readSpectrum(...)

[tobiasko]

refactor rawDiag::readScans()

arguments

rawfile : path to raw file
scans : numeric vector for selection based on scan index
filter : scan filter for logical selection of scans (e.g. MS, MS2, +, HCD, ...)

returns

S3 object, nested list of type Spectrum (not peaklist)

for FTMS scans the list should contain vectors for: mz, intensity, resolution, noise, charge

In addition header information is needed:

• raw file
• scan#
• RT (Scan Start Time)
• NL (normalized level = base beak intensity)
• TIC (Total Ion Current)
• Base Peak Mass
• Scan Mode (e.g. FTMS + c NSI Full ms [350.0000 -1800.000]
• Scan Low Mass
• Scan High Mass

[tobiasko]

Potentially interesting:

==== Diagnostic Data: ==== as shown in Freestyle

contains attributes like AGC Fill, HCD Energy eV, ...

==== Instrument data ==== as shown in Freestyle

contains attributes like Multiple Injection, Charge State, Ion Injection Time (ms), AGC Target, ...

The BIG question: How much scan meta data do we want to extract by default???

[tobiasko]

complete scan header example c&p from Freestyle:

Total Ion Current:	53435.391	
Scan Low Mass:	100	
Scan High Mass:	1335	
Scan Start Time (Min):	20.72	
Scan Number:	12939	
Base Peak Intensity:	6354.29	
Base Peak Mass:	303.27	
Scan Mode:	FTMS + c NSI Full ms2 [email protected] [100.0000-1335.0000]	
======= Instrument data =====	
	
Multiple Injection:	h 	
Multi Inject Info:	IT=55 	
AGC:	On	
Micro Scan Count:	1	
Scan Segment:	1	
Scan Event:	2	
Master Index:	0	
Charge State:	2	
Monoisotopic M/Z:	0.0000	
Ion Injection Time (ms):	55.000	
Max. Ion Time (ms):	55.00	
FT Resolution:	30000	
MS2 Isolation Width:	1.40	
MS2 Isolation Offset:	0.00	
AGC Target:	100000	
HCD Energy:	27.00	
Analyzer Temperature:	30.02	
=== Mass Calibration: ===:	
	
Conversion Parameter B:	211692985.2249	
Conversion Parameter C:	-97213762.9727	
Temperature Comp. (ppm):	-5.72	
RF Comp. (ppm):	-0.22	
Space Charge Comp. (ppm):	-0.01	
Resolution Comp. (ppm):	0.07	
Number of Lock Masses:	2	
Lock Mass #1 (m/z):	371.1010	
Lock Mass #2 (m/z):	445.1200	
Lock Mass #3 (m/z):	0.0000	
LM Search Window (ppm):	15.0	
LM Search Window (mmu):	0.0	
Number of LM Found:	0	
Last Locking (sec):	0.1	
LM m/z-Correction (ppm):	-1.20	
=== Ion Optics Settings: ===:	
	
S-Lens RF Level:	60.00	
S-Lens Voltage (V):	21.00	
Skimmer Voltage (V):	15.00	
Inject Flatapole Offset (V):	5.00	
Bent Flatapole DC (V):	2.00	
MP2 and MP3 RF (V):	633.00	
Gate Lens Voltage (V):	0.88	
C-Trap RF (V):	1010.0	
====  Diagnostic Data:  ====:	
	
Dynamic RT Shift (min):	0.00	
Intens Comp Factor:	0.5575	
Res. Dep. Intens:	1.000	
CTCD NumF:	0	
CTCD Comp:	1.739	
CTCD ScScr:	0.000	
RawOvFtT:	16263.9	
LC FWHM parameter:	15.0	
Rod:	0	
PS Inj. Time (ms):	13.595	
AGC PS Mode:	-2	
AGC PS Diag:	0	
HCD Energy eV:	31.338	
AGC Fill:	0.01	
Injection t0:	0.000	
t0 FLP:	0.00	
Access Id:	0	
Analog Input 1 (V):	0.000	
Analog Input 2 (V):	0.000	

[cpanse]

omit.spectrum = FALSE

[tobiasko]

Hi CP,

I checked the details of the current implementation. Currently, some important items are missing in the list/S3 object returned by readSpectrum(...):

*Total Ion Current
*Scan Low Mass
*Scan High Mass
*Base Peak Intensity
*Base Peak Mass

further down the list you should also see a key:value pair ======= Instrument data =====:NA, similar to Mass Calibration, Ion Optics Settings, Diagnostic Data. I could not find it.

Regarding those key:value pairs that are used by thermo to structure the list. Would it be possible to use them as branch points for nesting the list in R?

====  Diagnostic Data:  ====:: chr ""
=== Ion Optics Settings: ===:: chr ""
=== Mass Calibration: ===:: chr ""
=== Instrument data ===:: chr ""

And we should think about where to place the peak lists/attributes in the returned object!

The basic peak list is two numeric vectors:

*position (mz)
*intensity

but there should be additional vectors like:

resolution, noise, charge, background

and the peak flags. As discussed before, maybe having a dedicated object for the peak lists would help, since the vectors would need to stick to certain names, be of equal length and types. omit.spectrum = TRUE would simply not populate this peak list object slot with data.

What do you think?

 sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rawR_0.0.1

loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2   

[tobiasko]

After reading the S3 OOP chapter in Master Hadleys book of whisdom I realized the following: ˋreadSpectrum()ˋ is equal to one of the 3 essential functions, the ˋmyclass()ˋor helper function in case users create class instances. I would therefore rename ˋreadSpectrum()ˋ to ˋSpectrumˋ

[tobiasko]

Or if we incl. the package name in the object name as you suggest ˋrawRSpectrum()ˋ

[tobiasko]

See section 13.3.3 of Hadleys book of wisdom.

[tobiasko]

13.3.3 also answers your question regarding the usage of the validator. The helper function calls the low level constructor ˋnew_myclass() and the validator.

[tobiasko]

The final goal should be that people only interact with two well crafted objects: rawRSpectrum and rawRChromatogram

[tobiasko]

[cpanse]

no idea what is meant with helper in that context

…

On Thu, Sep 17, 2020 at 10:09 AM Tobias Kockmann ***@***.***> wrote: 13.3.3 also answers your question regarding the usage of the validator. The helper function calls the low level constructor ˋnew_myclass() and the validator. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABFMYY76XKJFOE6J7OTVSGLSGG74JANCNFSM4QKNXNOA> .

[tobiasko]

[cpanse]

ahh

[cpanse]

brain wash

[tobiasko]

Something I came across:

readChromatogram() returns a rawRchromatogramSet which is basically a list of rawRchromatogram objects.

readSpectrum() behaves differently:

it returns a plain list instead of a rawRspectrumSet.

Could you fix that @cpanse ???

[tobiasko]

status quo: only peak flags are missing.