ADAT Content

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
SOMAmerReferenceSource	SOMAmer metadata version used during analysis
AssayType	Assay types used
AssayVersion	Version of the Illumina Protein Prep assay
AssayRobot	Liquid handling robot
RunId	Unique identifier for the run (created by sequencing instrument)
Instrument Type	Instrument used for sequencing
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
CreatedDate	Date the run was performed
StudyOrganism	Sample organism (human)
StudyMatrix	Matrix used in study (serum or plasma)
CalibratorId	Lot number(s) of the calibrator samples
ProcessSteps	The process steps that occurred to produced the counts in the current ADAT
PlateRefCorr_PassFlag	PASS/FLAG for each plate. If greater than 70% of Blank Samples have RefCorr_PassFlag = FLAG, PlateRefCorr_PassFlag shall be WARNING. Otherwise, it shall have the value "PASS".
PlateSOMAmerNormReads_PassFlag	PASS/FLAG for each plate. If greater than 70% of Blank Samples have SOMAmerNormReads_PassFlag = FLAG, PlateSOMAmerNormReads_PassFlag shall be WARNING. Otherwise, it shall have the value "PASS".
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.
PlatformSpecificCalibrateTailPercent_PassFlag	PASS/WARNING for each plate. If PlatformSpecificCalibrateTailPercent for a plate is greater than .15, this value shall be "WARNING". If it's less than or equal to .15, it shall be "PASS".
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".
MedianPercentCV	Median Percent CV metric for each plate, providing: (sample Standard Deviation of calibrator samples/Mean of calibrator samples)*100 (sample Standard Deviation of QC samples/Mean of QC samples)*100
MedianS2B	Median Signal to Background metric for each plate, providing: Median Calibrator/Median Blank Median QC/Median Blank
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
MatrixTubeBarcode	Matrix tube barcode scanned during library prep
BatchID	User-provided batch 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
ControlID	ID of the calibrator, QC, or blank lot (applied to controls only).
ProbePlate	Probe plate lot number, from library prep
SOMAmerBeadPlate	SOMAmer bead plate lot number. Last two digits indicate the master mix lot number.
WellPosition	Location of the sample on the 96 well plate (A1-H12)
Project	(Optional) User-provided project identifier
SOMAmerReads	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.
SOMAmerNormReads	Number of normalized counts human SOMAmer reads at plate scale normalization step (excluding control reads)
SOMAmerNormReads_PassFlag	This flag indicates whether a blank sample meets the specifications for number of normalized SOMAmer reads. For blank samples: SOMAmerNormReads ≤ 40 million = PASS SOMAmerNormReads > 40 million = FLAG Not applied to non-blank samples.
RefCorr	Spearman correlation value for comparing samples to the plasma or serum reference.
RefCorr_PassFlag	This flag indicates if a blank sample meets the specification for comparison to a serum or plasma reference. For blank samples: RefCorr < 0.6 = PASS RefCorr > 0.6 = FLAG Not applied to non-blank samples.
EmpericalHybTemp	This indicates the actual hybridization temperature of a sample, obtained empirically from a set of 78 temperature controls.
HybNorm_1_ScaleFactor	The hybridization control scale factor
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.
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.
RowCheck_PassFlag	This flag indicates whether all row scale factors are within the specified acceptance criteria range.

SOMAmer Metadata

Metric	Description
SeqId	Unique sequence identifier for the SOMAmer
SeqIdVersion	SOMAmer sequence version
SomaId	Somalogic-provided identifier
Target	Protein target identifier
TargetFullName	Protein target full name
Type	Target type (protein)
UniProt	UniProt identifier
EntrezGeneID	Entrez Gene identifier
EntrezGeneSymbol	Entrez Gene symbol
HybControl	True is the SOMAmer is a hyb control, 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
PlatfromSpecificCalibrate_<PlateId>_PassFlag	Pass Flag for Platform Specific Calibration
PlatformSpecificCalibrate_<PlateId>_ScaleFactor	Scale Factor for Platform Specific Calibration
CrossPlatformCalibrate_<PlateId>_ScaleFactor	Scale Factor for Cross Platform Calibration
QCCheck_<PlateId>_PassFlag	Pass Flag for QC Check
QCCheck_<PlateId>_ScaleFactor	Scale Factor for QC Check
Dilution	Dilution group classification for the SOMAmer
DRC_Level	Compression of SOMAmer range that occurred during the assay.
References	References used in the analysis.
Units	Units of matrix content