Service Data Formats
General MS Service Information
We provide your MS data
Starting end of July 2026, we have changed the way we supply your mass spectra.
Therefore, this part of our website briefly summarizes how we provide data of our instruments.
It will also give detailed advice on what software may be used to open original files from our insturments.
Dedicated New Course on Moodle
In addition, there tutorials in a dedicated Moodle course "Mass Spectral Data: Access and Analysis Software".
There, you find lecture slides and tutorial videos for perusal.
So far, there are
- A lecture video on the numerous data formats in MS (based on our instrumentation)
- A tutorial video on using Bruker Data Analysis Viewer software
- A tutorial video dealing with Thermo Fisher Scientific FreeStyle 1.8
This course will be kept alive during the semesters to come.
Below, you find the tabulated facts.
Ionization Methods and Availability by Instruments
There are various combinations of instruments and ionization methods. Some are unique to an instrument while other can be offered and two or three instruments. Instruments may vary in respect to their ability to offer high resolution and accurate mass, tandem MS, etc.
|
Instrument |
Ionization methods |
Operational modes |
|
Bruker Autoflex Speed |
LDI, MALDI |
Spectra in linear or reflector mode |
|
Bruker timsTOFflex |
ESI, APCI, |
HR mass spectra and tandem mass spectra for all methods; combinations with TIMS possible |
|
JEOL AccuTOF GCx |
EI,
FI, FD, LIFDI |
LR and HR mass spectra,
LR mass spectra |
|
Thermo Exploris 240 |
ESI, APCI,
LIFDI |
HR mass spectra and tandem mass spectra,
HR mass spectra |
|
Thermo Q-Exactive |
ESI, APCI |
HR mass spectra and tandem mass spectra |
Folders and Filenames on the Servers
In order to locate files on the servers of OCI and ACI, you will need to understand the naming conventions and the directories where to look in.
|
Instrument |
Data folder on server |
File names |
Analyze using
|
|
Bruker Autoflex Speed |
/ms/autoflex |
aut34567_samplename |
DataAnalysisViewer |
|
Bruker timsTOFflex |
/ms/timstof (formerly both in /autoflex) |
tims56789_samplename |
DataAnalysisViewer
|
|
JEOL AccuTOF GCx |
/ms/accutof |
jat12345_samplename |
MS Axcel |
|
Thermo Q-Exactive |
/ms/qexactive |
qex0468_samplename |
FreeStyle |
|
Thermo Exploris 240 |
/ms/exploris |
ex0579_samplename |
FreeStyle
|
|
Our short names in blue |
|
|
|
Ion Current Versus Time
When dealing with mass spectral data, you will need a basic understanding of ion current versus time and its dependence on the selection of one of the above combinations.
The table provides a first overlook.
|
Ion current |
Reason |
Occurrence |
Currently delivered by
|
|
No ion current recorded |
Individual spectra (often generated at kHz rate) are accumulated to yield one final output spectrum |
LDI, MALDI |
timsTOFflex and Autoflex Speed |
|
Ion current is (essentially) constant in time |
Admission from reservoir inlet |
EI, FI |
AccuTOF |
|
|
Admission from syringe pump |
ESI, APCI |
timsTOFflex, Q-Exactive, Exploris |
|
Ion current varies in time |
Fractionation during admission from direct probe or other heating-ramped sample supply |
EI, FD, LIFDI, APFD, DART |
AccuTOF, timsTOFflex, Exploris |
|
|
Admission via chromatograph to separate by components |
GC-MS, LC-MS |
AccuTOF |
|
|
Ion mobility separation being part of procedure |
TIMS |
timsTOFflex |
Confused?
Please refer to the Moodle course "Mass Spectral Data: Access and Analysis Software".
