ADAT Content - 6k

This page describes the output from the 6k Illumina Protein Prep assay, which differs slightly from the 9.5k assay. Do not reference this page unless your analysis was created on DRAGEN Protein Quantification v1.8 or earlier.

The primary output file of DRAGEN Protein Quantification is the ADAT. One ADAT is produced for each normalization step performed. The final ADAT produced (<output_file_prefix>_Step7_FinalNormStep_MedNormExt.adat) has the normalized counts at the end of the full normalization process.

There are four key components to the ADAT: the header, SOMAmer metadata, sample metadata, and counts.

ADAT Layout

ADAT Header

Metric	Description
Version	Version of the software used during analysis
Title	User reference for the anlaysis
OutputDirectory	Not applicable
SOMAmerReferenceSource	SOMAmer metadata version used during analysis
AssayType	Assay types used
SiteId	Not applicable
AssayVersion	Version of the Illumina Protein Prep assay (for 6k product, value will be Illumina Protein Kit 1.0)
AssayRobot	Liquid handling robot
RunId	Unique identifier for the run (created by sequencing instrument)
Instrument Type	Instrument used for sequencing
NGSLot	Internal reference for control samples
Flowcell	Flowcell used for sequencing
YieldDemux	Total number of reads that are demultiplexed
YieldQ30Demux	Total number of reads that are demultiplexed with a passing QC score
Q30WeightedMean	Q30 primary sequencing metric, comuted as the Q30 weighted mean across lanes
CreatedBy	Not applicable
EnteredBy	Not applicable
ExpDate	Not applicable
CreatedDate	Date the run was performed
Notes	Not applicable
StudyOrganism	Sample organism (human)
StudyMatrix	Matrix used in study (serum or plasma)
CalibratorId	Lot number(s) of the calibrator samples
ReportConfig	Configuration used for normalization
ProcessSteps	The process steps that occurred to produced the counts in the current ADAT
PlatformSpecificPlateScale_ScaleFactor	Scale factors for the PlateScale normalization step, when compared to a platform specific reference. The reference is based on data from the sequencing instrumented used for the run.
PlatformSpecificCalibrateTailPercent	Percent of Platform Specific Calibration scale factors in tails (outside of the acceptable range of 0.6-1.4) for each plate when compared to a reference. The platform specific reference is based on data from the sequencing instrument used for the run.
CrossPlatformPlateScale_ScaleFactor	Scale factors for the PlateScale normalization step, when compared to a universal reference made with NovaSeq X data.
CrossPlatformCalibrateTailPercent	Percent of Cross Platform Calibration scale factors in tails (outside of the acceptable range of 0.6-1.4) for each plate when compared to a reference. The cross platform reference is based on data from NovaSeq X runs.
QCCheckTailPercent	Percent of QC scale factors in tails for each plate.
QCCheckTailPercent_PassFlag	PASS/FAIL for each plate. If QCCheckTailPercent for a plate is greater than .15, this value shall be "FAIL". If it's less than or equal to .15, it shall be "PASS".
GeneratedBy	Version of SomaData parser used to write ADAT (ex. SomaData_1.0.0)

Sample Metadata

Metric	Description
SampleID	Sample identifier
PlateId	Unique plate identifier
InputType	Sample type specified in manifest file. Examples: Plasma_Calibrator, Plasma_QC, Plasma, Serum_Calibrator, Serum_ QC, Serum, Blank
MatrixTube	Matrix used. Examples: Plasma, Serum
SampleType	Type of sample processed. Examples: Plasma, Serum, Blank, QC, Calibrator
CalibratorId	Calibrator lot/ID.
WellPosition	Location of the sample on the 96 well plate (A1-H12)
SOMAmer Reads	Number of raw counts human SOMAmer reads (excluding control reads)
SOMAmerReads_PassFlag	This flag indicates whether a non-blank sample meets specifications for number of SOMAmer reads. For non-blank samples: SOMAmerReads ≥ 10 million = PASS SOMAmerReads < 10 million = FLAG Not applied to blank samples.
HybNorm_1_ScaleFactor	The hybridization control scale factor for hyb plate 1
HybNorm_2_ScaleFactor	The hybridization control scale factor for hyb plate 2
HybNorm_PassFlag	This flag indicates whether the HybNorm_1_ScaleFactor is within the specified acceptance criteria range of 0.4–2.5.
MedNormInt_5e-05_ScaleFactor	The MedNormInt scale factor for the 0.005% dilution group
MedNormInt_0.005_ScaleFactor	The MedNormInt scale factor for the 0.5% dilution group
MedNormInt_0.2_ScaleFactor	The MedNormInt scale factor for the 20% dilution group
MedNormInt_PassFlag	This flag indicates whether all dilution group scale factors are within the specified acceptance criteria range of 0.4–2.5 for the MedNormInt step. Applies to blank and calibrator samples.
MedNormExt_5e-05_ScaleFactor	The MedNormExt scale factor for the 0.005% dilution group
MedNormExt_0.005_ScaleFactor	The MedNormExt scale factor for the 0.5% dilution group
MedNormExt_0.2_ScaleFactor	The MedNormExt scale factor for the 20% dilution group
MedNormExt_PassFlag	This flag indicates whether all dilution group scale factors are within the specified acceptance criteria range of 0.4–2.5 for the MedNormExt step. Applied to QC and serum/plasma samples.
ANML_5e-05_ScaleFactor	The ANML scale factor for the 0.005% dilution group. Note: ANML norm is not output.
ANML_0.005_ScaleFactor	The ANML scale factor for the 0.5% dilution group. Note: ANML norm is not output.
ANML_0.2_ScaleFactor	The ANML scale factor for the 20% dilution group. Note: ANML norm is not output.
ANML_5e-05_fraction_used	Fraction of probes in 0.005% dilution group used to compute corresponding ANML scale factor.
ANML_0.005_fraction_used	Fraction of probes in 0.5% dilution group used to compute corresponding ANML scale factor.
ANML_0.2_fraction_used	Fraction of probes in 20% dilution group used to compute corresponding ANML scale factor.
RowCheck_PassFlag	This flag indicates whether all row scale factors are within the specified acceptance criteria range.
PlateRunDate	Not applicable
SampleNotes	Not applicable
Barcode	Not applicable

SOMAmer Metadata

Metric	Description
SeqId	Unique sequence identifier for the SOMAmer
SeqIdVersion	SOMAmer sequence version
SomaId	Somalogic-provided identifier
Target	Protein target identifier
Target Full Name	Protein target full name
Type	Target type (protein)
UniProt	UniProt identifier
EntrezGeneID	Entrez Gene identifier
EntrezGeneSymbol	Entrez Gene symbol
HybControl	True if the SOMAmer is a hyb control, else False
MedNormControl	True if the SOMAmer is used during MedNormExt normalization, else False
LoD.Plasma	Limit of detection for plasma SOMAmers
LoD.Serum	Limit of detection for serum SOMAmers
Organism	Organism (e.g. Human, Mouse) of the SOMAmer
PlatformSpecificCalibrate_<PlateId>_ScaleFactor	Scale Factor for Platform Specific Calibration
PlatformSpecificCalibrate_<PlateId>_PassFlag	Flag to indicates whether the PlatformSpecificCalibrate scale factor for this SeqId was in the acceptance criteria range of 0.6-1.4. Note: this flag is only used for evaluating the PlatformSpecificCalibrateTailPercent and should not be used to exclude SOMAmers from analysis.
CrossPlatformCalibrate_<PlateId>_ScaleFactor	Scale Factor for Cross Platform Calibration
CrossPlatformCalibrate_<PlateId>_PassFlag	Flag to indicates whether the CrossPlatformCalibrate scale factor for this SeqId was in the acceptance criteria range of 0.6-1.4. Note: this flag is only used for evaluating the CrossPlatformCalibrateTailPercent and should not be used to exclude SOMAmers from analysis.
QCCheck_<PlateId>_ScaleFactor	Scale Factor for QC Check
QCCheck_<PlateId>_PassFlag	Flag to indicates whether the QCCheck scale factor for this SeqId was in the acceptance criteria range of 0.8-1.2. Note: this flag is only used for evaluating the QCCheckTailPercent and should not be used to exclude SOMAmers from analysis.
ColCheck_<PlateId>_PassFlag	This flag indicates whether all SOMAmer scale factors are within the specified acceptance criteria range. Note: this flag should not be used to exclude SOMAmers from analysis.
Dilution	Dilution group classification for the SOMAmer
DRC	Compression of SOMAmer range that occurred during the assay.
HCG	Hybridization Control Group. Identifies the hybridization plate of the SOMAmer's NGS reporter.
BlackList	Identifies SOMAmers with low performing NGS reporters in product testing. SOMAmers with the value TRUE should be excluded from analysis.
References (Ref.*)	References available to the SW version used for analysis.
Units	Units of matrix content