tartare 1.12.0
Pierce HeLa protein digest standard (#1862824, Thermo Scientific) in 3% ACN, 0.1% FA
file name: 20190710_003_PierceHeLaProteinDigestStd.raw
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 …
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
Experiment 2 and 3 were executed in parrallel! All method details are listed below.
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)file name: 20190716_004_PierceHeLa.raw
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 …
The MS acquision was started directly after sample injection and lastet for 35 min. In summary, 5 different experiments were recorded:
Exp. #5 (MS) was executed the entire method duration! Method details are listed below.
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:The mzXML files were produced by using proteowizard software using the below-listed wrapper script.
"C:\Program Files (x86)\ProteoWizard\ProteoWizard 3.0.10200\msconvert" %1 --mzXML -z -o %~dp1\msconvert_mzXMLThe 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 |
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.rawLoading tartare data using Bioconductor ExperimentHub
(fl <- system.file("extdata", "metadata.csv", package='tartare'))## [1] "/tmp/RtmprlVA3u/Rinst2f273e71ad6615/tartare/extdata/metadata.csv"metadata <- read.csv(fl, stringsAsFactors=FALSE)| Title | SourceType | RDataPath | Notes |
|---|---|---|---|
| Q Exactive HF-X mzXML | mzXML | tartare/20190710_003_PierceHeLaProteinDigestStd.mzXML | md5=44cdee961107b3e6f755b5401d20b407 |
| Q Exactive HF-X raw | raw | tartare/20190710_003_PierceHeLaProteinDigestStd.raw | md5=21becaaa165d8aec00a48a2ace61ee20 |
| Fusion Lumos mzXML | mzXML | tartare/20190716_004_PierceHeLa.mzXML | md5=6f7485fc3b5864bac51a215200a52101 |
| Fusion Lumos raw | raw | tartare/20190716_004_PierceHeLa.raw | md5=055f6133b2e1c18fd33fa2c08fbaa8da |
| Q Exactive HF Orbitrap raw | raw | tartare/20181113_010_autoQC01.raw | md5=a1f5df9627cf9e0d51ec1906776957ab |
query and load tartare package data from aws s3
library(ExperimentHub)
eh <- ExperimentHub();
query(eh, "tartare")## ExperimentHub with 5 records
## # snapshotDate(): 2022-10-24
## # $dataprovider: Functional Genomics Center Zurich (FGCZ)
## # $species: NA
## # $rdataclass: Spectra
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH3219"]]'
##
## title
## EH3219 | Q Exactive HF-X mzXML
## EH3220 | Q Exactive HF-X raw
## EH3221 | Fusion Lumos mzXML
## EH3222 | Fusion Lumos raw
## EH4547 | Q Exactive HF Orbitrap raw#### 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)More example code snippets are shown in the package vignette of the MsBackendRawFileReader package.
Here is the compiled output of sessionInfo():
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ExperimentHub_2.6.0 AnnotationHub_3.6.0 BiocFileCache_2.6.0
## [4] dbplyr_2.2.1 BiocGenerics_0.44.0 knitr_1.40
## [7] BiocStyle_2.26.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.9 png_0.1-7
## [3] Biostrings_2.66.0 assertthat_0.2.1
## [5] digest_0.6.30 utf8_1.2.2
## [7] mime_0.12 GenomeInfoDb_1.34.0
## [9] R6_2.5.1 stats4_4.2.1
## [11] RSQLite_2.2.18 evaluate_0.17
## [13] httr_1.4.4 highr_0.9
## [15] pillar_1.8.1 zlibbioc_1.44.0
## [17] rlang_1.0.6 curl_4.3.3
## [19] jquerylib_0.1.4 blob_1.2.3
## [21] S4Vectors_0.36.0 rmarkdown_2.17
## [23] stringr_1.4.1 RCurl_1.98-1.9
## [25] bit_4.0.4 shiny_1.7.3
## [27] compiler_4.2.1 httpuv_1.6.6
## [29] xfun_0.34 pkgconfig_2.0.3
## [31] htmltools_0.5.3 tidyselect_1.2.0
## [33] KEGGREST_1.38.0 GenomeInfoDbData_1.2.9
## [35] tibble_3.1.8 interactiveDisplayBase_1.36.0
## [37] bookdown_0.29 IRanges_2.32.0
## [39] fansi_1.0.3 withr_2.5.0
## [41] crayon_1.5.2 dplyr_1.0.10
## [43] later_1.3.0 bitops_1.0-7
## [45] rappdirs_0.3.3 jsonlite_1.8.3
## [47] xtable_1.8-4 lifecycle_1.0.3
## [49] DBI_1.1.3 magrittr_2.0.3
## [51] cli_3.4.1 stringi_1.7.8
## [53] cachem_1.0.6 XVector_0.38.0
## [55] promises_1.2.0.1 bslib_0.4.0
## [57] ellipsis_0.3.2 filelock_1.0.2
## [59] generics_0.1.3 vctrs_0.5.0
## [61] tools_4.2.1 bit64_4.0.5
## [63] Biobase_2.58.0 glue_1.6.2
## [65] purrr_0.3.5 BiocVersion_3.16.0
## [67] fastmap_1.1.0 yaml_2.3.6
## [69] AnnotationDbi_1.60.0 BiocManager_1.30.19
## [71] memoise_2.0.1 sass_0.4.2Kockmann, Tobias, and Christian Panse. 2021. “The rawrr R Package: Direct Access to Orbitrap Data and Beyond” 20 (4): 2028–34. https://doi.org/10.1021/acs.jproteome.0c00866.
Shofstahl, Jim. 2015. “Reading Files using the C# file reader.” http://planetorbitrap.com/rawfilereader#.WjkqIUtJmL4.