> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/dragen-protein-quantification/output-files/adat-content-9.5k.md). # ADAT Content - 9.5k This page describes the output from the 9.5k SomaSeq Discovery assay, which differs slightly from the 6k assay. Use this for ADATs made on DRAGEN Protein Quantification v2.0 and higher. The primary output file of DRAGEN Protein Quantification is the ADAT. One ADAT is produced for each normalization step performed. The final ADAT produced (\\_Step3\_SampleNorm.adat) has the normalized counts at the end of the full normalization process. Supported sample types: **Plasma**, **Serum**, **CSF**, and **MultiMatrix** (with user-defined tissue types). 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 analysis | | SOMAmerReferenceSource | SOMAmer metadata version used during analysis | | AssayType | Assay types used | | AssayVersion | Version of the SomaSeq Discovery assay (e.g., SomaSeq Discovery v2) | | 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, computed as the Q30 weighted mean across lanes | | CreatedDate | Date the run was performed | | StudyOrganism | Sample organism (human) | | StudyMatrix | Matrix used in study (Serum, Plasma, CSF, or MultiMatrix) | | CalibratorId | Lot number(s) of the calibrator samples per plate (JSON format, e.g., `{"PlateId":"240320B"}`) | | ProcessSteps | The process steps that occurred to produced the counts in the current ADAT | | HybQC\_Ref | Reference value for Hyb QC calculation | | HybQC\_Delta | Threshold delta for HybQC pass/flag determination. If a sample's HybQC value is less than or equal to this threshold, the sample receives 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 instrument 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 is less than or equal to .15, it shall be "PASS". | | PlatformSpecificQCCheckTailPercent | Percent of QC scale factors in tails for each plate from comparing Serum QC samples on MultiMatrix plates to their corresponding calibration samples after plate scaling. This is only reported for MultiMatrix. | | PlatformSpecificQCCheckTailPercent\_PassFlag | PASS/WARNING for each plate. If PlatformSpecificQCCheckTailPercent for a plate is greater than .15, this value shall be "WARNING". If it is less than or equal to .15, it shall be "PASS". This is only reported for MultiMatrix. | | 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 is less than or equal to .15, it shall be "PASS". | | IntraPlateMedianCV |

Median Percent CV metric for each plate, computed after Sample Normalization, providing:

| | IntraPlateQ75CV | Same as IntraPlateMedianCV (above) but showing 75th percentile of Percent CV instead of median | | IntraPlateQ90CV | Same as IntraPlateMedianCV (above) but showing 90th percentile of Percent CV instead of median | | InterPlateMedianCV |

Median Percent CV metric across plates, providing:

Provided only if there are 4 or more plates in the analysis

| | InterPlateQ75CV | Same as InterPlateMedianCV (above) but showing 75th percentile of Percent CV instead of median | | InterPlateQ90CV | Same as InterPlateMedianCV (above) but showing 90th percentile of Percent CV instead of median | | MedianS2B |

Median Signal to Background metric for each plate based on human somamers after Plate Normalization, providing:

| | GeneratedBy | Version of SomaData parser used to write ADAT (ex. SomaData\_1.0.0) | ## Sample Metadata
MetricDescription
SampleIDSample identifier
PlateIdUnique plate identifier
MatrixTubeBarcodeMatrix tube barcode scanned during library prep
BatchIDUser-provided batch identifier
InputType

Sample type specified in manifest file.

Examples: Plasma, Serum, CSF, MultiMatrix-<tissuetype>, Blank

MatrixType

Matrix used.

Examples: Plasma, Serum, CSF

SampleType

Type of sample processed.

Examples: Plasma, Serum, CSF, Blank, QC, Calibrator

ControlThe control type for the sample. Values: Calibrator, QC, Blank, or empty (for non-control samples).
ControlIDID of the calibrator, QC, or blank lot (applied to controls only).
KitTypeKit type associated with the sample plate. Values: Plasma, Serum, CSF, or MultiMatrix.
ScriptsVersionVersion of ILASS automation scripts used during library prep (e.g., 3.2.7).
ProbePlateProbe plate lot number, from library prep
SOMAmerBeadPlateSOMAmer bead plate lot number. For Plasma/Serum/CSF: SBP1 barcode. For MultiMatrix: MBP barcode.
WellPositionLocation of the sample on the 96 well plate (A1-H12)
Project(Optional) User-provided project identifier. Multiple projects per plate are supported.
SOMAmerReadsNumber 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.

SOMAmerNormReadsNumber 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 ≤ 20 million = PASS
  • SOMAmerNormReads > 20 million = FLAG

Not applied to non-blank samples.

RefCorrSpearman correlation value for comparing samples to the plasma, serum, or CSF reference.
HybQCHyb QC metric value for the sample, representing the deviation from expected Tm control distribution. Replaces EmpiricalHybTemp from earlier versions.
HybQC_PassFlag

This flag indicates if a sample meets the specification for Hyb QC.

  • HybQC ≤ HybQC_Delta (from ADAT header) = PASS
  • HybQC > HybQC_Delta or missing = FLAG
HybNorm_1_ScaleFactorThe hybridization control scale factor
HybNorm_PassFlagThis flag indicates whether the HybNorm_1_ScaleFactor is within the specified acceptance criteria range of 0.4–2.5. CSF samples (excluding controls) have a different acceptance criteria range of 0.2-5.0.
MedNormInt_<dilution>_ScaleFactorThe MedNormInt scale factor for the dilution group
MedNormInt_PassFlagThis 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_<dilution>_ScaleFactorThe MedNormExt scale factor for the dilution group (Plasma/Serum/CSF only; not applicable to MultiMatrix)
MedNormExt_PassFlagThis flag indicates whether all dilution group scale factors are within the specified acceptance criteria range of 0.4–2.5 for the MedNormExt step. CSF samples (excluding controls) have a different acceptance criteria range of 0.125-8.0.
Applied to QC and serum/plasma/CSF samples. Not applicable to MultiMatrix.
CrossPlateMedNormInt_all_ScaleFactorThe CrossPlateMedNormInt scale factor specific to MultiMatrix samples
CrossPlateMedNormInt_PassFlagThis flag indicates whether the CrossPlateMedNormInt scale factor is within the specified acceptance criteria range of 0.4–2.5 for MultiMatrix samples
RowCheck_PassFlagThis flag indicates whether the sample's plate failed and if not 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 | | Target Full Name | Protein target full name | | Type | Target type (protein) | | UniProt ID | UniProt identifier | | Entrez Gene ID | Entrez Gene identifier | | Entrez Gene Symbol | Entrez Gene symbol | | HybControl | True if the SOMAmer is a hyb control, else False | | Organism | Organism (e.g. Human, Mouse) of the SOMAmer | | PlatformSpecificCalibrate\_\\_ScaleFactor | Scale Factor for Platform Specific Calibration | | CrossPlatformCalibrate\_\\_ScaleFactor | Scale Factor for Cross Platform Calibration | | QCCheck\_\\_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. For Plasma/Serum: includes `Ref.MedNormExt.{type}` and `Ref.QCCheck.{type}`. Bridging references follow the format `Ref.Bridging....v2`. | | Units | Units of matrix content | --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/dragen-protein-quantification/output-files/adat-content-9.5k.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.