Data Acquisition

You are here: Reference Content > Methods > Data Acquisition

The data acquisition method consists of the instrumental method and analytical sequence that encompass operator decisions used to analyze the samples, blanks, standards, and controls (see: Sample Information and Preparation, QC Spikes & Samples), and should be designed with the scope of the NTA experiment in mind (see: Objectives & Scope). Instrumental methods comprise a detailed list of conditions and parameters that are chosen for the acquisition of (high resolution) mass spectrometry raw data files (including conditions and parameters for associated chromatographic separations). When designing instrumental methods, NTA researchers should consider both the intended scope of the data acquisition process (i.e., minimally limited/operating in a non-targeted manner vs. limited to a specific suspect screening list) as well as the intended scope of subsequent data analysis.

Reporting the details of the data acquisition method enables readers to understand the results and reproduce the experiment. Just as the choices made during sample preparation can impact the scope of the NTA study, choices made with respect to the run order and instrumental analysis methods and settings can impact the detectable chemical space and the scope of the conclusions that can be drawn from the results. Accordingly, although data acquisition information can be mundane (and details can often be listed in the Supporting Information, rather than the main manuscript), complete details should be included as an essential part of an NTA manuscript. We recommend that researchers consider (in advance) and report/discuss the potential or observed impact of data acquisition method and parameter choices on the final scope of their NTA results. This section primarily provides information regarding the reporting of the methods and associated settings; additional details on reporting the performance of data acquisition methods can be found in the section on QA/QC Metrics.

It is important to note that instruments from different manufacturers and different acquisition modes will have some specific/unique parameters and terminology; researchers should be aware of these differences both when developing new methods across instruments and when reporting settings from their study.

Analytical Sequence

You are here: Reference Content > Methods > Data Acquisition > Analytical Sequence

The analytical sequence encompasses both the analytical run order and the use of single vs. multiple analytical batches. Run order is the arrangement of the samples, replicates, blanks, standards, and QC samples (see: Sample Information and Preparation, QC Spikes & Samples) as they are sequentially analyzed by the instrument. Ideally, instrumental analysis of a sample should not depend on or be impacted by the previous analysis, but problems such as background contamination, sample carry-over, instrument fouling, or even increasing instrument sensitivity, can impact the results of an NTA workflow. Therefore, we recommend that the run order be considered when designing the study and described when reporting the data acquisition method. Although a table of all samples arranged in their run order would effectively provide this information, the general pattern of the run order (for example: blank-QC-sample-blank, the number of samples between analyses of blanks/QCs, use of analytical replicates, randomization of sample types and/or field/analytical replicates, use of single vs. multiple analytical batches, etc.) is sufficient for reporting. Researchers should also report on any observed impacts due to run order (for example: observed carry-over in blanks, increased or decreased peak area response for spiked QC samples over the course of the analytical batch, etc.)

As a general guideline, the instrumental analysis of one blank for every 7-12 samples within a sequence is acceptable, but smaller sample sets will benefit from a higher frequency, as multiple blank samples are required to assess the variability of contamination. The same guideline can be applied to the periodic analysis of QC samples that are used to assess instrument performance. Additionally, it is recommended that a solvent blank be used to assess carry-over contamination from one sample to the next during instrument injection (especially after samples or standards that are known to be particularly concentrated; at minimum, via periodic analysis throughout the sequence). Ultimately, the researcher should consider the intent of the blank or QC sample(s) (e.g., to assess carry-over, to detect background contamination from sample preparation, to evaluate chromatographic variability, etc.) in deciding their run-order and distribution of blank samples through the run.

Chromatography

You are here: Reference Content > Methods > Data Acquisition > Chromatography

While not required for all NTA, chromatography is frequently used to separate and improve detection of individual components (compounds) in complex mixtures, such as environmental or food samples. NTA can be performed with gas chromatography (GC) or liquid chromatography (LC), but also other separation techniques such as capillary electrophoresis (CE) and ion mobility spectrometry (IMS).

The parameters of a chromatographic method can be separated into two distinct sections: parameters relevant to the sample and sample introduction (Table 2.1) and those relevant to chromatography and other separations (Table 2.2). These tables are not meant to be comprehensive of all variants of those parameters and terminologies, but rather representative/illustrative.

We encourage that all information in the tables below should be reported if applicable and if possible; however we realize this may not be reasonable for all studies given the variable goals of NTA research. However, we have distinguished between parameters and information that we suggest are essential and should be reported in the main manuscript (MM) vs. are less critical (i.e., although they provide valuable supplementary information about the methods) and thus could be reported in the supplemental information (SI).

Table 2.1 Sample and Sample Introduction
Method
LC Parameter
GC Parameter
Reported Location
Sample
Final solvent
MM
Sample spiking (e.g., QC spikes, chemical standards, etc.)
MM
Derivatization reaction conditions (reaction type, chemical details, time, temp)
MM
Type of vial used (deactivated vs. normal glass)
SI
Sample Introduction
Direct injection parameters
MM
Injection volume
MM
Injector/autosampler type: [large volume injection (LVI), flow thru, online solid phase extraction (SPE), non-LVI, direct injection/infusion]
Injector type: [Automatic Liquid Sampler (ALS), Programmed Temperature Vaporization (PTV), Split/Splitless (SSPL), Cold On-Column (COC), direct injection/infusion]
MM
n/a
Split ratios

[Split/pressure program/purge time and flow]
[Backflush use, start time/duration]
MM
Washes: procedures, parts washed (e.g., seals for LC), solvents, number of cycles
SI
Needle wash: volume, time, solvent
SI
Needle information: needle depth, draw speed
SI
Autosampler temperature
Injector temperature/program (temperature programmed injectors)
SI
Loop size/system delay volume
Injection liner type/manufacturer/Part #
SI
Table 2.2: Chromatography and Other Separations
Method
LC Parameter
GC Parameter
Reported Location
Instrument
Manufacturer & Model
MM
Acquisition software and version
SI
Column
Column manufacturer, part #, lot #
MM
Stationary phase, length, inner diameter (ID), particle size (LC), film thickness (GC)
MM
Guard column and dimensions
Retention gap/pre-column and dimensions
MM
Pore size
n/a
SI
Column startup, conditioning, shutdown method
n/a
SI
2-dimensional mode
Same details as for first dimension
Modulator type

MM
2nd dimension column (see Column), temperature program, and modulation time (and other related specific parameters)
Mobile phase
Solvent prep recipe + stability indication (e.g., pressure/response variability)
Gas (type, purity)
MM
Column temperature
n/a
MM
Isocratic vs. gradient program
Isothermal vs. gradient program
MM
Solvent program
Temperature program
MM
Flow rate
Flow rate
MM
Pressure (as diagnostic)
Pressure (w/ flow or pressure control type)
SI
pH of eluents and adjustment procedure
n/a
SI
Pump type (binary, quaternary)
n/a
SI
Other
n/a
Transfer line temperature
SI
Other Chromatography
CE and Capillary Electrokinetic Chromatography
(CEC) specific parameters
MM
Ion mobility (IM)
Manufacturer & model
n/a
MM
Type [(low pressure) drift tube, travelling wave, trapped, high-field asymmetric waveform, etc.]
Gas
IM resolution [full width-half maximum (FWHM)]
Voltages
n/a
SI
Acquisition software and version
Calibration type and standards
Multiplexed?
Drift time
Trapping time
Trap radio frequency (RF)
Electric field strength (V/cm)

Mass Spectrometry

You are here: Reference Content > Methods > Data Acquisition > Mass Spectrometry

Mass spectrometry is essential to NTA studies to detect and identify unknown chemical compounds. Mass spectrometers often have varied settings, but the parameters can be clustered between LC- and GC-coupled mass spectrometers and are detailed in Table 2.3 below. This table is not meant to be comprehensive of all variants of those parameters and terminologies, but rather representative/illustrative. We encourage that all information in the tables below should be reported if applicable and if possible; however we realize this may not be reasonable for all studies given the variable goals of NTA research. However, we have distinguished between parameters and information that we suggest should be reported in the main manuscript (MM) vs. the supplemental information (SI).

Table 2.3 Mass Spectrometry
Method
LC-coupled MS Parameter
GC-coupled MS Parameter
Reported Location
General
Manufacturer & Model
MM
Ionization mode and polarity
MM
Acquisition type [MS1/full scan, multiple reaction monitoring (MRM), MS/MS, MSn, data dependent (DDA), data independent (DIA), All ion]
Acquisition type [Scan, selected ion monitoring (SIM), MRM, MS, MS/MS]
MM
Ion source (vendor specific)
MM
Scan range (for full scan, MS/MS)
MM
Data acquisition or scan rate; resolving power
MM
Acquisition software and version
SI
Vacuum pressure (all stages must be in spec)
SI
Ion Source
Source/vaporizer temperature
Ion source temperature
MM
Spray voltage (kV)
EI: electron energy (eV), emission current (µA)
MM
Other gases: aux/sweep gas flow
CI: reagent gas, flow
SI
Sheath gas temp/flow
n/a
SI
Nebulizer pressure
n/a
SI
Ion transfer capillary/optics, S-lens, temp/RF level (%)
n/a
SI
Discharge current (µA) for atmospheric pressure chemical ionization (APCI)
n/a
SI
In-source collision induced dissociation (CID) or declustering potential (eV)
n/a
SI
Analyzer
Data type (profile, centroid)
MM
Isolation window (Da)
MM
Theoretical resolution (MS and/or MSn) @ mass and given acquisition speed
MM
Collision energy(ies) [e.g., stepped Normalized-Collision-Energy (NCE), eV]
MM
Fragmentation mode to include exclusion/inclusion/priority/triggered MRM lists or data dependent MS2 (Top N)
SI
DDA-exclusion time
SI
DDA/MRM-number of ions to fragment
SI
DDA intensity thresholds, trigger events (e.g., apex)
SI
Skimmer/fragmentor/lens voltages
SI
Automatic gain control and other related like max ion time (msec) for MS and/or MSn
SI
Other voltages/temperatures (vendor specific)
SI
Nozzle/cone voltage
n/a
SI
Tuning/mass calibration
Tune type (auto, manual, low mass, etc.)
SI
Tuning requirements/parameters if manual
SI
Tuning compound(s) and source
SI
Compound concentration
SI
Solvent composition
SI
Frequency
SI
Vendor specific tuning parameters
SI
Mass accuracy correction
Reference compounds, source, and introduction technique (i.e., separate reference probe)
SI
Compound concentration
SI
Solvent composition
SI
Infusion method
SI
Correction method/usage
SI
Flow rate
SI

References & Other Relevant Literature

Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., . . . Viant, M. R. (2007). Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics, 3(3), 211-221. doi:10.1007/s11306-007-0082-2