Key Fields

Liability Metric Fields

Field Name

Type

Description

liability_string_cdr1_aa_1

string

‘+’ concatenated string of identified liabilities by type (e.g., ‘YYY - Polyspecificity + ‘DG - Isomerization’) within chain_1 CDR1 (e.g., LCDR1 if orientation is 5’ VL and 3’ VH).

liability_string_cdr2_aa_1

string

‘+’ concatenated string of identified liabilities by type (e.g., ‘YYY - Polyspecificity + ‘DG - Isomerization’) within chain_1 CDR2 (e.g., LCDR2 if orientation is 5’ VL and 3’ VH).

liability_string_cdr3_aa_1

string

‘+’ concatenated string of identified liabilities by type (e.g., ‘YYY - Polyspecificity + ‘DG - Isomerization’) within chain_1 CDR3 (e.g., LCDR3 if orientation is 5’ VL and 3’ VH).

liability_string_cdr1_aa_2

string

‘+’ concatenated string of identified liabilities by type (e.g., ‘YYY - Polyspecificity + ‘DG - Isomerization’) within chain_2 CDR1 (e.g., HCDR1 if orientation is 5’ VL and 3’ VH).

liability_string_cdr2_aa_2

string

‘+’ concatenated string of identified liabilities by type (e.g., ‘YYY - Polyspecificity + ‘DG - Isomerization’) within chain_2 CDR2 (e.g., HCDR2 if orientation is 5’ VL and 3’ VH).

liability_string_cdr3_aa_2

string

‘+’ concatenated string of identified liabilities by type (e.g., ‘YYY - Polyspecificity + ‘DG - Isomerization’) within chain_2 CDR3 (e.g., HCDR3 if orientation is 5’ VL and 3’ VH).

liability_quant_cdr1_aa_1

integer

Total count of liabilities identified within chain_1 CDR1 (e.g., LCDR1 if orientation is 5’ VL and 3’ VH), each liability counted only once per CDR, even if multiple of same liability found in single CDRs.

liability_quant_cdr2_aa_1

integer

Total count of liabilities identified within chain_1 CDR2 (e.g., LCDR2 if orientation is 5’ VL and 3’ VH), each liability counted only once per CDR, even if multiple of same liability found in single CDRs.

liability_quant_cdr3_aa_1

integer

Total count of liabilities identified within chain_1 CDR3 (e.g., LCDR3 if orientation is 5’ VL and 3’ VH), each liability counted only once per CDR, even if multiple of same liability found in single CDRs.

liability_quant_cdr1_aa_2

integer

Total count of liabilities identified within chain_1 CDR1 (e.g., LCDR1 if orientation is 5’ VL and 3’ VH), each liability counted only once per CDR, even if multiple of same liability found in single CDRs.

liability_quant_cdr2_aa_2

integer

Total count of liabilities identified within chain_1 CDR2 (e.g., LCDR2 if orientation is 5’ VL and 3’ VH), each liability counted only once per CDR, even if multiple of same liability found in single CDRs.

liability_quant_cdr3_aa_2

integer

Total count of liabilities identified within chain_1 CDR3 (e.g., LCDR3 if orientation is 5’ VL and 3’ VH), each liability counted only once per CDR, even if multiple of same liability found in single CDRs.

liability_quant_chain_1

integer

Total count of liabilities identified across all chain_1 CDRs (e.g., LCDR1-3 if orientation is 5’ VL and 3’ VH).

liability_quant_chain_2

integer

Total count of liabilities identified across all chain_2 CDRs (e.g., HCDR1-3 if orientation is 5’ VL and 3’ VH).

liability_quant_lcdr1_3_hcdr1_3

integer

Total count of liabilities identified across all VH and VL CDRs, only in SANGER/PacBio.

Biophysical Metric Fields

Field Name

Type

Description

cdr3_aa_1_charge

float

Net charge of chain_1 CDR3 at pH 7(e.g., LCDR3 if orientation is 5’ VL and 3’ VH).

cdr3_aa_2_charge

float

Net charge of chain_2 CDR3 at pH 7 (e.g., HCDR3 if orientation is 5’ VL and 3’ VH).

merged_cdrs_1_charge

float

Net charge of chain_1 CDR1-3 (e.g., LCDR1-3 if orientation is 5’ VL and 3’ VH).

merged_cdrs_2_charge

float

Net charge of chain_2 CDR1-3 (e.g., HCDR1-3 if orientation is 5’ VL and 3’ VH).

merged_cdrs_1_2_charge

float

Net charge of LCDR1-3 + HCDR1-3, only relevant to PacBio/SANGER sequencing.

cdr3_aa_1_hydropathy

float

Parker hydropathy of chain_1 CDR3 (e.g., LCDR3 if orientation is 5’ VL and 3’ VH).

cdr3_aa_2_hydropathy

float

Parker hydropathy of chain_2 CDR3 (e.g., HCDR3 if orientation is 5’ VL and 3’ VH).

merged_cdrs_1_hydropathy

float

Parker hydropathy of chain_1 CDR1-3 (e.g., LCDR1-3 if orientation is 5’ VL and 3’ VH).

merged_cdrs_2_hydropathy

float

Parker hydropathy of chain_2 CDR1-3 (e.g., HCDR1-3 if orientation is 5’ VL and 3’ VH).

merged_cdrs_1_2_hydropathy

float

Parker hydropathy LCDR1-3 + HCDR1-3, only relevant to PacBio/SANGER sequencing.

cdr3_aa_1_hydropathy

float

Parker hydropathy of chain_1 CDR3 (e.g., LCDR3 if orientation is 5’ VL and 3’ VH).

cdr3_aa_1_length

integer

Length of chain_1 CDR3 (e.g., LCDR3 if orientation is 5’ VL and 3’ VH).

cdr3_aa_2_length

integer

Length of chain_2 CDR3 (e.g., HCDR3 if orientation is 5’ VL and 3’ VH).

merged_cdrs_1_length

integer

Length of chain_1 CDR1-3 (e.g., LCDR1-3 if orientation is 5’ VL and 3’ VH).

merged_cdrs_2_length

integer

Length of chain_2 CDR1-3 (e.g., HCDR1-3 if orientation is 5’ VL and 3’ VH).

merged_cdrs_1_2_length

integer

Length LCDR1-3 + HCDR1-3, only relevant to PacBio/SANGER sequencing.

Identifier Fields

Field Name

Type

Description

id

string

If SANGER, will be a ‘:’ separated concatenated list of all sequences that match by given region of interest (default = ‘Full-Length, Including Framework’). If NGS, the ‘id’ contains the string ‘NGS’ + ‘sample_name’ + ‘barcode_group’ (e.g., ‘NGS-tri3-tri’).

sample_name

string

If NGS, is derived from the ‘barcode file’, if supplied, under the 1st column. This is used to identify the unique barcode population. If the dataset passes through any downstream processing that conducts enrichment calculation from two distinct populations, sample_name takes on single value from either the early (less_stringent) or late (more_stringent) round population. If SANGER, the sample_name takes on name ‘Sanger’, which should not be modified.

barcode_round

string

If NGS, this is derived from the ‘barcode file’, if supplied, under the 4th column. Takes on values of either ‘early, ‘late’, or ‘’. This field is used to assess enrichment from ‘early’ (less stringent) to ‘late’ (more stringent) rounds of selection by the ‘barcode_group’.

barcode_group

string

If NGS, this is derived from the ‘barcode file’, if supplied, under the 5th column. This is how individual populations are grouped together for enrichment or relative abundance calculations. If SANGER, the barcode_group will always be assigned the name “Sanger”, which should not be modified.

well_id

string

‘:’ separated concatenated string of all ‘id’ field values from SANGER that overlap to given NGS clone by the region of interest (ROI). Only relevant in context of SANGER.

seq_id

string

‘_’ separated string of the enumerated list of sequences by unique integer by sequence and the barcode_group, if the number of unique barcode_groups > 1 then it takes on value of unique_integer and barcode_group (e.g., 33_tri). If the number of barcode_groups <= 1 then it is assigned name unique integer + ‘empty’ (e.g., ‘21_nan’ or ‘21_id’). If barcode_group updatd by Modify Sample Name or Barcode Group FLOE, the seq_id is updated as well.

Overlap Fields of NGS to SANGER or NGS

Field Name

Type

Description

overlap_to_sanger

boolean

True/False indicates whether a given NGS sequence overlaps to SANGER.

overlap_to_ngs

boolean

True/False indicates whether a given SANGER (and NGS, but less relevant) sequence overlaps to NGS.

overlay_roi

string

If used in context of SANGER population this ROI reflects the overlap region of interest (ROI) used to map to SANGER populations (e.g., ‘CDR3 Chain_2 (Downstream Chain)’).

Enrichment, Abundance, and Relative Abundance Fields

Field Name

Type

Description

count

integer

Non-redundant VH+VL (PacBio) [VL or VH if Illumina] count of aa sequences by sample_name. If fold enrichment is calculated using ‘NGS Pipeline’ or ‘Enrichment and Relative Abundance Calculation’ then count takes on sum of the barcode.

processed_roi

string

Indicates the region of interest (ROI) that was processed for enrichment and clustering and different from overlay_roi.

count_roi_early

float

Early (less stringent) round region of interest (ROI) count or pseudo count as specified in ‘barcode_group’ and/or ‘barcode_round’, if specified, across the entire population otherwise (if given value found in ‘late’ but not in ‘early’, assigned a pseudo count calculated by min(‘late’ round roi count) / correction factor called the ‘Early Round Absence Penalty’).

count_roi_final

float

Late/Final (more stringent) round region of interest (ROI) count or pseudo count as specified in ‘barcode_group’ and/or ‘barcode_round’, or pseudo count, if specified, across the entire population otherwise (if given value found in ‘early’ but not in ‘late’, assigned a pseudo count calculated by min(‘early’ round roi count) / correction factor called the ‘Late Round Absence Penalty’).

percent_roi_early

float

Early (less stringent) round region of interest (ROI) relative abundance calculated by count_roi_early * 100 / sum(count_roi_early) using the barcode_group and/or barcode_round, if specified, or across entire population otherwise. Distinct full-length sequences sharing the same ROI will have the same value.

percent_roi_final

float

Late/Final (more stringent) round region of interest (ROI) relative abundance calculated by count_roi_final * 100 / sum(count_roi_final) using the barcode_group and/or barcode_round, if specified, or across entire population otherwise. Distinct full-length sequences sharing the same ROI will have the same value.

fold_enrichment_roi

float

Relative fold enrichment of the region of interest (ROI) calculated by percent_roi_final / percent_roi_early. Distinct full-length sequences sharing the same ROI will have the same value. Full-length sequences only keep a single copy of the full-length sequence from early or late. The relative enrichment by ROI, e.g., percent_roi_final and percent_roi_early, will be retained for each full-length, but results in reduced dataset relative to combined input.

log2_enrichment

float

log2(fold_enrichment_roi).

round_enrich

string

takes on value of ‘early’, ‘late’, or ‘both’. If assigned ‘early’ the given region of interest (ROI) is only found in early but not late and assigned a pseudo count for count_roi_late and percent_roi_late based on the correction factor ‘Early Round Absence Penalty’. If assigned ‘late’ the given ROI is only found in late but not early and assigned a pseudo count for count_roi_early and percent_roi_early based on the correction factor ‘Late Round Absence Penalty’. If assigned ‘both’ the given ROI is found in both rounds and no pseudo values assigned to early or late.

Scaffold / Germline Call Fields

Field Name

Type

Description

match_name_1

string

The scaffold of chain_1 (upstream/5’ chain) receiving the highest number of votes in either the specified species database (e.g., human, mouse, alpaca or rabbit) or, if provided, closest match to user-provided custom database file.

match_name_2

string

The scaffold of chain_2 (downstream/3’ chain) receiving the highest number of votes in either the specified species database (e.g., human, mouse, alpaca or rabbit) or, if provided, user provides the custom database file.

match_name_1_2

string

The scaffold of chain_1 and chain_2.

Clustering Fields

Annotation Fields

Field Name

Type

Description

read

string

DNA of the read from the NGS or SANGER source. If only AA sequence processed (SANGER), this field will contain AA not DNA.

fr1_1

string

DNA Framework 1 of the 5’ (upstream) chain (e.g., Light Chain Framework 1 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

fr1_aa_1

string

Amino Acid Framework 1 of the 5’ (upstream) chain (e.g., Light Chain Framework 1 if orientation is 5’ VL and 3’ VH).

cdr1_1

string

DNA CDR1 of the 5’ (upstream) chain (e.g., LCDR1 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

cdr1_aa_1

string

Amino Acid CDR1 of the 5’ (upstream) chain (e.g., LCDR1 if orientation is 5’ VL and 3’ VH).

fr2_1

string

DNA Framework 2 of the 5’ (upstream) chain (e.g., Light Chain Framework 2 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

fr2_aa_1

string

Amino Acid Framework 2 of the 5’ (upstream) chain (e.g., Light Chain Framework 2 if orientation is 5’ VL and 3’ VH).

cdr2_1

string

DNA CDR2 of the 5’ (upstream) chain (e.g., LCDR2 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

cdr2_aa_1

string

Amino Acid CDR2 of the 5’ (upstream) chain (e.g., LCDR2 if orientation is 5’ VL and 3’ VH).

fr3_1

string

DNA Framework 3 of the 5’ (upstream) chain (e.g., Light Chain Framework 3 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

fr3_aa_1

string

Amino Acid Framework 3 of the 5’ (upstream) chain (e.g., Light Chain Framework 3 if orientation is 5’ VL and 3’ VH).

cdr3_1

string

DNA CDR3 of the 5’ (upstream) chain (e.g., LCDR3 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

cdr3_aa_1

string

Amino Acid CDR3 of the 5’ (upstream) chain (e.g., LCDR3 if orientation is 5’ VL and 3’ VH).

fr4_1

string

DNA Framework 4 of the 5’ (upstream) chain (e.g., Light Chain Framework 4 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

fr4_aa_1

string

Amino Acid Framework 4 of the 5’ (upstream) chain (e.g., Light Chain Framework 4 if orientation is 5’ VL and 3’ VH).

cdr1_2

string

DNA CDR1 of the 3’ (downstream) chain (e.g., HCDR1 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

cdr1_aa_2

string

Amino Acid CDR1 of the 3’ (downstream) chain (e.g., HCDR1 if orientation is 5’ VL and 3’ VH).

cdr2_2

string

DNA CDR2 of the 3’ (downstream) chain (e.g., HCDR2 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

cdr2_aa_2

string

Amino Acid CDR2 of the 3’ (downstream) chain (e.g., HCDR2 if orientation is 5’ VL and 3’ VH).

cdr3_2

string

DNA CDR3 of the 3’ (downstream) chain (e.g., HCDR3 if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

cdr3_aa_2

string

Amino Acid CDR3 of the 3’ (downstream) chain (e.g., HCDR3 if orientation is 5’ VL and 3’ VH).

sequence_1

string

DNA of the 5’ (upstream) chain (e.g., Light Chain if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

sequence_aa_1

string

Amino Acid of the 5’ (upstream) chain (e.g., Light Chain if orientation is 5’ VL and 3’ VH).

sequence_2

string

DNA of the 3’ (downstream) chain (e.g., Heavy Chain if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

sequence_aa_2

string

Amino Acid of the 3’ (downstream) chain (e.g., Heavy Chain if orientation is 5’ VL and 3’ VH).

merged_cdrs_1

string

DNA of the 5’ (upstream) concatenated chain 1 CDRs (e.g., Light Chain if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

merged_cdrs_aa_1

string

Amino Acid of the 5’ (upstream) concatenated chain 1 CDRs (e.g., Light Chain if orientation is 5’ VL and 3’ VH).

merged_cdrs_2

string

DNA of the 3’ (downstream) concatenated chain 2 CDRs (e.g., Heavy Chain if orientation is 5’ VL and 3’ VH). If only AA sequence processed (SANGER), this field will contain AA not DNA.

merged_cdrs_aa_2

string

Amino Acid of the 3’ (downstream) concatenated chain 2 CDRs (e.g., Heavy Chain if orientation is 5’ VL and 3’ VH).

merged_cdrs_1_2

string

DNA of the 5’ and 3’ (upstream and downstream) concatenated chain 1+2 CDRs. If only AA sequence processed (SANGER), this field will contain AA not DNA.

merged_cdrs_aa_1_2

string

Amino Acid of the 5’ and 3’ (upstream and downstream) concatenated chain 1+2 CDRs.

Sequence Quality Fields

Field Name

Type

Description

votes_1

integer

IgMather annotation score for chain 1. Minimum number of matching K-mers for germline assignment. Increased numbers make the algorithm more stringent at the expense of not annotating some sequences (default is votes for DNA).

votes_2

integer

IgMather annotation score for chain 2. Minimum number of matching K-mers for germline assignment. Increased numbers make the algorithm more stringent at the expense of not annotating some sequences (default is votes for DNA).

functional_1

string

IgMather-based functionality assessment at the 5’ upstream, chain 1. Takes on values of ‘functional’, ‘truncation, ‘frame-shift’, or ‘stop-codon’. Looks for truncations (values below the ‘Minimum chain length’ threshold), frame-shifts (non-zero % modulus value across the VH and VL specified DNA sequence), and stop codons (translated dna resulting in stop codon).

functional_2

string

IgMather-based functionality assessment at the 3’ downstream, chain 2. Takes on values of ‘functional’, ‘truncation, ‘frame-shift’, or ‘stop-codon’. Looks for truncations (values below the ‘Minimum chain length’ threshold), frame-shifts (non-zero % modulus value across the VH and VL specified DNA sequence), and stop codons (translated dna resulting in stop codon).

sequence_issue

string

Downstream (post-igmatcher) functionality assessment for missing regions (e.g., no cdr1_aa_1 present) or aberrant letters (e.g., ‘X’).

Special Fields to Add to Upload (Use in Analyze Tool Only)

Field Name

Type

Description

on_rate

float

Any KD values can be included in a downloaded AbXtract Excel, CSV, or TSV if provided column name matches ‘on_rate’ (case-sensitive). This value is typically derived from kinetics binding experiment (e.g., SPR). The first phase in molecular interaction wherein binding occurs when analyte and ligand collide from diffusion. Occurs when the two molecules have appropriate orientation and sufficient energy to form the interaction. The rate ka describes rate of complex formation (number of complexes formed per second in a one molar solution of ligand and analyte) in units M^-1s^-1. This modified AbXtract file may be uploaded using the ‘Upload AbXtract Compatible File’ FLOE.

off_rate

float

Any KD values can be included in a downloaded AbXtract Excel, CSV, or TSV if provided column name matches ‘off_rate’ (case-sensitive). This value is typically derived from kinetics binding experiment (e.g., SPR). After binding the ligand and analyte remain bound, and when flow over surface of chip is replaced by buffer only, free concentration of analyte drops to zero and complex starts to dissociate at given rate. This describes the stability of the complex (fraction that decays per second) in units of s^-1. This modified AbXtract file may be uploaded using the ‘Upload AbXtract Compatible File’ FLOE.

KD

float

Any KD values can be included in a downloaded AbXtract Excel, CSV, or TSV if provided column name matches ‘KD’ (case-sensitive). This value is typically derived from kinetics binding experiment (e.g., SPR). After a long enough period for analyte binds to ligand a steady state is attained, with net rate of binding is zero. Kd is the dissociation equilibrium constant of kd/ka = KD and in unities of Molar concentration (M). This modified AbXtract file may be uploaded using the ‘Upload AbXtract Compatible File’ FLOE.

integer_field

int

Any integer values can be included in a downloaded AbXtract Excel, CSV, or TSV if provided column name matches ‘integer_field’ (case-sensitive). This modified AbXtract file may be uploaded using the ‘Upload AbXtract Compatible File’ FLOE.

float_field

float

Any float values can be included in a downloaded AbXtract Excel, CSV, or TSV if provided column name matches ‘float_field’ (case-sensitive). This modified AbXtract file may be uploaded using the ‘Upload AbXtract Compatible File’ FLOE.

string_field

string

Any string values can be included in a downloaded AbXtract Excel, CSV, or TSV if provided column name matches ‘string_field’ (case-sensitive). This modified AbXtract file may be uploaded using the ‘Upload AbXtract Compatible File’ FLOE.

bool_field

bool

Any bool (True/False) values can be included in a downloaded AbXtract Excel, CSV, or TSV if provided column name matches ‘bool_field’ (case-sensitive). This modified AbXtract file may be uploaded using the ‘Upload AbXtract Compatible File’ FLOE.