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DRAGEN Protein Quantification
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DRAGEN Protein Quantification
  • Get Started
    • Introduction
    • Prerequisites
      • Illumina Protein Prep Automation System Output Files
  • Run Setup
    • Run Planning with the BSSH Run Planner Tool
    • Sample Sheet Fields
    • Local Sample Sheet Generation Tool
    • Lane Splitting and Multi-Analysis by Project
  • Counting and Normalization
    • Cloud Autolaunch Secondary Analysis
      • Accessing Cloud Results
    • Local Secondary Analysis
    • Normalization Summary
    • QC Summary
    • Interpretation of Results
    • Metrics Appendix
  • Output Files
    • Output Structure
    • DRAGEN Report
    • ADAT Content
  • After Counting and Normalization
    • Using the ADAT
    • Illumina Connected Multiomics Walkthrough
  • References
    • FAQs
    • Documentation Revision History
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  • ADAT Header
  • Sample Metadata
  • SOMAmer Metadata

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  1. Output Files

ADAT Content

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Last updated 1 month ago

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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 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

ADAT Layout