Processing Thermo Log files

Mass Spectrometry
Thermo
Log files
Author

Josue Baeza

Published

June 6, 2024

Modified

June 24, 2024

Background

Thermo mass spectrometers record daily log files that contain a lot of valuable information regarding the status of each instrument. The log files record data for temperature, pressure, voltages, etc. from numerous guages. Visualizing this data longitudinally can help assess instrument performance.

In this blog post, I will show you were to find the log files, how to import and visualize them.

Supported Instruments

  • Q-Exactive family instruments
  • Exploris family instruments

Note: Orbitrap Eclipse instruments do generate log files, however, this blog post will only focus on the instruments above because I don’t have access to Eclipse log files

Directories

Data is located in the following directories for the different instruments

Q Exactive

C:\ProgramData\Thermo\Exactive\Log

Exploris

C:\ProgramData\Thermo\Exploris\Log

Tribrids

C:\Thermo\Instruments\TNG\OrbitrapXXXXX\X.X\System\logs

where OrbitrapXXXXX can be OrbitrapFusion or OrbitrapEclipse and X.X is the software tune version.

Reading a log file

Libraries used

library(tidyverse)
library(janitor)
library(lubridate)
library(kableExtra)
# directory where I keep the log files
directory <- "QEHFX_logfiles/"

# Reading the log files in the directory
filelist <- list.files(directory, pattern = "InstrumentTemperature", full.names = TRUE)

# plucking a single log file to demonstrate
file <- filelist[29]

Importing a single file

logfile <- read.delim2(file, sep = "\t", header = FALSE)

During the file import, I’m using header = FALSE. The instrument log files do not always have the first row with the header information, if at all.

Additionally, the header row is often embedded multiple times in a single log file. Scroll down and see how many times this log file has the header information. This will need to be cleaned up in subsequent steps.

V1 V2 V3 V4 V5 V6 V7
1524590456 2018-04-24 11:19:05 28.8252314815 2.86308390141e-09 2.90075086435e-10 3.07164356907 0.000580532871567
1524591356 2018-04-24 11:34:04 28.8356481481 2.84303745373e-09 2.92634111611e-10 3.07164356907 0.000605535107192
1524592256 2018-04-24 11:49:04 28.8460648148 2.78373634155e-09 2.90075086435e-10 3.02877246651 0.000677598898499
1524593156 2018-04-24 12:04:04 28.8564814815 2.84303745373e-09 2.90075086435e-10 3.05013269694 0.000556562965495
1524594056 2018-04-24 12:19:04 28.8668981481 2.84303745373e-09 2.87538439409e-10 3.00756182283 0.000391660741639
1524594956 2018-04-24 12:34:04 28.8773148148 2.80336465311e-09 2.95215712354e-10 3.05013269694 0.000588750089782
1524595856 2018-04-24 12:49:04 28.8877199074 2.86308390141e-09 2.90075086435e-10 3.07164356907 0.000592902213365
1524596756 2018-04-24 13:04:04 28.8981481481 2.88327169793e-09 2.8502397484e-10 2.98649971834 0.000692036414077
1524597656 2018-04-24 13:19:04 28.9085532407 2.84303745373e-09 2.92634111611e-10 3.02877246651 0.000497371550805
1524598556 2018-04-24 13:34:04 28.9189699074 2.84303745373e-09 2.90075086435e-10 3.02877246651 0.000560488091375
1524599456 2018-04-24 13:49:04 28.9293865741 2.84303745373e-09 2.95215712354e-10 3.07164356907 0.000601294514827
1524600356 2018-04-24 14:04:04 28.9398032407 2.84303745373e-09 2.90075086435e-10 3.05013269694 0.000663462583626
1524601256 2018-04-24 14:19:04 28.9502199074 2.84303745373e-09 2.8502397484e-10 3.00756182283 0.000682377622808
1524602156 2018-04-24 14:34:04 28.9606365741 2.88327169793e-09 2.90075086435e-10 3.00756182283 0.00054879498479
1524603056 2018-04-24 14:49:04 28.9710416667 2.84303745373e-09 2.90075086435e-10 3.05013269694 0.000601294514827
1524603956 2018-04-24 15:04:04 28.9814583333 2.84303745373e-09 2.87538439409e-10 3.02877246651 0.000663462583626
1524604856 2018-04-24 15:19:04 28.991875 2.86308390141e-09 2.87538439409e-10 2.98649971834 0.00040000580842
1524605756 2018-04-24 15:34:04 29.0022916667 2.84303745373e-09 2.92634111611e-10 3.00756182283 0.000572430341531
1524606656 2018-04-24 15:49:04 29.0127083333 2.84303745373e-09 2.90075086435e-10 2.98649971834 0.000592902213365
1524607556 2018-04-24 16:04:04 29.0231365741 2.86308390141e-09 2.92634111611e-10 3.0933061453 0.000618437168518
1524608456 2018-04-24 16:19:04 29.0335532407 2.86308390141e-09 2.90075086435e-10 3.02877246651 0.000645071856343
1524609356 2018-04-24 16:34:04 29.0439583333 2.84303745373e-09 2.87538439409e-10 3.00756182283 0.000663462583626
1524610256 2018-04-24 16:49:04 29.0543865741 2.84303745373e-09 2.87538439409e-10 3.05013269694 0.000627190907393
1524611156 2018-04-24 17:04:04 29.0647916667 2.84303745373e-09 2.90075086435e-10 2.98649971834 0.000580532871567
1524612056 2018-04-24 17:19:04 29.0752083333 2.82313136521e-09 2.90075086435e-10 2.96558511281 0.000658816322274
1524612956 2018-04-24 17:34:04 29.085625 2.86308390141e-09 2.8502397484e-10 3.02877246651 0.000556562965495
1524613856 2018-04-24 17:49:04 29.0960416667 2.84303745373e-09 2.90075086435e-10 3.05013269694 0.000614106222379
1524614756 2018-04-24 18:04:04 29.1064583333 2.84303745373e-09 2.90075086435e-10 3.0933061453 0.000588750089782
1524615656 2018-04-24 18:19:04 29.116875 2.86308390141e-09 2.90075086435e-10 2.98649971834 0.000564440898963
1524616556 2018-04-24 18:34:04 29.1272916667 2.84303745373e-09 2.87538439409e-10 2.98649971834 0.000622798658387
1524617456 2018-04-24 18:49:04 29.1376967593 2.96545641142e-09 2.87538439409e-10 3.05013269694 0.000622798658387
1524618356 2018-04-24 19:04:04 29.1481134259 2.84303745373e-09 2.87538439409e-10 3.05013269694 0.000658816322274
1524619256 2018-04-24 19:19:04 29.1585300926 2.84303745373e-09 2.87538439409e-10 2.98649971834 0.000692036414077
1524620156 2018-04-24 19:34:04 29.1689467593 2.82313136521e-09 2.87538439409e-10 2.9241942741 0.000687190048774
1524621056 2018-04-24 19:49:04 29.1793634259 2.84303745373e-09 2.90075086435e-10 3.05013269694 0.000668141612449
1524621956 2018-04-24 20:04:04 29.1897800926 2.86308390141e-09 2.87538439409e-10 3.05013269694 0.000721840854675
1524622856 2018-04-24 20:19:04 29.2001851852 2.88327169793e-09 2.92634111611e-10 3.05013269694 0.000752928905008
1524623756 2018-04-24 20:34:04 29.2106018519 2.84303745373e-09 2.87538439409e-10 2.98649971834 0.000706781548007
1524624656 2018-04-24 20:49:04 29.2210185185 2.84303745373e-09 2.8502397484e-10 3.02877246651 0.000726931592642
1524625556 2018-04-24 21:04:03 29.2314351852 2.86308390141e-09 2.8502397484e-10 3.02877246651 0.000711766081146
1524626456 2018-04-24 21:19:03 29.2418518519 2.86308390141e-09 2.90075086435e-10 3.02877246651 0.000983406805692
1524627356 2018-04-24 21:34:03 29.2522685185 2.86308390141e-09 2.90075086435e-10 3.07164356907 0.000463617785196
1524628256 2018-04-24 21:49:03 29.2626851852 2.88327169793e-09 3.03097968396e-10 2.98649971834 0.000408528682503
1524629156 2018-04-24 22:04:03 29.2731018519 2.88327169793e-09 3.05771880663e-10 3.00756182283 0.000790894520766
1524630056 2018-04-24 22:19:03 29.2835185185 2.84303745373e-09 2.95215712354e-10 3.02877246651 0.0012934943445
1524630956 2018-04-24 22:34:03 29.2939236111 2.84303745373e-09 2.95215712354e-10 3.07164356907 0.000504411652696
1524631856 2018-04-24 22:49:03 29.3043402778 2.84303745373e-09 3.00447438944e-10 3.02877246651 0.00111601682998
1524632756 2018-04-24 23:04:03 29.3147569444 2.86308390141e-09 3.00447438944e-10 3.07164356907 0.000758238889528
1524633656 2018-04-24 23:19:03 29.3251736111 2.84303745373e-09 2.92634111611e-10 3.0933061453 0.00153113886434
1524634556 2018-04-24 23:34:03 29.3355902778 2.86308390141e-09 2.90075086435e-10 3.07164356907 0.000716785767397
1524635456 2018-04-24 23:49:03 29.3460069444 2.84303745373e-09 2.97820087826e-10 3.02877246651 0.00122277866402
Time [sec] Date Up-Time [days] Vacuum 1 (HV) [mbar] Vacuum 2 (UHV) [mbar] Vacuum 3 (Fore) [mbar] Vacuum 4/humidity [mbar]
1524636356 2018-04-25 00:04:03 29.3564236111 2.84303745373e-09 2.87538439409e-10 3.05013269694 0.00118055826489
1524637256 2018-04-25 00:19:03 29.3668402778 2.88327169793e-09 2.97820087826e-10 2.9448169733 0.000956147444247
1524638156 2018-04-25 00:34:03 29.3772569444 2.84303745373e-09 2.95215712354e-10 3.02877246651 0.00170135859296
1524639056 2018-04-25 00:49:03 29.3876736111 2.88327169793e-09 3.00447438944e-10 2.98649971834 0.000711766081146
1524639956 2018-04-25 01:04:03 29.3980902778 2.84303745373e-09 2.97820087826e-10 3.02877246651 0.00115592902863
1524640856 2018-04-25 01:19:03 29.4085069444 2.86308390141e-09 2.90075086435e-10 3.05013269694 0.00144743109464
1524641756 2018-04-25 01:34:03 29.4189236111 2.84303745373e-09 3.00447438944e-10 3.02877246651 0.000696916958072
1524642656 2018-04-25 01:49:03 29.4293402778 2.84303745373e-09 3.03097968396e-10 3.00756182283 0.0013492022156
1524643556 2018-04-25 02:04:03 29.4397569444 2.86308390141e-09 2.90075086435e-10 3.00756182283 0.00124008662297
1524644456 2018-04-25 02:19:03 29.4501736111 2.84303745373e-09 2.95215712354e-10 3.02877246651 0.000687190048774
1524645356 2018-04-25 02:34:03 29.4605787037 2.86308390141e-09 2.97820087826e-10 3.00756182283 0.001499195688
1524646256 2018-04-25 02:49:03 29.4709953704 2.84303745373e-09 2.90075086435e-10 3.02877246651 0.000836633496975
1524647156 2018-04-25 03:04:03 29.481412037 2.84303745373e-09 2.95215712354e-10 2.98649971834 0.00118888407901
1524648056 2018-04-25 03:19:03 29.4918287037 2.86308390141e-09 2.92634111611e-10 3.02877246651 0.0021911440399
1524648956 2018-04-25 03:34:03 29.5022453704 2.86308390141e-09 2.92634111611e-10 3.00756182283 0.000802089326745
1524649856 2018-04-25 03:49:03 29.512662037 2.86308390141e-09 2.97820087826e-10 2.98649971834 0.00132105466785
1524650756 2018-04-25 04:04:03 29.5230671296 2.84303745373e-09 2.90075086435e-10 2.96558511281 0.00123140223489
1524651656 2018-04-25 04:19:03 29.5334837963 2.86308390141e-09 2.95215712354e-10 2.96558511281 0.000824956556062
1524652556 2018-04-25 04:34:03 29.543900463 2.84303745373e-09 2.97820087826e-10 2.98649971834 0.00179975148628
1524653456 2018-04-25 04:49:02 29.5543171296 2.86308390141e-09 3.00447438944e-10 3.00756182283 0.00099732654859
1524654356 2018-04-25 05:04:02 29.5647337963 2.86308390141e-09 2.97820087826e-10 3.02877246651 0.00106993706447
1524655256 2018-04-25 05:19:02 29.575150463 2.90360183997e-09 2.92634111611e-10 2.98649971834 0.00202814027835
1524656156 2018-04-25 05:34:02 29.5855671296 2.86308390141e-09 2.95215712354e-10 3.00756182283 0.000813442590873
1524657056 2018-04-25 05:49:02 29.5959722222 2.84303745373e-09 3.00447438944e-10 2.98649971834 0.00153113886434
1524657956 2018-04-25 06:04:02 29.6063888889 2.86308390141e-09 2.90075086435e-10 2.98649971834 0.00202814027835
1524658856 2018-04-25 06:19:02 29.6168055556 2.84303745373e-09 2.95215712354e-10 2.96558511281 0.000936199948219
1524659756 2018-04-25 06:34:02 29.6272222222 2.86308390141e-09 2.92634111611e-10 3.00756182283 0.00182522627232
1524660656 2018-04-25 06:49:02 29.6376388889 2.84303745373e-09 2.87538439409e-10 3.00756182283 0.000854459542992
1524661556 2018-04-25 07:04:02 29.6480671296 2.86308390141e-09 2.95215712354e-10 3.07164356907 0.0013492022156
1524662456 2018-04-25 07:19:02 29.6584837963 2.86308390141e-09 2.90075086435e-10 2.98649971834 0.00157479098931
1524663356 2018-04-25 07:34:02 29.668900463 2.86308390141e-09 2.95215712354e-10 2.96558511281 0.00135871738075
1524664256 2018-04-25 07:49:02 29.6793055556 2.86308390141e-09 2.95215712354e-10 2.98649971834 0.00191726130892
1524665156 2018-04-25 08:04:02 29.6897222222 2.80336465311e-09 2.87538439409e-10 3.00756182283 0.00202814027835
1524666056 2018-04-25 08:19:02 29.7001388889 2.84303745373e-09 2.87538439409e-10 3.02877246651 0.00208596170458
1524666956 2018-04-25 08:34:02 29.7105555556 2.82313136521e-09 2.8502397484e-10 2.98649971834 0.00185106164411
1524667856 2018-04-25 08:49:02 29.7209722222 2.84303745373e-09 2.95215712354e-10 3.00756182283 0.0021757993496
1524668756 2018-04-25 09:04:02 29.7313888889 2.84303745373e-09 2.92634111611e-10 2.96558511281 0.00213040703156
1524669656 2018-04-25 09:19:02 29.7418055556 2.84303745373e-09 2.90075086435e-10 3.00756182283 0.00210067282044
1524670556 2018-04-25 09:34:02 29.7522106481 2.86308390141e-09 2.92634111611e-10 2.96558511281 0.00197192162236
1524671456 2018-04-25 09:49:02 29.7626273148 2.84303745373e-09 3.03097968396e-10 3.02877246651 0.00197192162236
1524672356 2018-04-25 10:04:02 29.7730439815 2.84303745373e-09 2.95215712354e-10 2.96558511281 0.00191726130892
1524673256 2018-04-25 10:19:02 29.7834606481 2.84303745373e-09 2.92634111611e-10 2.98649971834 0.0019858284776
1524674156 2018-04-25 10:34:02 29.7938773148 2.84303745373e-09 2.90075086435e-10 3.00756182283 0.00216056211893
1524675056 2018-04-25 10:49:02 29.8042939815 2.84303745373e-09 2.90075086435e-10 3.02877246651 0.0019858284776
1524675956 2018-04-25 11:04:02 29.8147106481 2.86308390141e-09 2.95215712354e-10 2.98649971834 0.00173760922921
1524676856 2018-04-25 11:19:02 29.8251157407 2.84303745373e-09 2.95215712354e-10 2.98649971834 0.00179975148628
1524677756 2018-04-25 11:34:02 29.8355324074 2.86308390141e-09 2.95215712354e-10 2.98649971834 0.00157479098931
1524678656 2018-04-25 11:49:02 29.8459490741 2.84303745373e-09 2.92634111611e-10 2.98649971834 0.00178714773743
1524679556 2018-04-25 12:04:02 29.8563657407 2.84303745373e-09 2.92634111611e-10 3.00756182283 0.00191726130892
1524680456 2018-04-25 12:19:02 29.8667824074 2.84303745373e-09 2.90075086435e-10 3.02877246651 0.00207135361139
1524681356 2018-04-25 12:34:02 29.8771990741 2.84303745373e-09 2.92634111611e-10 3.02877246651 0.00182522627232
1524682256 2018-04-25 12:49:02 29.8876157407 2.78373634155e-09 2.90075086435e-10 3.02877246651 0.00207135361139
1524683156 2018-04-25 13:04:02 29.8980324074 2.86308390141e-09 2.95215712354e-10 3.00756182283 0.00176220441564
1524684056 2018-04-25 13:19:02 29.9084490741 2.84303745373e-09 2.92634111611e-10 3.00756182283 0.00154193712645
1524684956 2018-04-25 13:34:02 29.9188541667 2.86308390141e-09 2.90075086435e-10 3.02877246651 0.00173760922921
1524685856 2018-04-25 13:49:02 29.9292708333 2.86308390141e-09 2.92634111611e-10 3.02877246651 0.00160834486534
1524686756 2018-04-25 14:04:02 29.9396875 2.86308390141e-09 2.92634111611e-10 3.00756182283 0.00158589710533
1524687656 2018-04-25 14:19:02 29.9501041667 2.86308390141e-09 2.95215712354e-10 2.98649971834 0.00137794949965
1524688556 2018-04-25 14:34:02 29.9605208333 2.86308390141e-09 2.97820087826e-10 2.98649971834 0.00171335731918
1524689456 2018-04-25 14:49:02 29.9709375 2.86308390141e-09 2.92634111611e-10 3.02877246651 0.00185106164411
1524690356 2018-04-25 15:04:02 29.9813541667 2.86308390141e-09 2.90075086435e-10 3.05013269694 0.00174986361079
1524691256 2018-04-25 15:19:02 29.9917592593 2.84303745373e-09 2.8502397484e-10 3.02877246651 0.00191726130892
1524692156 2018-04-25 15:34:01 30.0021875 2.86308390141e-09 2.92634111611e-10 3.02877246651 0.00177463225326
1524693056 2018-04-25 15:49:01 30.0126041667 2.84303745373e-09 2.92634111611e-10 2.98649971834 0.00158589710533
1524693956 2018-04-25 16:04:01 30.0230208333 2.84303745373e-09 2.92634111611e-10 2.96558511281 0.00156376264997
1524694856 2018-04-25 16:19:01 30.0334375 2.84303745373e-09 3.00447438944e-10 3.00756182283 0.00138766740324
1524695756 2018-04-25 16:34:01 30.0438541667 2.86308390141e-09 2.95215712354e-10 2.98649971834 0.00202814027835
1524696656 2018-04-25 16:49:01 30.0542708333 2.86308390141e-09 2.90075086435e-10 2.98649971834 0.0021911440399
1524697556 2018-04-25 17:04:01 30.0646875 2.82313136521e-09 2.90075086435e-10 2.98649971834 0.00190383463296
1524698456 2018-04-25 17:19:01 30.0750925926 2.86308390141e-09 2.90075086435e-10 3.00756182283 0.00171335731918
1524699356 2018-04-25 17:34:01 30.0855092593 2.84303745373e-09 2.8502397484e-10 2.98649971834 0.00189050198467
1524700256 2018-04-25 17:49:01 30.0959259259 2.84303745373e-09 2.8502397484e-10 2.96558511281 0.00204244361219
1524701156 2018-04-25 18:04:01 30.1063425926 2.84303745373e-09 2.82531498747e-10 2.96558511281 0.00189050198467
1524702056 2018-04-25 18:19:01 30.1167592593 2.84303745373e-09 2.8502397484e-10 3.02877246651 0.00191726130892
1524702956 2018-04-25 18:34:01 30.1271759259 2.84303745373e-09 2.87538439409e-10 3.00756182283 0.00193078267568
1524703856 2018-04-25 18:49:01 30.1375925926 2.84303745373e-09 2.8502397484e-10 2.9448169733 0.00193078267568
1524704756 2018-04-25 19:04:01 30.1480092593 2.84303745373e-09 2.87538439409e-10 2.9448169733 0.00172544066567
1524705656 2018-04-25 19:19:01 30.1584143519 2.86308390141e-09 2.87538439409e-10 2.9448169733 0.00174986361079
1524706556 2018-04-25 19:34:01 30.1688310185 2.86308390141e-09 2.87538439409e-10 2.9448169733 0.00170135859296
1524707456 2018-04-25 19:49:01 30.1792476852 2.88327169793e-09 2.90075086435e-10 2.98649971834 0.00171335731918
1524708356 2018-04-25 20:04:01 30.1896643519 2.84303745373e-09 2.87538439409e-10 2.96558511281 0.00190383463296
1524709256 2018-04-25 20:19:01 30.2000810185 2.84303745373e-09 2.87538439409e-10 2.98649971834 0.00190383463296
1524710156 2018-04-25 20:34:01 30.2104976852 2.86308390141e-09 2.87538439409e-10 2.98649971834 0.00197192162236
1524711056 2018-04-25 20:49:01 30.2209143519 2.84303745373e-09 2.87538439409e-10 2.96558511281 0.0020568478194
1524711956 2018-04-25 21:04:01 30.2313310185 2.84303745373e-09 2.87538439409e-10 3.02877246651 0.00202814027835
1524712856 2018-04-25 21:19:01 30.2417361111 2.86308390141e-09 2.8502397484e-10 2.96558511281 0.00126650899464
1524713756 2018-04-25 21:34:01 30.2521527778 2.86308390141e-09 2.95215712354e-10 3.00756182283 0.001619687618
1524714656 2018-04-25 21:49:01 30.2625694444 2.84303745373e-09 2.87538439409e-10 2.9448169733 0.0013492022156
1524715556 2018-04-25 22:04:01 30.2729861111 2.82313136521e-09 2.92634111611e-10 2.96558511281 0.00171335731918
1524716456 2018-04-25 22:19:01 30.2834027778 2.86308390141e-09 2.90075086435e-10 3.00756182283 0.00214543159534
1524717356 2018-04-25 22:34:01 30.2938194444 2.84303745373e-09 2.8502397484e-10 2.96558511281 0.000956147444247
1524718256 2018-04-25 22:49:01 30.3042361111 2.84303745373e-09 2.95215712354e-10 3.00756182283 0.00178714773743
1524719156 2018-04-25 23:04:01 30.3146527778 2.86308390141e-09 2.8502397484e-10 2.98649971834 0.00116408114659
1524720056 2018-04-25 23:19:01 30.3250578704 2.86308390141e-09 2.95215712354e-10 2.96558511281 0.00156376264997
1524720956 2018-04-25 23:34:01 30.335474537 2.86308390141e-09 2.8502397484e-10 2.9448169733 0.00168944389442
1524721856 2018-04-25 23:49:01 30.3458912037 2.86308390141e-09 2.95215712354e-10 3.00756182283 0.00144743109464
Time [sec] Date Up-Time [days] Vacuum 1 (HV) [mbar] Vacuum 2 (UHV) [mbar] Vacuum 3 (Fore) [mbar] Vacuum 4/humidity [mbar]
1524722756 2018-04-26 00:04:01 30.3563194444 2.84303745373e-09 2.90075086435e-10 2.96558511281 0.00208596170458
1524723656 2018-04-26 00:19:01 30.3667361111 2.86308390141e-09 2.87538439409e-10 2.9241942741 0.000903874608696
1524724556 2018-04-26 00:34:02 30.3771527778 2.86308390141e-09 2.92634111611e-10 3.00756182283 0.00172544066567
1524725456 2018-04-26 00:49:02 30.3875694444 2.84303745373e-09 2.95215712354e-10 2.9448169733 0.00113181361647
1524726356 2018-04-26 01:04:02 30.3979861111 2.84303745373e-09 2.92634111611e-10 3.00756182283 0.00186411614183
1524727256 2018-04-26 01:19:02 30.4083912037 2.86308390141e-09 2.92634111611e-10 2.9448169733 0.00106993706447
1524728156 2018-04-26 01:34:01 30.4188078704 2.86308390141e-09 2.87538439409e-10 2.96558511281 0.00201393711148
1524729056 2018-04-26 01:49:01 30.429224537 2.84303745373e-09 2.90075086435e-10 3.00756182283 0.000949451496312
1524729956 2018-04-26 02:04:01 30.4396412037 2.86308390141e-09 2.92634111611e-10 2.9448169733 0.00170135859296
1524730856 2018-04-26 02:19:01 30.4500578704 2.86308390141e-09 2.90075086435e-10 2.96558511281 0.000779855961325
1524731756 2018-04-26 02:34:01 30.460474537 2.84303745373e-09 2.90075086435e-10 2.9241942741 0.00164261366964
1524732656 2018-04-26 02:49:01 30.4708912037 2.84303745373e-09 2.92634111611e-10 2.98649971834 0.00100436013237
1524733556 2018-04-26 03:04:01 30.4812962963 2.84303745373e-09 2.92634111611e-10 2.9448169733 0.00171335731918
1524734456 2018-04-26 03:19:01 30.491712963 2.86308390141e-09 2.92634111611e-10 3.00756182283 0.00109273408063
1524735356 2018-04-26 03:34:01 30.5021296296 2.84303745373e-09 2.87538439409e-10 2.9448169733 0.00181244412229
1524736256 2018-04-26 03:49:01 30.5125462963 2.84303745373e-09 2.87538439409e-10 2.9241942741 0.000836633496975
1524737156 2018-04-26 04:04:01 30.522962963 2.86308390141e-09 2.92634111611e-10 2.9241942741 0.00131180325655
1524738056 2018-04-26 04:19:01 30.5333796296 2.84303745373e-09 2.8502397484e-10 3.00756182283 0.000819179344418
1524738956 2018-04-26 04:34:01 30.5437847222 2.88327169793e-09 2.92634111611e-10 2.9448169733 0.00121421548444
1524739856 2018-04-26 04:49:01 30.5542013889 2.90360183997e-09 2.82531498747e-10 2.96558511281 0.000747656106574
1524740756 2018-04-26 05:04:01 30.5646180556 2.86308390141e-09 2.90075086435e-10 2.96558511281 0.000866554087271
1524741656 2018-04-26 05:19:01 30.5750347222 2.86308390141e-09 2.92634111611e-10 2.9448169733 0.000622798658387
1524742556 2018-04-26 05:34:01 30.5854513889 2.86308390141e-09 2.92634111611e-10 2.9241942741 0.000819179344418
1524743456 2018-04-26 05:49:01 30.5958680556 2.90360183997e-09 2.92634111611e-10 2.98649971834 0.000522450966751
1524744356 2018-04-26 06:04:01 30.6062731481 2.86308390141e-09 2.95215712354e-10 2.9448169733 0.000605535107192
1524745256 2018-04-26 06:19:01 30.6167013889 2.86308390141e-09 2.92634111611e-10 2.9448169733 0.000357464512731
1524746156 2018-04-26 06:34:01 30.6271064815 2.84303745373e-09 2.95215712354e-10 2.9448169733 0.000391660741639
1524747056 2018-04-26 06:49:01 30.6375347222 2.86308390141e-09 2.95215712354e-10 2.9448169733 0.000264236779783
1524747956 2018-04-26 07:04:01 30.6479513889 2.82313136521e-09 2.92634111611e-10 2.96558511281 0.000347555841874
1524748856 2018-04-26 07:19:01 30.6583680556 2.86308390141e-09 2.82531498747e-10 3.00756182283 0.000249790884624
1524749756 2018-04-26 07:34:01 30.6687847222 2.84303745373e-09 2.87538439409e-10 3.11512149551 0.00040000580842
1524750656 2018-04-26 07:49:01 30.6792013889 2.84303745373e-09 2.8502397484e-10 3.00756182283 0.000504411652696
1524751556 2018-04-26 08:04:01 30.6896064815 2.84303745373e-09 2.80060818845e-10 2.96558511281 0.000497371550805
1524752456 2018-04-26 08:19:01 30.7000231481 2.84303745373e-09 2.80060818845e-10 2.98649971834 0.000529846058072
1524753356 2018-04-26 08:34:01 30.7104398148 2.86308390141e-09 2.80060818845e-10 2.98649971834 0.000476835333237
1524754256 2018-04-26 08:49:01 30.7208564815 2.84303745373e-09 2.87538439409e-10 2.96558511281 0.000426123087367
1524755156 2018-04-26 09:04:01 30.7312731481 2.82313136521e-09 2.82531498747e-10 3.00756182283 0.000426123087367
1524756056 2018-04-26 09:19:01 30.7416898148 2.86308390141e-09 2.8502397484e-10 3.02877246651 0.0004539456222
1524756956 2018-04-26 09:34:01 30.7521064815 2.84303745373e-09 2.8502397484e-10 2.9448169733 0.000444475243389
1524757856 2018-04-26 09:49:01 30.7625115741 2.86308390141e-09 2.82531498747e-10 2.96558511281 0.000483584752913
1524758756 2018-04-26 10:04:01 30.7729398148 2.86308390141e-09 2.82531498747e-10 3.13709069713 0.000460371046871
1524759656 2018-04-26 10:19:00 30.7833449074 2.86308390141e-09 2.82531498747e-10 3.00756182283 0.000450766618512
1524760556 2018-04-26 10:34:01 30.7937615741 2.84303745373e-09 2.82531498747e-10 3.00756182283 0.000473496031768
1524761456 2018-04-26 10:49:01 30.8041782407 2.86308390141e-09 2.8502397484e-10 3.02877246651 0.000470180115593
1524762356 2018-04-26 11:04:00 30.8145949074 2.84303745373e-09 2.82531498747e-10 2.98649971834 0.000470180115593
1524763256 2018-04-26 11:19:01 30.8250115741 2.84303745373e-09 2.8502397484e-10 3.00756182283 0.000504411652696
1524764156 2018-04-26 11:34:00 30.8354282407 2.82313136521e-09 2.82531498747e-10 2.96558511281 0.000486995204464
1524765056 2018-04-26 11:49:00 30.8458449074 2.80336465311e-09 2.82531498747e-10 3.00756182283 0.000441362561233
1524765956 2018-04-26 12:04:00 30.85625 2.84303745373e-09 2.87538439409e-10 3.02877246651 0.000435202439068
1524766856 2018-04-26 12:19:00 30.8666666667 2.86308390141e-09 2.8502397484e-10 2.96558511281 0.000493888433187
1524767756 2018-04-26 12:34:00 30.8770833333 2.86308390141e-09 2.87538439409e-10 2.98649971834 0.000493888433187
1524768656 2018-04-26 12:49:00 30.8875 2.86308390141e-09 2.8502397484e-10 3.00756182283 0.000504411652696
1524769556 2018-04-26 13:04:00 30.8979166667 2.86308390141e-09 2.87538439409e-10 2.96558511281 0.00051879221674
1524770456 2018-04-26 13:19:00 30.9083333333 2.86308390141e-09 2.8502397484e-10 2.96558511281 0.000438271677344
1524771356 2018-04-26 13:34:00 30.91875 2.86308390141e-09 2.90075086435e-10 3.0933061453 0.000457147045616
1524772256 2018-04-26 13:49:00 30.9291550926 2.86308390141e-09 2.87538439409e-10 2.96558511281 0.000497371550805
1524773156 2018-04-26 14:04:00 30.9395949074 2.84303745373e-09 2.90075086435e-10 2.96558511281 0.000529846058072
1524774056 2018-04-26 14:19:00 30.95 2.84303745373e-09 2.82531498747e-10 3.00756182283 0.000631614132463
1524774956 2018-04-26 14:34:00 30.9604166667 2.88327169793e-09 2.82531498747e-10 3.00756182283 0.000658816322274
1524775856 2018-04-26 14:49:00 30.9708333333 2.84303745373e-09 2.80060818845e-10 2.96558511281 0.000592902213365
1524776756 2018-04-26 15:04:00 30.98125 2.84303745373e-09 2.80060818845e-10 2.96558511281 0.000592902213365
1524777656 2018-04-26 15:19:00 30.9916666667 2.84303745373e-09 2.80060818845e-10 2.98649971834 0.000507968984669
1524778556 2018-04-26 15:34:00 31.0020833333 2.84303745373e-09 2.82531498747e-10 2.98649971834 0.00051879221674
1524779456 2018-04-26 15:49:00 31.0125 2.86308390141e-09 2.80060818845e-10 3.00756182283 0.000544951746315
1524780356 2018-04-26 16:04:00 31.0229050926 2.84303745373e-09 2.8502397484e-10 3.00756182283 0.000511551404505
1524781256 2018-04-26 16:19:00 31.0333217593 2.86308390141e-09 2.8502397484e-10 2.96558511281 0.00040000580842
1524782156 2018-04-26 16:34:00 31.0437384259 2.86308390141e-09 2.90075086435e-10 3.00756182283 0.000457147045616
1524783056 2018-04-26 16:49:00 31.0541550926 2.84303745373e-09 2.90075086435e-10 3.02877246651 0.000411409805761
1524783956 2018-04-26 17:04:00 31.0645717593 2.86308390141e-09 2.92634111611e-10 2.9448169733 0.000429128294076
1524784856 2018-04-26 17:19:00 31.0749884259 2.86308390141e-09 2.90075086435e-10 3.0933061453 0.000405667735894
1524785756 2018-04-26 17:34:00 31.0854050926 2.86308390141e-09 2.92634111611e-10 2.98649971834 0.000388917922056
1524786656 2018-04-26 17:49:00 31.0958101852 2.86308390141e-09 2.90075086435e-10 2.96558511281 0.000378137384288
1524787556 2018-04-26 18:04:00 31.1062268519 2.86308390141e-09 2.92634111611e-10 2.98649971834 0.000435202439068
1524788456 2018-04-26 18:19:00 31.1166435185 2.86308390141e-09 2.8502397484e-10 3.00756182283 0.000438271677344
1524789356 2018-04-26 18:34:00 31.1270601852 2.86308390141e-09 2.90075086435e-10 3.02877246651 0.000466887420943
1524790256 2018-04-26 18:49:00 31.1374768519 2.84303745373e-09 2.87538439409e-10 2.9448169733 0.000466887420943
1524791156 2018-04-26 19:04:00 31.1478935185 2.86308390141e-09 2.87538439409e-10 2.96558511281 0.000460371046871
1524792056 2018-04-26 19:19:00 31.1583101852 2.86308390141e-09 2.8502397484e-10 2.96558511281 0.000444475243389
1524792956 2018-04-26 19:34:00 31.1687268519 2.86308390141e-09 2.87538439409e-10 3.00756182283 0.000391660741639
1524793856 2018-04-26 19:49:00 31.1791319444 2.84303745373e-09 2.90075086435e-10 2.96558511281 0.00040000580842
1524794756 2018-04-26 20:04:00 31.1895486111 2.84303745373e-09 2.90075086435e-10 2.98649971834 0.000386194310574
1524795656 2018-04-26 20:19:00 31.1999652778 2.86308390141e-09 2.87538439409e-10 2.9448169733 0.000423138926269
1524796556 2018-04-26 20:34:00 31.2103819444 2.86308390141e-09 2.87538439409e-10 2.96558511281 0.000375489269447
1524797456 2018-04-26 20:48:59 31.2207986111 2.86308390141e-09 2.8502397484e-10 2.96558511281 0.000429128294076
1524798356 2018-04-26 21:03:59 31.2312268519 2.86308390141e-09 2.87538439409e-10 3.02877246651 0.000473496031768
1524799256 2018-04-26 21:18:59 31.2416319444 2.84303745373e-09 2.82531498747e-10 2.98649971834 0.000541135422229
1524800156 2018-04-26 21:33:59 31.2520486111 2.84303745373e-09 2.82531498747e-10 3.02877246651 0.00052613551987
1524801056 2018-04-26 21:48:59 31.2624652778 2.86308390141e-09 2.77611744532e-10 2.98649971834 0.000490429708013
1524801956 2018-04-26 22:03:59 31.2728819444 2.84303745373e-09 2.82531498747e-10 3.00756182283 0.000490429708013
1524802856 2018-04-26 22:18:59 31.2832986111 2.84303745373e-09 2.82531498747e-10 2.98649971834 0.000486995204464
1524803756 2018-04-26 22:33:59 31.2937152778 2.86308390141e-09 2.82531498747e-10 3.00756182283 0.000497371550805
1524804656 2018-04-26 22:48:59 31.3041319444 2.84303745373e-09 2.82531498747e-10 3.00756182283 0.000490429708013
1524805556 2018-04-26 23:03:59 31.314537037 2.84303745373e-09 2.82531498747e-10 2.96558511281 0.000504411652696
1524806456 2018-04-26 23:18:59 31.3249537037 2.86308390141e-09 2.87538439409e-10 2.98649971834 0.000497371550805
1524807356 2018-04-26 23:33:59 31.3353703704 2.86308390141e-09 2.82531498747e-10 3.02877246651 0.000504411652696
1524808256 2018-04-26 23:48:59 31.345787037 2.84303745373e-09 2.80060818845e-10 2.98649971834 0.000572430341531
Time [sec] Date Up-Time [days] Vacuum 1 (HV) [mbar] Vacuum 2 (UHV) [mbar] Vacuum 3 (Fore) [mbar] Vacuum 4/humidity [mbar]
1524809156 2018-04-27 00:03:59 31.3562037037 2.84303745373e-09 2.80060818845e-10 2.96558511281 0.000486995204464
1524810056 2018-04-27 00:18:59 31.3666203704 2.84303745373e-09 2.77611744532e-10 3.0933061453 0.000497371550805
1524810956 2018-04-27 00:33:59 31.377037037 2.86308390141e-09 2.82531498747e-10 3.02877246651 0.000541135422229
1524811856 2018-04-27 00:48:59 31.3874537037 2.86308390141e-09 2.80060818845e-10 3.02877246651 0.000605535107192
1524812756 2018-04-27 01:03:59 31.3978587963 2.82313136521e-09 2.80060818845e-10 3.00756182283 0.000588750089782
1524813656 2018-04-27 01:18:59 31.408275463 2.86308390141e-09 2.82531498747e-10 3.00756182283 0.000580532871567
1524814556 2018-04-27 01:33:59 31.4186921296 2.86308390141e-09 2.82531498747e-10 3.00756182283 0.000592902213365
1524815456 2018-04-27 01:48:59 31.4291087963 2.86308390141e-09 2.82531498747e-10 2.96558511281 0.00054879498479
1524816356 2018-04-27 02:03:59 31.439525463 2.84303745373e-09 2.8502397484e-10 2.96558511281 0.000584627043727
1524817256 2018-04-27 02:18:59 31.4499421296 2.84303745373e-09 2.8502397484e-10 2.96558511281 0.000568421583481
1524818156 2018-04-27 02:33:59 31.4603587963 2.84303745373e-09 2.8502397484e-10 2.98649971834 0.000597083619542
1524819056 2018-04-27 02:48:59 31.4707638889 2.86308390141e-09 2.82531498747e-10 3.02877246651 0.000572430341531
1524819956 2018-04-27 03:03:59 31.4811805556 2.86308390141e-09 2.80060818845e-10 2.9448169733 0.000572430341531
1524820856 2018-04-27 03:18:59 31.4915972222 2.84303745373e-09 2.8502397484e-10 3.02877246651 0.000580532871567
1524821756 2018-04-27 03:33:59 31.5020138889 2.84303745373e-09 2.8502397484e-10 2.98649971834 0.00052613551987
1524822656 2018-04-27 03:48:59 31.5124305556 2.86308390141e-09 2.8502397484e-10 2.96558511281 0.000560488091375
1524823556 2018-04-27 04:03:59 31.5228472222 2.84303745373e-09 2.82531498747e-10 3.00756182283 0.000572430341531
1524824456 2018-04-27 04:18:59 31.533275463 2.86308390141e-09 2.80060818845e-10 3.00756182283 0.000601294514827
1524825356 2018-04-27 04:33:59 31.5436921296 2.84303745373e-09 2.82531498747e-10 2.96558511281 0.000560488091375
1524826256 2018-04-27 04:48:59 31.5541087963 2.84303745373e-09 2.82531498747e-10 2.96558511281 0.000537345824051
1524827156 2018-04-27 05:03:59 31.5645138889 2.84303745373e-09 2.8502397484e-10 2.96558511281 0.000609805606071
1524828056 2018-04-27 05:18:59 31.5749305556 2.84303745373e-09 2.8502397484e-10 3.00756182283 0.000636068552055
1524828956 2018-04-27 05:33:59 31.5853472222 2.86308390141e-09 2.82531498747e-10 3.02877246651 0.000601294514827
1524829856 2018-04-27 05:48:58 31.5957638889 2.86308390141e-09 2.8502397484e-10 3.00756182283 0.000618437168518
1524830756 2018-04-27 06:03:58 31.6061805556 2.86308390141e-09 2.8502397484e-10 3.02877246651 0.000605535107192
1524831656 2018-04-27 06:18:58 31.6165972222 2.86308390141e-09 2.82531498747e-10 2.9448169733 0.000605535107192
1524832556 2018-04-27 06:33:58 31.6270023148 2.86308390141e-09 2.72777658575e-10 2.96558511281 0.000672853639833
1524833456 2018-04-27 06:48:58 31.6374189815 2.84303745373e-09 2.8502397484e-10 2.96558511281 0.000737221028119
1524834356 2018-04-27 07:03:58 31.6478356481 2.84303745373e-09 2.82531498747e-10 3.02877246651 0.000848475720468
1524835256 2018-04-27 07:18:58 31.6582523148 2.86308390141e-09 2.8502397484e-10 3.00756182283 0.000878819825145
1524836156 2018-04-27 07:33:58 31.6686689815 2.86308390141e-09 2.82531498747e-10 3.05013269694 0.000742420233808
1524837056 2018-04-27 07:48:58 31.6790856481 2.88327169793e-09 2.82531498747e-10 2.98649971834 0.000813442590873
1524837956 2018-04-27 08:03:58 31.6895023148 2.84303745373e-09 2.82531498747e-10 3.02877246651 0.000721840854675
1524838856 2018-04-27 08:18:58 31.6999074074 2.86308390141e-09 2.8502397484e-10 3.07164356907 0.00065420259892
1524839756 2018-04-27 08:33:58 31.7103356481 2.84303745373e-09 2.87538439409e-10 2.9448169733 0.000580532871567
1524840656 2018-04-27 08:48:58 31.7207407407 2.84303745373e-09 2.87538439409e-10 2.88338112966 0.000732058232724
1524841556 2018-04-27 09:03:58 31.7311574074 2.86308390141e-09 2.82531498747e-10 2.96558511281 0.000854459542992
1524842456 2018-04-27 09:18:58 31.7415740741 2.84303745373e-09 2.80060818845e-10 2.98649971834 0.00088501764759
1524843356 2018-04-27 09:33:58 31.7519907407 2.84303745373e-09 2.8502397484e-10 2.96558511281 0.00111601682998
1524844256 2018-04-27 09:48:58 31.7624074074 2.84303745373e-09 2.82531498747e-10 3.02877246651 0.000962890614942
1524845156 2018-04-27 10:03:58 31.7728240741 2.86308390141e-09 2.8502397484e-10 2.98649971834 0.000878819825145
1524846056 2018-04-27 10:18:58 31.7832407407 2.86308390141e-09 2.82531498747e-10 2.96558511281 0.000903874608696
1524846956 2018-04-27 10:33:58 31.7936458333 2.86308390141e-09 2.8502397484e-10 2.98649971834 0.00077439459138
1524847856 2018-04-27 10:48:58 31.8040625 2.84303745373e-09 2.8502397484e-10 3.00756182283 0.000891259179794
1524848756 2018-04-27 11:03:58 31.8144791667 2.84303745373e-09 2.92634111611e-10 3.00756182283 0.00108508160971
1524849656 2018-04-27 11:18:58 31.8249074074 2.86308390141e-09 2.82531498747e-10 3.00756182283 0.00114783400036
1524850556 2018-04-27 11:33:58 31.8353240741 2.86308390141e-09 2.80060818845e-10 2.98649971834 0.00100436013237
1524851456 2018-04-27 11:48:58 31.8457407407 2.86308390141e-09 2.80060818845e-10 3.02877246651 0.00104027914367
1524852356 2018-04-27 12:03:58 31.8561458333 2.84303745373e-09 2.82531498747e-10 3.00756182283 0.00108508160971
1524853256 2018-04-27 12:18:58 31.8665625 2.86308390141e-09 2.80060818845e-10 3.05013269694 0.00127544097096
1524854156 2018-04-27 12:33:58 31.8769791667 2.84303745373e-09 2.82531498747e-10 3.00756182283 0.00104761564797
1524855056 2018-04-27 12:48:58 31.8873958333 2.84303745373e-09 2.8502397484e-10 2.96558511281 0.000903874608696
1524855956 2018-04-27 13:03:58 31.8978125 2.84303745373e-09 2.87538439409e-10 2.96558511281 0.000878819825145
1524856856 2018-04-27 13:18:58 31.9082291667 2.84303745373e-09 2.8502397484e-10 2.90371599668 0.000819179344418
1524857756 2018-04-27 13:33:58 31.9186458333 2.88327169793e-09 2.87538439409e-10 2.98649971834 0.000929643693586
1524858656 2018-04-27 13:48:58 31.9290625 2.82313136521e-09 2.8502397484e-10 2.9448169733 0.00101144332006
1524859556 2018-04-27 14:03:58 31.9394791667 2.86308390141e-09 2.87538439409e-10 2.98649971834 0.00109273408063
1524860456 2018-04-27 14:18:58 31.9498842593 2.84303745373e-09 2.8502397484e-10 2.9448169733 0.00108508160971

Cleaning up header

These are the steps being performed in the following chunk.

  1. Indexing the rows in a single log file that contain the header-row
  2. Removing Non-ASCII characters from header
  3. Assigning a header-row as column names
  4. Removing all header-rows from log file
  5. Cleaning up column names using the janitor package
# Indexing the header-rows
index <- grep("[a-z]", logfile[,3])

# Removing Non-ASCII characters
logfile[index[1],] <- iconv(logfile[index[1],], "utf-8", "ascii", sub = "")

# Assigning new column name
names(logfile) <- logfile[index[1],]

# Removing header-rows
logfile <- logfile[-index,]

# Cleaning column names
logfile <- logfile %>% clean_names(case = "snake")

Formatting data types

The next step is to convert the dataframe to numeric and the date column to datetime. During the data import, the header-rows being present forced all columns to import as character type.

# Creating a vector of date-time. I need to deal with this separately
date_column <- logfile$date

# Removing the date column from the data frame
logfile$date <- NA

# Need to convert the entire data frame to numeric
logfile <- as.data.frame(sapply(logfile, FUN = as.numeric))

# Now that the data frame is numeric, I can add back the date-time
logfile$date <- date_column
 
# Formatting date-time using lubridate
logfile$date <- ymd_hms(logfile$date)

Putting it all together

This is the function used to import individual log files into a dataframe.

import_orbitrap_logfiles <- function(file){
  
  # Loading libraries
  require(tidyverse)
  require(janitor)
  require(lubridate)
  
  # Importing log file
  logfile <- read.delim2(file, sep = "\t", header = FALSE)
  
  # Indexing the header-rows
  index <- grep("[a-z]", logfile[,3])
  
  # Removing Non-ASCII characters
  logfile[index[1],] <- iconv(logfile[index[1],], "utf-8", "ascii", sub = "")
  
  # Assigning new column name
  names(logfile) <- logfile[index[1],]
  
  # Removing header-rows
  logfile <- logfile[-index,]
  
  # Cleaning column names
  logfile <- logfile %>% clean_names(case = "snake") 
  
  # Creating a vector of date-time. I need to deal with this separately
  date_column <- logfile$date
  
  # Removing the date-time from the dataframe
  logfile$date <- NA
  
  # Need to convert the entire dataframe to numeric
  logfile <- as.data.frame(sapply(logfile, FUN = as.numeric))
  
  # Now that the dataframe is numeric, I can add back the date-time
  logfile$date <- date_column
  
  # Formatting date-time
  logfile$date <- ymd_hms(logfile$date)
  
  # return dataframe
  return(logfile)
  
}

Reading many log files

# directory where log files are kept
directory <- "QEHFX_logfiles/"

# Reading the log files in the directory
filelist <- list.files(directory, pattern = "InstrumentTemperature", full.names = TRUE)

# function to read in log files with some error handling
read_logfile_to_df <- function(x){
  tryCatch(import_orbitrap_logfiles(x),
           error = function(e) NA,
           warning = function(w) NA)
}

# importing log files and saving as a list
log <- filelist %>% 
  lapply(read_logfile_to_df) 

# Removing log files that generated an error
# I can go back and investigate why this happened later
log <- log[which(!is.na(log))]

# Concatenated files
data <- log %>% 
  bind_rows()

Instrument readbacks

The log files record numerous instrument readbacks including:

  • Ambient temperature
  • Analyzer temperature
  • CEPS Peltier temperature
  • Fore vacuum pressure
  • High vacuum pressure
  • Ultra high vacuum pressure

Below is the full list of readbacks that are available for the QE-HFX.

Note: The list of readbacks for each instrument will vary slightly depending on model and tune version

Instrument Readbacks
up_time_days
vacuum_1_hv_mbar
vacuum_2_uhv_mbar
vacuum_3_fore_mbar
vacuum_4_humidity_mbar
turbo1_temp_bearing_r_c
turbo1_temp_motor_r_c
turbo1_temp_bottompart_r_c
turbo1_temp_powerstage_r_c
turbo1_temp_electronics_r_c
turbo1_volt_r_v
turbo1_curr_r_a
turbo2_temp_bearing_r_c
turbo2_temp_motor_r_c
turbo2_temp_bottompart_r_c
turbo2_temp_powerstage_r_c
turbo2_temp_electronics_r_c
turbo2_volt_r_v
turbo2_curr_r_a
turbo3_temp_bearing_r_c
turbo3_temp_motor_r_c
turbo3_temp_bottompart_r_c
turbo3_temp_powerstage_r_c
turbo3_temp_electronics_r_c
turbo3_volt_r_v
turbo3_curr_r_a
ambient_temperature_raw_c
ambient_humidity_result_percent
capillary_temperature_c
itv_gas_pressure_actual_bar
ios_heatsink_temperature_c
inj_flat_ampl_vpp
inj_flat_freq_k_hz
bent_flat_freq_k_hz
ios_rf2_3_freq_k_hz
ctrap_rf_amp_vpp
ctrap_amp_current_a
ctrap_freq_m_hz
ce_pos_electronics_temperature_act_c
ce_neg_electronics_temperature_act_c
analyzer_temperature_sensor_c
analyzer_temp_sensor_filtered_c
analyzer_temperature_with_delay_model_c
ceps_peltier_temperature_sensor_c
quad_detector_temperature_c

Ambient Temperature

The ambient_temperature_raw_c provides a measure of the ambient temperature. This sensor is located at the back of the instrument.

Code 
data %>% 
  ggplot(aes(x = date)) +
  geom_line(aes(y = ambient_temperature_raw_c)) +
  theme_bw(base_size = 22) +
  labs(x = NULL,
       y = expression('Temp ('~degree*C*')')) +
  scale_x_datetime(date_breaks = "3 month", 
                   date_minor_breaks = "1 month",
                   date_labels = "%b%y")

Ultra High (UHV) Vacuum pressure

Using vacuum_2_uhv_mbar to plot the UHV pressure can be useful to visualize instrument bake-out procedures. Each time there is a large spike in pressure, it coincides with an instrument venting and bake-out process.

Code 
data %>% 
  ggplot(aes(x = date)) +
  geom_line(aes(y = vacuum_2_uhv_mbar)) +
  theme_bw(base_size = 22) +
  scale_y_log10() +
  labs(x = NULL,
       y = expression('Pressure (mbar)')) +
  scale_x_datetime(date_breaks = "3 month", 
                   date_minor_breaks = "1 month",
                   date_labels = "%b%y")

Orbitrap Temperature

Another way to visualize bake-out procedures is to plot the Orbitrap temperature directly using analyzer_temperature_sensor_c.

Code 
data %>% 
  ggplot(aes(x = date)) +
  geom_line(aes(y = analyzer_temperature_sensor_c)) +
  theme_bw(base_size = 22) +
  scale_y_log10() +
  labs(x = NULL,
       y = expression('Temp ('~degree*C*')')) +
  scale_x_datetime(date_breaks = "3 month", 
                   date_minor_breaks = "1 month",
                   date_labels = "%b%y")

But Why!?!?!

Original problem

This project started when I was a postdoc in the Garcia lab. In 2018, we had a new QE HF-X installed. Some time after installation, we began to notice that the mass accuracy would quickly drift, even with a recent mass calibration. The mass accuracy drift would occur most on samples that were run overnight. The hypothesis was that the temperature of the room fluctuated between at different times of the day. So the beginnings of this analysis script was prompted by this question.

The plot below is how the temperature fluctuated between the day and night time.

Code 
data %>% 
  filter(date >= as.Date("2018-10-01"),
         date <= as.Date("2018-10-26")) %>%
  ggplot(aes(x = date)) +
  geom_line(aes(y = ambient_temperature_raw_c)) +
  expand_limits(y = 0) +
  theme_bw(base_size = 22) +
  labs(x = NULL,
       y = expression('Temp ('~degree*C*')')) +
  scale_x_datetime(date_breaks = "1 week", 
                   limits = as_datetime(c("2018-10-01", "2018-12-15")),
                   date_labels = "%d-%b")

First solution attempt

Using this data, we were able to show the building manager that instrument performance (mass accuracy) was affected by the room temperature. This data was taken to the building manager to find a solution for the problem. It turned out that the AC vents were pointing directly to the top of the instrument. The maintenance team flipped the direction of the vents to see if it solved the problem—it helped, sort of.

See below.

Code 
data %>% 
  filter(date >= as.Date("2018-10-01"),
         date <= as.Date("2018-11-07")) %>%
  ggplot(aes(x = date)) +
  geom_line(aes(y = ambient_temperature_raw_c)) +
  expand_limits(y = 0) +
  theme_bw(base_size = 22) +
  labs(x = NULL,
       y = expression('Temp ('~degree*C*')')) +
  scale_x_datetime(date_breaks = "1 week", 
                   limits = as_datetime(c("2018-10-01", "2018-12-15")),
                   date_labels = "%d-%b")

Second solution attempt

We went back to the building manager to show that it wasn’t fully resolved. This time, they changed the vents to point further away from the building and towards the doorway. Another factor to this saga was that the thermostat to the room was directly behind the QE HF-X. Therefore a work order was placed to change the location of the thermostat to a different part of the room.

With this work, we finally reached a steady state in temperature.

Code 
data %>% 
  filter(date >= as.Date("2018-10-01"),
         date <= as.Date("2018-12-15")) %>%
  ggplot(aes(x = date)) +
  geom_line(aes(y = ambient_temperature_raw_c)) +
  expand_limits(y = 0) +
  theme_bw(base_size = 22) +
  labs(x = NULL,
       y = expression('Temp ('~degree*C*')')) +
  scale_x_datetime(date_breaks = "1 week", 
                   limits = as_datetime(c("2018-10-01", "2018-12-15")),
                   date_labels = "%d-%b")

Conclusions

Analyzing data from the instrument log files gave us the evidence we needed to show the building manager that our instrument performance issues stemmed from a facilities problem.

Since 2018, I’ve used this log file analysis to help troubleshoot or prevent potential issues even before they were real failures. This can be a valuable tool to any mass spectrometrist looking to understand how their instrument is performing.