raw file spec. meta data

[tobiasko]

thermo raw files contain lots of metadata in different containers. This issue will deal with how to make them accessible in R using the Spectra class or a raw specific extension.

[tobiasko]

This is what Freestyle reports when asking for the scan header of a raw file file recorded on the LUMOS_1:

Scan Header 15237 - 20190701_18_autoQC4L

Total Ion Current:	191256784	
Scan Low Mass:	350	
Scan High Mass:	1500	
Scan Start Time (Min):	40.76	
Scan Number:	15237	
Base Peak Intensity:	7325822	
Base Peak Mass:	522.79	
Scan Mode:	FTMS + c ESI Full ms [350.0000-1500.0000]	
======= Instrument data =====	
				
Scan Description:	                	
AGC:	On          	
Micro Scan Count:	1	
Ion Injection Time (ms):	1.270	
Elapsed Scan Time (sec):	0.275	
Average Scan by Inst:	No	
Orbitrap Resolution:	120000	
API Process Delay:	-1.000	
Dependency Type:	0	
Multi Inject Info:	                                	
Master Scan Number:	-1	
Monoisotopic M/Z:	-1.0000	
Charge State:	0	
HCD Energy:	                         	
HCD Energy eV:	                         	
MS2 Isolation Width:	-1.00	
SPS Masses:	                                                                                                                                	
SPS Masses Continued:	                                                                                                                                	
Access ID:	0	
Conversion Parameter I:	0.000000	
Conversion Parameter A:	0.000000	
Conversion Parameter B:	211801469.281149	
Conversion Parameter C:	-8020593.145370	
Conversion Parameter D:	0.000000	
Conversion Parameter E:	0.000000	
Temperature Comp. (ppm):	-7.06	
RF Comp. (ppm):	0.00	
Space Charge Comp. (ppm):	-0.26	
Resolution Comp. (ppm):	-0.13	
Number of LM Found:	0	
LM Correction (ppm):	0.00	
RawOvFtT:	506252.4	
Injection t0:	0.000	
Reagent Ion Injection Time (ms):	0.000	
FAIMS Voltage On:	No	
FAIMS CV:	0.000	

all metadata comes in key, value pairs

The corresponding file header:

Sample Name		
Comment		
Seq Row	3	
Sample Type	Unknown	
Path	D:\Data2San\p3000\Proteomics\LUMOS_1\pgehrig_20190701_autoQC	
Cal Level		
Cal File		
Inj Volume	2	
Sample Weight	0	
Sample Volume	0	
Sample Id	"1:B,2"	
Istd Amount	0	
CD Factor	1	
Bar Code		
Bar Code Status	0	
Inst Method	C:\Xcalibur\methods\__autoQC\trap\autoQC4L_APD.meth	
Proc Method		
User Text1		
User Text2		
User Text3		
User Text4		
User Text5		
Tray Index	80	
Tray Name	ANSI-48Vial2mLHolder/ANSI-48Vial2mLHolder	
Tray Shape	Rectangular	
Vial Index	47	
Vials Per Tray	48	
Vials Per TrayX	8	
Vials Per TrayY	6	
Instrument Name	Orbitrap Fusion Lumos	
Instrument Model	Orbitrap Fusion Lumos	
Instrument Number	FSN20583	
Instrument SoftWare	3.1.2412.25	
Instrument Hardware		
Flags		
Mass Tolerance	0.5 amu	
Created by	Administrator	

[tobiasko]