Center Zurich email: cp@fgcz.ethz.ch - name: Tobias Kockmann affiliation: Functional Genomics Center Zurich email: tobias.Kockmann@fgcz.ethz.ch package: tartare output: BiocStyle::html_document abstract: | The tartare package provides raw files recorded on different Liquid Chromatography Mass Spectrometry (LC-MS) instruments. All included MS instruments are manufactured by Thermo Fisher Scientific and belong to the Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their common origin and shared hardware components (e.g. Orbitrap mass analyser), the above instruments tend to write data in different "dialects" in a shared binary file format (.raw). The intention behind tartare is to provide complex but slim real-world files that can be used to make code robust with respect to this diversity. In other words, it is intended for enhanced unit testing. The package is considered to be used with the "*[rawDiag](https://github.com/fgcz/rawDiag)*" package [@Trachsel2018] and the "*[Spectra](https://github.com/rformassspectrometry/Spectra)*" MsBackends. vignette: > %\VignetteIndexEntry{make and use tartare data} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} bibliography: - tartare.bib --- ```{r initial, echo=FALSE, warning=FALSE, message=FALSE} library(BiocStyle) ``` # Sample description Pierce HeLa protein digest standard (#1862824, Thermo Scientific) in 3% ACN, 0.1% FA # Data recording ## Q Exactive HF-X file name: `20190710_003_PierceHeLaProteinDigestStd.raw` ### LC 200 ng sample were seperated on a linear gradient from 5 to 35% B in 20 min using a binary mobile phase composed of A) 0.1% FA in water, B) 0.1% FA in ACN. The stationary phase was ... ### MS The MS acquision was started 18 min post sample injection and lastet only 4 min. Be aware that spray voltage and source gas was turned on at 18.5 min (see Tunefiles section of the method). This means the first 30 s were recorded without ESI. In summary, 4 different experiments were recorded * Full MS / dd-MS² (TopN) * PRM * Targeted-SIM * DIA Experiment 2 and 3 were executed in parrallel! All method details are listed below. ```{txt} Method of Q Exactive HF-X Overall method settings Global Settings Use lock masses best Lock mass injection ― Chrom. peak width (FWHM) 15 s Time Method duration 4.00 min Customized Tolerances (+/-) Lock Masses ― Inclusion ― Exclusion ― Neutral Loss ― Mass Tags ― Dynamic Exclusion ― Experiments Full MS / dd-MS² (TopN) General Runtime 0 to 1 min Polarity positive In-source CID 0.0 eV Default charge state 2 Inclusion ― Exclusion ― Tags ― Full MS Microscans 1 Resolution 120,000 AGC target 3e6 Maximum IT 100 ms Number of scan ranges 1 Scan range 200 to 2000 m/z Spectrum data type Centroid dd-MS² / dd-SIM Microscans 1 Resolution 30,000 AGC target 1e5 Maximum IT 50 ms Loop count 5 MSX count 1 TopN 5 Isolation window 1.4 m/z Isolation offset 0.0 m/z Scan range 200 to 2000 m/z Fixed first mass ― (N)CE / stepped (N)CE nce: 30 Spectrum data type Centroid dd Settings Minimum AGC target 8.00e3 Intensity threshold 1.6e5 Apex trigger ― Charge exclusion unassigned, 1, 5 - 8, >8 Multiple charge states all Peptide match preferred Exclude isotopes on Dynamic exclusion 10.0 s If idle .. do not pick others PRM General Runtime 1 to 2 min Polarity positive In-source CID 0.0 eV Dynamic RT off Default charge state 2 Inclusion on MS² Microscans 1 Resolution 30,000 AGC target 2e5 Maximum IT 100 ms Loop count 11 MSX count 1 MSX isochronous ITs on Isolation window 4.0 m/z Isolation offset 0.0 m/z Fixed first mass ― (N)CE / stepped (N)CE nce: 35 Spectrum data type Centroid Full MS — SIM General Runtime 1 to 2 min Polarity positive In-source CID 0.0 eV Full MS — SIM Microscans 1 Resolution 120,000 AGC target 3e6 Maximum IT 200 ms Number of scan ranges 2 Scan range 1 150 to 1000 m/z Scan range 2 1000 to 2000 m/z Spectrum data type Centroid Targeted-SIM General Runtime 2 to 3 min Polarity positive In-source CID 0.0 eV Inclusion on SIM Microscans 1 Resolution 240,000 AGC target 5e4 Maximum IT 200 ms MSX count 5 Isolation window 4.0 m/z Isolation offset 0.0 m/z Scan range 150 to 2000 m/z Spectrum data type Centroid DIA General Runtime 3 to 4 min Polarity positive In-source CID 0.0 eV Default charge state 2 DIA Microscans 1 Resolution 30,000 AGC target 1e6 Maximum IT auto Loop count 11 MSX count 1 MSX isochronous ITs on Isolation window 20.0 m/z Isolation offset 0.0 m/z Fixed first mass 100.0 m/z (N)CE / stepped (N)CE nce: 30 Spectrum data type Centroid Setup Tunefiles General Switch Count 2 Base Tunefile C:\Xcalibur\methods\nogas_novoltage_nano.mstune Element 1 At 0.50 min New Tunefile C:\Xcalibur\methods\default_nano.mstune Element 2 At 34.50 min New Tunefile C:\Xcalibur\methods\nogas_novoltage_nano.mstune Contact Closure General Used True Start in Closed False Switch Count 2 Element 1 At 0.50 min Switches to Open Element 2 At 34.50 min Switches to Closed Syringe General Used False Start in OFF True Stop at end of run False Switch Count 0 Pump setup Syringe type Hamilton Flow rate 3.000 µL/min Inner diameter 2.303 mm Volume 250 µL Divert Valve A General Used False Start in 1-2 True Switch Count 0 Divert Valve B General Used False Start in 1-2 True Switch Count 0 Lock Masses 2 entries Mass Polarity Start End Comment [m/z] [min] [min] 371.10124 Positive 445.12002 Positive Inclusion List 16 entries Mass Formula Species CS Polarity Start End (N)CE MSX ID Comment [m/z] [M] [z] [min] [min] 487.25671 2 Positive 1.00 3.00 28 LGGNEQVTR (light) 644.82261 2 Positive 1.00 3.00 28 GAGSSEPVTGLDAK (light) 683.82789 2 Positive 1.00 3.00 28 VEATFGVDESNAK (light) 547.29804 2 Positive 1.00 3.00 28 YILAGVENSK (light) 669.83806 2 Positive 1.00 3.00 28 TPVISGGPYEYR (light) 683.85371 2 Positive 1.00 3.00 28 TPVITGAPYEYR (light) 699.33842 2 Positive 1.00 3.00 28 DGLDAASYYAPVR (light) 726.83571 2 Positive 1.00 3.00 28 ADVTPADFSEWSK (light) 622.85351 2 Positive 1.00 3.00 28 GTFIIDPGGVIR (light) 636.86916 2 Positive 1.00 3.00 28 GTFIIDPAAVIR (light) 776.92975 2 Positive 1.00 3.00 28 LFLQFGAQGSPFLK (light) 410.00000 2 Positive 3.00 4.00 28 window1 430.00000 2 Positive 3.00 4.00 28 window2 450.00000 2 Positive 3.00 4.00 28 window3 470.00000 2 Positive 3.00 4.00 28 window4 490.00000 2 Positive 3.00 4.00 28 window5 Exclusion List (no entries) Neutral Losses (no entries) Mass Tags (no entries) ``` ## Fusion Lumos file name: `20190716_004_PierceHeLa.raw` ### LC 200 ng sample were seperated on a linear gradient from 5 to 35% B in 20 min using a binary mobile phase composed of A) 0.1% FA in water, B) 0.1% FA in ACN. The stationary phase was ... ### MS The MS acquision was started directly after sample injection and lastet for 35 min. In summary, 5 different experiments were recorded: * Exp. 1 Orbitrap HCD - High Load (greater than 500 ng) * Exp. 2 ETD Data-Dependent Decision Tree * Exp. 3 Glycopeptide - Enriched * Exp. 4 TMT Quan Pierce TKO Standard QC MS3 SPS * Exp. 5 MS Exp. #5 (MS) was executed the entire method duration! Method details are listed below. ```{txt} Method Summary Method Settings Application Mode: Peptide Method Duration (min): 35 Global Parameters Ion Source Use Ion Source Settings from Tune: True FAIMS Mode: Not Installed MS Global Settings Advanced Peak Determination: False Default Charge State: 1 Internal Mass Calibration: Off Experiment#1 [Orbitrap HCD - High Load (greater than 500 ng)] Start Time (min): 20 End Time (min): 21 Cycle Time (sec): 3 Master Scan: MS OT Detector Type: Orbitrap Orbitrap Resolution: 60000 Mass Range: Normal Use Quadrupole Isolation: True Scan Range (m/z): 375-1500 RF Lens (%): 30 AGC Target: 4.0e5 Maximum Injection Time (ms): 50 Microscans: 1 Data Type: Centroid Polarity: Positive Source Fragmentation: Disabled Scan Description: Filters: MIPS Monoisotopic Peak Determination: Peptide Charge State Include charge state(s): 2-7 Include undetermined charge states: False Include charge states 25 and higher: False Dynamic Exclusion Exclude after n times: 1 Exclusion duration (s): 60 Mass Tolerance: ppm Low: 10 High: 10 Exclude Isotopes: True Perform dependent scan on single charge state per precursor only: False Intensity Filter Type: Intensity Threshold Intensity Threshold: 5.0e4 Data Dependent Data Dependent Mode: Cycle Time Time between Master Scans (sec): 3 Scan Event Type 1: Scan: ddMS² OT HCD Isolation Mode: Quadrupole Isolation Window (m/z): 1.6 Isolation Offset: Off Activation Type: HCD Collision Energy Mode: Fixed HCD Collision Energy (%): 30 Detector Type: Orbitrap Scan Range Mode: Auto: m/z Normal Orbitrap Resolution: 15000 First Mass (m/z): 110 AGC Target: 5.0e4 Inject Ions for All Available Parallelizable Time: False Maximum Injection Time (ms): 30 Microscans: 1 Data Type: Centroid Use EASY-IC™: False Scan Description: Experiment#2 [ETD Data-Dependent Decision Tree] Start Time (min): 21 End Time (min): 22 Cycle Time (sec): 3 Master Scan: MS OT Detector Type: Orbitrap Orbitrap Resolution: 120000 Mass Range: Normal Use Quadrupole Isolation: True Scan Range (m/z): 350-1500 RF Lens (%): 30 AGC Target: 4.0e5 Maximum Injection Time (ms): 50 Microscans: 1 Data Type: Centroid Polarity: Positive Source Fragmentation: Disabled Scan Description: Filters: MIPS Monoisotopic Peak Determination: Peptide Dynamic Exclusion Exclude after n times: 1 Exclusion duration (s): 60 Mass Tolerance: ppm Low: 10 High: 10 Exclude Isotopes: True Perform dependent scan on single charge state per precursor only: False Exclude Within Cycle: False Intensity Filter Type: Intensity Threshold Intensity Threshold: 1.0e4 Data Dependent Data Dependent Mode: Cycle Time Time between Master Scans (sec): 3 Scan Event Type 1: Charge State Include charge state(s): 3 Include undetermined charge states: False Include charge states 25 and higher: False Precursor Selection Range Mass Range (m/z): 350-650 OR Charge State Include charge state(s): 4 Include undetermined charge states: False Include charge states 25 and higher: False Precursor Selection Range Mass Range (m/z): 350-900 OR Charge State Include charge state(s): 5 Include undetermined charge states: False Include charge states 25 and higher: False Precursor Selection Range Mass Range (m/z): 350-950 OR Charge State Include charge state(s): 6-8 Include undetermined charge states: False Include charge states 25 and higher: False Sort by Charge Precursor Priority: Highest Charge State Sort by m/z Precursor Priority: Lowest m/z Scan: ddMS² IT ETD Scan Priority: 1 Isolation Mode: Quadrupole Isolation Window (m/z): 2 Isolation Offset: Off Activation Type: ETD Use Calibrated Charge-Dependent ETD Parameters: True ETD Supplemental Activation: False Detector Type: Ion Trap Scan Range Mode: Auto: m/z Normal Ion Trap Scan Rate: Rapid First Mass (m/z): 120 AGC Target: 1.0e4 Inject Ions for All Available Parallelizable Time: True Maximum Injection Time (ms): 100 Microscans: 1 Data Type: Centroid Scan Description: Scan Event Type 2: Charge State Include charge state(s): 2 Include undetermined charge states: False Include charge states 25 and higher: False OR Charge State Include charge state(s): 3 Include undetermined charge states: False Include charge states 25 and higher: False Precursor Selection Range Mass Range (m/z): 650-1200 OR Charge State Include charge state(s): 4 Include undetermined charge states: False Include charge states 25 and higher: False Precursor Selection Range Mass Range (m/z): 900-1200 OR Charge State Include charge state(s): 5 Include undetermined charge states: False Include charge states 25 and higher: False Precursor Selection Range Mass Range (m/z): 950-1200 Scan: ddMS² IT CID Scan Priority: 1 Isolation Mode: Quadrupole Isolation Window (m/z): 2 Isolation Offset: Off Activation Type: CID Collision Energy Mode: Fixed CID Collision Energy (%): 30 CID Activation Time (ms): 10 Activation Q: 0.25 Multistage Activation: False Detector Type: Ion Trap Scan Range Mode: Auto: m/z Normal Ion Trap Scan Rate: Rapid AGC Target: 1.0e4 Inject Ions for All Available Parallelizable Time: True Maximum Injection Time (ms): 35 Microscans: 1 Data Type: Centroid Scan Description: Experiment#3 [Glycopeptide - Enriched] Start Time (min): 22 End Time (min): 23 Cycle Time (sec): 3 Master Scan: MS OT Detector Type: Orbitrap Orbitrap Resolution: 120000 Mass Range: Normal Use Quadrupole Isolation: True Scan Range (m/z): 350-1800 RF Lens (%): 30 AGC Target: 4.0e5 Maximum Injection Time (ms): 50 Microscans: 1 Data Type: Centroid Polarity: Positive Source Fragmentation: Disabled Scan Description: Filters: MIPS Monoisotopic Peak Determination: Peptide Charge State Include charge state(s): 2-8 Include undetermined charge states: False Include charge states 25 and higher: False Dynamic Exclusion Exclude after n times: 1 Exclusion duration (s): 60 Mass Tolerance: ppm Low: 10 High: 10 Exclude Isotopes: True Perform dependent scan on single charge state per precursor only: False Intensity Filter Type: Intensity Threshold Intensity Threshold: 5.0e4 Data Dependent Data Dependent Mode: Cycle Time Time between Master Scans (sec): 3 Scan Event Type 1: Sort by Charge Precursor Priority: Highest Charge State Sort by m/z Precursor Priority: Lowest m/z Scan: ddMS² OT EThcD Isolation Mode: Quadrupole Isolation Window (m/z): 3 Isolation Offset: Off Activation Type: ETD Use Calibrated Charge-Dependent ETD Parameters: True ETD Supplemental Activation: True SA Collision Energy Type: EThcD SA Collision Energy (%): 15 Detector Type: Orbitrap Scan Range Mode: Auto: m/z Normal Orbitrap Resolution: 60000 First Mass (m/z): 120 AGC Target: 5.0e4 Inject Ions for All Available Parallelizable Time: False Maximum Injection Time (ms): 118 Microscans: 1 Data Type: Centroid Use EASY-IC™: False Scan Description: Experiment#4 [TMT Quan Pierce TKO Standard QC MS3 SPS] Start Time (min): 23 End Time (min): 24 Cycle Time (sec): 2 Master Scan: MS OT Detector Type: Orbitrap Orbitrap Resolution: 120000 Mass Range: Normal Use Quadrupole Isolation: False Scan Range (m/z): 375-1500 RF Lens (%): 30 AGC Target: 4.0e5 Maximum Injection Time (ms): 50 Microscans: 1 Data Type: Centroid Polarity: Positive Source Fragmentation: Disabled Scan Description: Filters: MIPS Monoisotopic Peak Determination: Peptide Charge State Include charge state(s): 2-6 Include undetermined charge states: False Include charge states 25 and higher: False Dynamic Exclusion Exclude after n times: 1 Exclusion duration (s): 60 Mass Tolerance: ppm Low: 10 High: 10 Exclude Isotopes: True Perform dependent scan on single charge state per precursor only: True Exclude Within Cycle: True Intensity Filter Type: Intensity Threshold Intensity Threshold: 5.0e3 Data Dependent Data Dependent Mode: Cycle Time Time between Master Scans (sec): 2 Scan Event Type 1: Charge State Include charge state(s): 2 Include undetermined charge states: False Include charge states 25 and higher: False Scan: ddMS² IT CID Scan Priority: 1 Isolation Mode: Quadrupole Isolation Window (m/z): 1.2 Isolation Offset: Off Activation Type: CID Collision Energy Mode: Fixed CID Collision Energy (%): 35 CID Activation Time (ms): 10 Activation Q: 0.25 Multistage Activation: False Detector Type: Ion Trap Scan Range Mode: Auto: m/z Normal Ion Trap Scan Rate: Turbo AGC Target: 1.0e4 Inject Ions for All Available Parallelizable Time: False Maximum Injection Time (ms): 50 Microscans: 1 Data Type: Centroid Scan Description: Filters: Precursor Selection Range Selection Range Mode: Mass Range Mass Range (m/z): 400-1200 Isobaric Tag Loss Exclusion Reagent: TMT Precursor Ion Exclusion Exclusion mass width: m/z Low: 50 High: 5 Data Dependent Data Dependent Mode: Scans Per Outcome Scan Event Type 1: Scan: ddMS³ OT HCD MSⁿ Level: 3 Synchronous Precursor Selection: True Number of SPS Precursors: 5 MS Isolation Window (m/z): 1.3 MS2 Isolation Window (m/z): 2 Isolation Offset: Off Activation Type: HCD HCD Collision Energy (%): 65 Detector Type: Orbitrap Scan Range Mode: Define m/z range Orbitrap Resolution: 50000 Scan Range (m/z): 100-500 AGC Target: 1.0e5 Inject Ions for All Available Parallelizable Time: False Maximum Injection Time (ms): 105 Microscans: 1 Data Type: Centroid Use EASY-IC™: False Scan Description: Number of Dependent Scans: 5 Scan Event Type 2: Charge State Include charge state(s): 3 Include undetermined charge states: False Include charge states 25 and higher: False Scan: ddMS² IT CID Scan Priority: 1 Isolation Mode: Quadrupole Isolation Window (m/z): 0.7 Isolation Offset: Off Activation Type: CID Collision Energy Mode: Fixed CID Collision Energy (%): 35 CID Activation Time (ms): 10 Activation Q: 0.25 Multistage Activation: False Detector Type: Ion Trap Scan Range Mode: Auto: m/z Normal Ion Trap Scan Rate: Turbo AGC Target: 1.0e4 Inject Ions for All Available Parallelizable Time: False Maximum Injection Time (ms): 50 Microscans: 1 Data Type: Centroid Scan Description: Filters: Precursor Selection Range Selection Range Mode: Mass Range Mass Range (m/z): 400-1200 Isobaric Tag Loss Exclusion Reagent: TMT Precursor Ion Exclusion Exclusion mass width: m/z Low: 50 High: 5 Data Dependent Data Dependent Mode: Scans Per Outcome Scan Event Type 1: Scan: ddMS³ OT HCD MSⁿ Level: 3 Synchronous Precursor Selection: True Number of SPS Precursors: 10 MS Isolation Window (m/z): 0.7 MS2 Isolation Window (m/z): 2 Isolation Offset: Off Activation Type: HCD HCD Collision Energy (%): 65 Detector Type: Orbitrap Scan Range Mode: Define m/z range Orbitrap Resolution: 50000 Scan Range (m/z): 100-500 AGC Target: 1.0e5 Inject Ions for All Available Parallelizable Time: False Maximum Injection Time (ms): 105 Microscans: 1 Data Type: Centroid Use EASY-IC™: False Scan Description: Number of Dependent Scans: 10 Scan Event Type 3: Charge State Include charge state(s): 4-6 Include undetermined charge states: False Include charge states 25 and higher: False Scan: ddMS² IT CID Scan Priority: 1 Isolation Mode: Quadrupole Isolation Window (m/z): 0.5 Isolation Offset: Off Activation Type: CID Collision Energy Mode: Fixed CID Collision Energy (%): 35 CID Activation Time (ms): 10 Activation Q: 0.25 Multistage Activation: False Detector Type: Ion Trap Scan Range Mode: Auto: m/z Normal Ion Trap Scan Rate: Turbo AGC Target: 1.0e4 Inject Ions for All Available Parallelizable Time: False Maximum Injection Time (ms): 50 Microscans: 1 Data Type: Centroid Scan Description: Filters: Precursor Selection Range Selection Range Mode: Mass Range Mass Range (m/z): 400-1200 Isobaric Tag Loss Exclusion Reagent: TMT Precursor Ion Exclusion Exclusion mass width: m/z Low: 50 High: 5 Data Dependent Data Dependent Mode: Scans Per Outcome Scan Event Type 1: Scan: ddMS³ OT HCD MSⁿ Level: 3 Synchronous Precursor Selection: True Number of SPS Precursors: 10 MS Isolation Window (m/z): 0.5 MS2 Isolation Window (m/z): 2 Isolation Offset: Off Activation Type: HCD HCD Collision Energy (%): 65 Detector Type: Orbitrap Scan Range Mode: Define m/z range Orbitrap Resolution: 50000 Scan Range (m/z): 100-500 AGC Target: 1.0e5 Inject Ions for All Available Parallelizable Time: False Maximum Injection Time (ms): 105 Microscans: 1 Data Type: Centroid Use EASY-IC™: False Scan Description: Number of Dependent Scans: 10 Experiment#5 [MS] Start Time (min): 0 End Time (min): 35 Master Scan: MS OT Detector Type: Orbitrap Orbitrap Resolution: 120000 Mass Range: Normal Use Quadrupole Isolation: True Scan Range (m/z): 350-2000 RF Lens (%): 30 AGC Target: 2.0e5 Maximum Injection Time (ms): 50 Microscans: 1 Data Type: Centroid Polarity: Positive Source Fragmentation: Disabled Scan Description: ``` # mzXML conversion The mzXML files were produced by using proteowizard software using the below-listed wrapper script. ```{bat} "C:\Program Files (x86)\ProteoWizard\ProteoWizard 3.0.10200\msconvert" %1 --mzXML -z -o %~dp1\msconvert_mzXML ``` The software versions are: |software release | Q Exactive HF-X | Fusion Lumos | |:---------------------|:------------------------|:---------------------| |ProteoWizard | 3.0.10200 (2016-11-17) | 3.0.18109-390173050 | |ProteoWizard MSData | 3.0.10200 (2016-11-17) | | |ProteoWizard Analysis | 3.0.10112 (2016-10-19) | | |Build date: | Nov 17 2016 10:59:56 | | # Uploading to S3 ``` cp@fgcz-148:~ > aws --profile AnnotationContributor s3 cp tartare s3://annotation-contributor/tartare --recursive --acl public-read upload: tartare/20190710_003_PierceHeLaProteinDigestStd.mzXML to s3://annotation-contributor/tartare/20190710_003_PierceHeLaProteinDigestStd.mzXML upload: tartare/20190710_003_PierceHeLaProteinDigestStd.raw to s3://annotation-contributor/tartare/20190710_003_PierceHeLaProteinDigestStd.raw upload: tartare/20190716_004_PierceHeLa.mzXML to s3://annotation-contributor/tartare/20190716_004_PierceHeLa.mzXML upload: tartare/20190716_004_PierceHeLa.raw to s3://annotation-contributor/tartare/20190716_004_PierceHeLa.raw ``` # Loading `r Biocpkg("tartare")` data using Bioconductor `r Biocpkg("ExperimentHub")` load metadata ```{r} (fl <- system.file("extdata", "metadata.csv", package='tartare')) metadata <- read.csv(fl, stringsAsFactors=FALSE) ``` ```{r eval=TRUE, echo=FALSE} library(knitr) kable(metadata[,c(1,5,15,16)]) ``` query and load `r Biocpkg("tartare")` package data from aws s3 ```{r echo=TRUE, message=FALSE, warning=FALSE, eval=TRUE} library(ExperimentHub) eh <- ExperimentHub(); query(eh, "tartare") #### code snippets to be continued # load(query(eh, c("NestLink", "F255744.RData"))[[1]]) # dim(F255744) # load(query(eh, c("NestLink", "WU160118.RData"))[[1]]) # dim(WU160118) ``` # Session info Here is the compiled output of `sessionInfo()`: ```{r sessionInfo, echo=FALSE} sessionInfo() ``` # References