Output

The output you can expect after running READ depends on the version of READ you are running (e.g. READ for Chimerys, READ for DIA-NN, etc.) and the input files - more specifically if you supply a resolution file from the Resolution GUI Tool or not.

Below you can find a breakdown of all version and input combinations.

Please note that columns containing a {reporter} placeholder exist once for every reporter (so in total 18-times) with reporters being:

Expand to show reporter labels!

TMTpro-126
TMTpro-127N
TMTpro-127C
TMTpro-128N
TMTpro-128C
TMTpro-129N
TMTpro-129C
TMTpro-130N
TMTpro-130C
TMTpro-131N
TMTpro-131C
TMTpro-132N
TMTpro-132C
TMTpro-133N
TMTpro-133C
TMTpro-134N
TMTpro-134C
TMTpro-135N

The Resolution GUI Tool output columns are:

Expand to show column names!

Resolution
TIC
126 Resolution
126 Intensity
126 Noise
127N Resolution
127N Intensity
127N Noise
127C Resolution
127C Intensity
127C Noise
128N Resolution
128N Intensity
128N Noise
128C Resolution
128C Intensity
128C Noise
129N Resolution
129N Intensity
129N Noise
129C Resolution
129C Intensity
129C Noise
130N Resolution
130N Intensity
130N Noise
130C Resolution
130C Intensity
130C Noise
131N Resolution
131N Intensity
131N Noise
131C Resolution
131C Intensity
131C Noise
132N Resolution
132N Intensity
132N Noise
132C Resolution
132C Intensity
132C Noise
133N Resolution
133N Intensity
133N Noise
133C Resolution
133C Intensity
133C Noise
134N Resolution
134N Intensity
134N Noise
134C Resolution
134C Intesntiy
134C Noise
135N Resolution
135N Intensity
135N Noise

Generated (Output) Files

The following (output) files will be generated by all READ versions:

• If a RAW file was provided as input, READ will download ThermoRawFileParser into your current working directory.
• If a RAW file was provided as input, READ will generate the corresponding .mzML file via ThermoRawFileParser.exe -i RAW_FILE in the RAW file directory.
• If quantification via OpenMS was selected (default), a corresponding .mzML.consensusXML file will be generated in the .mzML file directory.

READ for Chimerys DIA & READ for Chimerys DDA

The following output files will be generated by READ for Chimerys:

• {psm_table_name}_purity_tmt_quant.txt and
  {psm_table_name}_purity_tmt_quant.parquet:
  • The PSM table with annotated PSM quantities. Created in the same directory as the input PSM table.
  • The *.txt file is tab-delimited.
• {psm_table_name}_purity_tmt_quant_conditions.txt and
  {psm_table_name}_purity_tmt_quant_conditions.parquet:
  • The PSM table with annotated PSM quantities and condition based annotations. Created in the same directory as the input PSM table.
  • The *.txt file is tab-delimited.

If a protein table was provided, READ for Chimerys will also generate:

• {protein_table_name}_purity_tmt_quant.txt and
  {protein_table_name}_purity_tmt_quant.parquet:
  • The protein table with annotated protein quantities. Created in the same directory as the input protein table.
  • The *.txt file is tab-delimited.

NOTE

READ for Chimerys always creates both .txt and .parquet files with the same suffixes. Files with the same suffix but different file format extensions are always identical and only differ in file format!

READ for Spectronaut

The following output files will be generated by READ for Spectronaut:

• {main_report}_purity_tmt_quant.csv and
  {main_report}_purity_tmt_quant.parquet:
  • The main report with annotated precursor- and protein-level quantities. Created in the same directory as the input report.
  • The *.csv file is comma-delimited (,).

NOTE

READ for Spectronaut always creates both .csv and .parquet files with the same suffix. Files with the same suffix but different file format extensions are always identical and only differ in file format!

READ for DIA-NN

The following output file will be generated by READ for DIA-NN:

• {main_report}_purity_tmt_quant.parquet:
  • The main report with annotated precursor- and protein-level quantities. Created in the same directory as the input report.

Generated Columns with the Resolution GUI Tool Output

The following output will be produced by READ if a resolution file from the Resolution GUI Tool is provided.

---

READ for Chimerys DIA & READ for Chimerys DDA

PSM Table

Quantification:

• Annotated {reporter}:
  • PSM-level reporter quantification (noise subtracted if specified).

PSM statistics:

• Co-Isolation Purity:
  • Precursor co-isolation purity of the PSM.
• Parsed MS2 Scan Number:
  • The scan number of the MS2 scan that the PSM was associated with.

Condition statistics:

• Condition_S_{condition}:
  • Total signal for condition {condition},
    e.g. sum of all signal for each reporter in the condition, guaranteed to be a float.
• Condition_N_{condition}:
  • Total noise for condition {condition},
    e.g. sum of all noise for each reporter in the condition, guaranteed to be a float.
• Condition_SN_{condition}:
  • Total signal-to-noise for condition {condition},
    e.g. Condition_S_{condition} divided by Condition_N_{condition}, guaranteed to be a float.

Annotated Resolution GUI Tool columns:

• RESGUI_{colname}:
  • Annotated Resolution GUI Tool columns from the resolution file, where {colname} is the column name of each column in the file.

Protein Table

Quantification:

• Annotated protein-level {reporter}:
  • Protein-level aggregated reporter quantification after filtering.
• Annotated protein-level {reporter} (unfiltered):
  • Protein-level aggregated reporter quantification without filtering.

Reporter statistics per protein:

• Annotated mean {reporter} S (unfiltered):
  • Annotated mean reporter signal for the protein considering all {reporter} reporters, may be NaN.
• Annotated mean {reporter} S (filtered):
  • Annotated mean reporter signal for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated median {reporter} S (unfiltered):
  • Annotated median reporter signal for the protein considering all {reporter} reporters, may be NaN.
• Annotated median {reporter} S (filtered):
  • Annotated median reporter signal for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated min {reporter} S (unfiltered):
  • Annotated minimum reporter signal for the protein considering all {reporter} reporters, may be NaN.
• Annotated min {reporter} S (filtered):
  • Annotated minimum reporter signal for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated max {reporter} S (unfiltered):
  • Annotated maximum reporter signal for the protein considering all {reporter} reporters, may be NaN.
• Annotated max {reporter} S (filtered):
  • Annotated maximum reporter signal for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated mean {reporter} S/N (unfiltered):
  • Annotated mean reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated mean {reporter} S/N (filtered):
  • Annotated mean reporter signal-to-noise for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated median {reporter} S/N (unfiltered):
  • Annotated median reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated median {reporter} S/N (filtered):
  • Annotated median reporter signal-to-noise for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated min {reporter} S/N (unfiltered):
  • Annotated minimum reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated min {reporter} S/N (filtered):
  • Annotated minimum reporter signal-to-noise for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated max {reporter} S/N (unfiltered):
  • Annotated maximum reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated max {reporter} S/N (filtered):
  • Annotated maximum reporter signal-to-noise for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated mean {reporter} resolution (unfiltered):
  • Annotated mean reporter resolution for the protein considering all {reporter} reporters, may be NaN.
• Annotated mean {reporter} resolution (filtered):
  • Annotated mean reporter resolution for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated median {reporter} resolution (unfiltered):
  • Annotated median reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated median {reporter} resolution (filtered):
  • Annotated median reporter resolution for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated min {reporter} resolution (unfiltered):
  • Annotated minimum reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated min {reporter} resolution (filtered):
  • Annotated minimum reporter resolution for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated max {reporter} resolution (unfiltered):
  • Annotated maximum reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated max {reporter} resolution (filtered):
  • Annotated maximum reporter resolution for the protein considering only {reporter} reporters that pass filtering, may be NaN.

PSM/Precursor statistics per protein:

• Annotated mean purity:
  • Mean precursor co-isolation purity of all precursors associated with the protein, may be NaN.
• Annotated median purity:
  • Median precursor co-isolation purity of all precursors associated with the protein, may be NaN.
• Annotated number of PSMs (unfiltered):
  • Total number of PSMs per protein, always a positive integer or zero.
• Annotated number of PSMs (filtered):
  • Number of PSMs per protein that pass filtering, always a positive integer or zero.

---

READ for Spectronaut & READ for DIA-NN

Main Report

Quantification:

• Annotated {reporter}:
  • Precursor-level reporter quantification (noise subtracted if specified).
• Annotated protein-level {reporter}:
  • Protein-level aggregated reporter quantification after filtering.
• Annotated protein-level {reporter} (unfiltered):
  • Protein-level aggregated reporter quantification without filtering.

Precursor statistics:

• Co-Isolation Purity:
  • Precursor co-isolation purity.
• Parsed MS2 Scan Number:
  • The scan number of the MS2 scan that the precursor was associated with.

Condition statistics:

• Condition_S_{condition}:
  • Total signal for condition {condition},
    e.g. sum of all signal for each reporter in the condition, guaranteed to be a float.
• Condition_N_{condition}:
  • Total noise for condition {condition},
    e.g. sum of all noise for each reporter in the condition, guaranteed to be a float.
• Condition_SN_{condition}:
  • Total signal-to-noise for condition {condition},
    e.g. Condition_S_{condition} divided by Condition_N_{condition}, guaranteed to be a float.

Annotated Resolution GUI Tool columns:

• RESGUI_{colname}:
  • Annotated Resolution GUI Tool columns from the resolution file, where {colname} is the column name of each column in the file.

Reporter statistics per protein:

• Annotated mean {reporter} S (unfiltered):
  • Annotated mean reporter signal for the protein considering all {reporter} reporters, may be NaN.
• Annotated mean {reporter} S (filtered):
  • Annotated mean reporter signal for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated median {reporter} S (unfiltered):
  • Annotated median reporter signal for the protein considering all {reporter} reporters, may be NaN.
• Annotated median {reporter} S (filtered):
  • Annotated median reporter signal for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated min {reporter} S (unfiltered):
  • Annotated minimum reporter signal for the protein considering all {reporter} reporters, may be NaN.
• Annotated min {reporter} S (filtered):
  • Annotated minimum reporter signal for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated max {reporter} S (unfiltered):
  • Annotated maximum reporter signal for the protein considering all {reporter} reporters, may be NaN.
• Annotated max {reporter} S (filtered):
  • Annotated maximum reporter signal for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated mean {reporter} S/N (unfiltered):
  • Annotated mean reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated mean {reporter} S/N (filtered):
  • Annotated mean reporter signal-to-noise for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated median {reporter} S/N (unfiltered):
  • Annotated median reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated median {reporter} S/N (filtered):
  • Annotated median reporter signal-to-noise for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated min {reporter} S/N (unfiltered):
  • Annotated minimum reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated min {reporter} S/N (filtered):
  • Annotated minimum reporter signal-to-noise for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated max {reporter} S/N (unfiltered):
  • Annotated maximum reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated max {reporter} S/N (filtered):
  • Annotated maximum reporter signal-to-noise for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated mean {reporter} resolution (unfiltered):
  • Annotated mean reporter resolution for the protein considering all {reporter} reporters, may be NaN.
• Annotated mean {reporter} resolution (filtered):
  • Annotated mean reporter resolution for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated median {reporter} resolution (unfiltered):
  • Annotated median reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated median {reporter} resolution (filtered):
  • Annotated median reporter resolution for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated min {reporter} resolution (unfiltered):
  • Annotated minimum reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated min {reporter} resolution (filtered):
  • Annotated minimum reporter resolution for the protein considering only {reporter} reporters that pass filtering, may be NaN.
• Annotated max {reporter} resolution (unfiltered):
  • Annotated maximum reporter signal-to-noise for the protein considering all {reporter} reporters, may be NaN.
• Annotated max {reporter} resolution (filtered):
  • Annotated maximum reporter resolution for the protein considering only {reporter} reporters that pass filtering, may be NaN.

Precursor statistics per protein:

• Annotated mean purity:
  • Mean precursor co-isolation purity of all precursors associated with the protein, may be NaN.
• Annotated median purity:
  • Median precursor co-isolation purity of all precursors associated with the protein, may be NaN.
• Annotated number of PSMs (unfiltered):
  • Total number of precursors (here denoted as PSMs) per protein, always a positive integer or zero.
• Annotated number of PSMs (filtered):
  • Number of precursors (here denoted as PSMs) per protein that pass filtering, always a positive integer or zero.

Protein filtering:

• Filter:Is_Ambiguous_PG: If the protein group is ambiguous, e.g. contains more than one protein,
  only available if config.PROTEIN.keep_ambiguous_protein_groups = false.

---

Generated Columns without the Resolution GUI Tool Output

The following output will be produced by READ if a resolution file from the Resolution GUI Tool is NOT provided.

---

READ for Chimerys DIA & READ for Chimerys DDA

PSM Table

Quantification:

• Annotated {reporter}:
  • PSM-level reporter quantification.

PSM statistics:

• Co-Isolation Purity:
  • Precursor co-isolation purity of the PSM.
• Parsed MS2 Scan Number:
  • The scan number of the MS2 scan that the PSM was associated with.

Protein Table

Quantification:

• Annotated protein-level {reporter}:
  • Protein-level aggregated reporter quantification after filtering.
• Annotated protein-level {reporter} (unfiltered):
  • Protein-level aggregated reporter quantification without filtering.

PSM/Precursor statistics per protein:

• Annotated mean purity:
  • Mean precursor co-isolation purity of all precursors associated with the protein, may be NaN.
• Annotated median purity:
  • Median precursor co-isolation purity of all precursors associated with the protein, may be NaN.
• Annotated number of PSMs (unfiltered):
  • Total number of PSMs per protein, always a positive integer or zero.
• Annotated number of PSMs (filtered):
  • Number of PSMs per protein that pass filtering, always a positive integer or zero.

The following columns will be created but all values will be NaN and can be ignored:

Expand to show column names!

Annotated mean {reporter} S (unfiltered)
Annotated mean {reporter} S (filtered)
Annotated median {reporter} S (unfiltered)
Annotated median {reporter} S (filtered)
Annotated min {reporter} S (unfiltered)
Annotated min {reporter} S (filtered)
Annotated max {reporter} S (unfiltered)
Annotated max {reporter} S (filtered)
Annotated mean {reporter} S/N (unfiltered)
Annotated mean {reporter} S/N (filtered)
Annotated median {reporter} S/N (unfiltered)
Annotated median {reporter} S/N (filtered)
Annotated min {reporter} S/N (unfiltered)
Annotated min {reporter} S/N (filtered)
Annotated max {reporter} S/N (unfiltered)
Annotated max {reporter} S/N (filtered)
Annotated mean {reporter} resolution (unfiltered)
Annotated mean {reporter} resolution (filtered)
Annotated median {reporter} resolution (unfiltered)
Annotated median {reporter} resolution (filtered)
Annotated min {reporter} resolution (unfiltered)
Annotated min {reporter} resolution (filtered)
Annotated max {reporter} resolution (unfiltered)
Annotated max {reporter} resolution (filtered)

---

READ for Spectronaut & READ for DIA-NN

Main Report

Quantification:

• Annotated {reporter}:
  • PSM-level reporter quantification.
• Annotated protein-level {reporter}:
  • Protein-level aggregated reporter quantification after filtering.
• Annotated protein-level {reporter} (unfiltered):
  • Protein-level aggregated reporter quantification without filtering.

Precursor statistics:

• Co-Isolation Purity:
  • Precursor co-isolation purity.
• Parsed MS2 Scan Number:
  • The scan number of the MS2 scan that the precursor was associated with.

Precursor statistics per protein:

• Annotated mean purity:
  • Mean precursor co-isolation purity of all precursors associated with the protein, may be NaN.
• Annotated median purity:
  • Median precursor co-isolation purity of all precursors associated with the protein, may be NaN.
• Annotated number of PSMs (unfiltered):
  • Total number of precursors (here denoted as PSMs) per protein, always a positive integer or zero.
• Annotated number of PSMs (filtered):
  • Number of precursors (here denoted as PSMs) per protein that pass filtering, always a positive integer or zero.

Protein filtering:

• Filter:Is_Ambiguous_PG: If the protein group is ambiguous, e.g. contains more than one protein,
  only available if config.PROTEIN.keep_ambiguous_protein_groups = false.

The following columns will be created but all values will be NaN and can be ignored:

Expand to show column names!

Annotated mean {reporter} S (unfiltered)
Annotated mean {reporter} S (filtered)
Annotated median {reporter} S (unfiltered)
Annotated median {reporter} S (filtered)
Annotated min {reporter} S (unfiltered)
Annotated min {reporter} S (filtered)
Annotated max {reporter} S (unfiltered)
Annotated max {reporter} S (filtered)
Annotated mean {reporter} S/N (unfiltered)
Annotated mean {reporter} S/N (filtered)
Annotated median {reporter} S/N (unfiltered)
Annotated median {reporter} S/N (filtered)
Annotated min {reporter} S/N (unfiltered)
Annotated min {reporter} S/N (filtered)
Annotated max {reporter} S/N (unfiltered)
Annotated max {reporter} S/N (filtered)
Annotated mean {reporter} resolution (unfiltered)
Annotated mean {reporter} resolution (filtered)
Annotated median {reporter} resolution (unfiltered)
Annotated median {reporter} resolution (filtered)
Annotated min {reporter} resolution (unfiltered)
Annotated min {reporter} resolution (filtered)
Annotated max {reporter} resolution (unfiltered)
Annotated max {reporter} resolution (filtered)