1 Sample description

Pierce HeLa protein digest standard (#1862824, Thermo Scientific) in 3% ACN, 0.1% FA

2 Data recording

2.1 Q Exactive HF-X

file name: 20190710_003_PierceHeLaProteinDigestStd.raw

2.1.1 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 …

2.1.2 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.

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)

2.2 Fusion Lumos

file name: 20190716_004_PierceHeLa.raw

2.2.1 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 …

2.2.2 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.

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:

3 mzXML conversion

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_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

4 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

5 Usage

Loading tartare data using Bioconductor ExperimentHub

(fl <- system.file("extdata", "metadata.csv", package='tartare'))
## [1] "/tmp/RtmpiBk7mN/Rinst2c0ecd3fcfb7bd/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(): 2022-04-19
## # $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.

6 Session info

Here is the compiled output of sessionInfo():

## R version 4.2.0 RC (2022-04-21 r82226)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 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_2.5.0 AnnotationHub_3.5.0 BiocFileCache_2.5.0
## [4] dbplyr_2.1.1        BiocGenerics_0.43.0 knitr_1.38         
## [7] BiocStyle_2.25.0   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8.3                  png_0.1-7                    
##  [3] Biostrings_2.65.0             assertthat_0.2.1             
##  [5] digest_0.6.29                 utf8_1.2.2                   
##  [7] mime_0.12                     R6_2.5.1                     
##  [9] GenomeInfoDb_1.33.0           stats4_4.2.0                 
## [11] RSQLite_2.2.12                evaluate_0.15                
## [13] httr_1.4.2                    highr_0.9                    
## [15] pillar_1.7.0                  zlibbioc_1.43.0              
## [17] rlang_1.0.2                   curl_4.3.2                   
## [19] jquerylib_0.1.4               blob_1.2.3                   
## [21] S4Vectors_0.35.0              rmarkdown_2.14               
## [23] stringr_1.4.0                 RCurl_1.98-1.6               
## [25] bit_4.0.4                     shiny_1.7.1                  
## [27] compiler_4.2.0                httpuv_1.6.5                 
## [29] xfun_0.30                     pkgconfig_2.0.3              
## [31] htmltools_0.5.2               tidyselect_1.1.2             
## [33] KEGGREST_1.37.0               GenomeInfoDbData_1.2.8       
## [35] tibble_3.1.6                  interactiveDisplayBase_1.35.0
## [37] bookdown_0.26                 IRanges_2.31.0               
## [39] fansi_1.0.3                   crayon_1.5.1                 
## [41] dplyr_1.0.8                   later_1.3.0                  
## [43] bitops_1.0-7                  rappdirs_0.3.3               
## [45] jsonlite_1.8.0                xtable_1.8-4                 
## [47] lifecycle_1.0.1               DBI_1.1.2                    
## [49] magrittr_2.0.3                cli_3.3.0                    
## [51] stringi_1.7.6                 cachem_1.0.6                 
## [53] XVector_0.37.0                promises_1.2.0.1             
## [55] bslib_0.3.1                   ellipsis_0.3.2               
## [57] filelock_1.0.2                generics_0.1.2               
## [59] vctrs_0.4.1                   tools_4.2.0                  
## [61] bit64_4.0.5                   Biobase_2.57.0               
## [63] glue_1.6.2                    purrr_0.3.4                  
## [65] BiocVersion_3.16.0            fastmap_1.1.0                
## [67] yaml_2.3.5                    AnnotationDbi_1.59.0         
## [69] BiocManager_1.30.17           memoise_2.0.1                
## [71] sass_0.4.1

References

Kockmann, 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.