Logo QCeltis

Introduction

Welcome to your QCeltis Quality Control Analysis Report! We are pleased to present to you a visual QC summary of your dataset. Representing high-dimensional omics data using plots helps us view large amounts of information at once to identifying patterns and trends across your samples and datasets. The QCeltis package monitors metrics based on the input datasets provided. For any concerns about or suggestions to improve this report, let the team know at GroupHeartBioinformaticsSupport@cshs.org, and we will consider your feedback. We are happy to support your computational needs.

The report is divided into 2 tabs:

  • ID-Free - When a mzML directory is provided as input, ID-Free Tab is populated with plots from ID-Free parameters extracted from your mzML files.
  • ID-Based - When a protein, peptide or precursor level intensity file is provided, ID-based Tab will be populated with ID-based parameters extracted from your quantified input.
{% if mzml_dir %}

ID-Free Metrics

The following ID-Free metrics have been extracted from the provided mzML files. Given thresholds have been applied and outlier analysis has been performed. If no outliers were found, outlier plots will not be plotted. If a grouping file was provided, additional groupwise plots will be included.

{% endif %} {% if total_ion_current %}

Total Ion Current

{{ tic_ms_plot_description }}

{{ tic_plot | safe }} {% if tic_ms1_outlier_plot or tic_ms2_outlier_plot %}
TIC Outliers
{% endif %} {% if tic_ms1_outlier_plot %}

MS1 TIC is expected to be consistent across replicate quality control samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with data acquisition and LC-MS instrument performance such as improper autosampler sample pickup. Please check the specific samples listed below.

{{ tic_ms1_outlier_plot | safe }}

{{ tic_ms1_outlier_description }}

{% endif %} {% if tic_ms2_outlier_plot %}

MS2 TIC is expected to be consistent across replicate quality control samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with data acquisition and LC-MS instrument performance such as improper autosampler sample pickup. Please check the specific samples listed below.

{{ tic_ms2_outlier_plot | safe }}

{{ tic_ms2_outlier_description }}

{% endif %} {% if groupwise_comparison %}
Groupwise TIC CV%

{{ tic_ms_cv_description }}

{% if tic_ms1_cv_plot %} {{ tic_ms1_cv_plot | safe }}

{{ tic_ms1_cv_description }}

{% endif %} {% if tic_ms2_cv_plot %} {{ tic_ms2_cv_plot | safe }}

{{ tic_ms2_cv_description }}

{% endif %} {% endif %}
{% endif %}
{% if ms2_ms1_spectral_ratio %}

Spectral Ratio

{% if ms2_ms1_spectral_ratio_plot %}

The number of spectra recorded in each mzML file is extracted. The spectral ratio represents the number of MS2 Spectra over the number of MS1 Spectra found in each file.

{{ ms2_ms1_spectral_ratio_plot | safe }} {% endif %} {% if ms2_ms1_spectral_ratio_outlier_plot %}
Spectral Ratio Outliers

MS2/MS1 Spectra Ratio is expected to be consistent across replicate quality control samples. Any outliers detected are highlighted in yellow. Outliers detected point to an issue with the mass spectrometry instrument performance. Please check experiment protocols for your instrument.

{{ ms2_ms1_spectral_ratio_outlier_plot | safe }}

{{ ms2_ms1_spectral_ratio_outlier_description }}

{% endif %}
{% endif %} {% if max_basepeak_intensity %}

Max Base Peak Intensity

The base peak intensity is the recorded intensity of the most intense peak from each spectrum in the mzML file. The Max Base Peak Intensity represents the highest recorded base peak intensity in each mzML file.

{% if max_basepeak_intensity_plot %} {{ max_basepeak_intensity_plot | safe }} {% endif %} {% if max_basepeak_intensity_outlier_plot %}
Max Base Peak Intensity Outliers

Max Base Peak Intensity is expected to be consistent across replicate quality control samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with data acquisition or instrument performance such as sample pickup or samples being dried out. Please check the specific samples listed below.

{{ max_basepeak_intensity_outlier_plot | safe }}

{{ max_basepeak_intensity_outlier_description }}

{% endif %}
{% endif %}

ID-Based Metrics

The following ID-Based metrics have been calculated and derived from the input search results that were provided. Given input thresholds have been applied and if grouping file was provided, additional groupwise plots will be included.


{% if protein_file %}

Protein Quantification

{% if protein_quant_plot %}

{{ protein_quant_description }}

{{ protein_quant_plot | safe }} {% endif %}
{% endif %} {% if peptide_file %}

Peptide Quantification

{% if peptide_quant_plot %}

{{ peptide_quant_description }}

{{ peptide_quant_plot | safe }} {% endif %}
{% endif %} {% if precursor_file %}

Precursor Quantification

{% if precursor_quant_plot %}

{{ precursor_quant_description }}

{{ precursor_quant_plot | safe }} {% endif %}
{% endif %}
{% if protein_file or peptide_file or precursor_file %}

Intensity CV% Cumulative Frequency

{% if cumulative_frequency_plot %}

{{ cumulative_frequency_description }}

{{ cumulative_frequency_plot | safe }} {% endif %}
{% endif %} {% if protein_file and groupwise_comparison %}

Percentage of Proteins Under CV%

{% if percentage_proteins_undercv_plot %}

{{ percentage_proteins_undercv_description }}

{{ percentage_proteins_undercv_plot | safe }} {% endif %}
{% endif %} {% if peptide_file and groupwise_comparison %}

Percentage of Peptides Under CV%

{% if percentage_peptides_undercv_plot %}

{{ percentage_peptides_undercv_description }}

{{ percentage_peptides_undercv_plot | safe }} {% endif %}
{% endif %} {% if precursor_file and groupwise_comparison %}

Percentage of Precursors Under CV%

{% if percentage_precursors_undercv_plot %}

{{ percentage_precursors_undercv_description }}

{{ percentage_precursors_undercv_plot | safe }} {% endif %}
{% endif %}
{% if protein_file and groupwise_comparison %}

PCA for Protein Intensities

{% if protein_pca_plot %}

{{ protein_pca_description }}

{{ protein_pca_plot | safe }} {% endif %}
{% endif %} {% if peptide_file and groupwise_comparison %}

PCA for Peptide Intensities

{% if peptide_pca_plot %}

{{ peptide_pca_description }}

{{ peptide_pca_plot | safe }} {% endif %}
{% endif %} {% if precursor_file and groupwise_comparison %}

PCA for Precursor Intensities

{% if precursor_pca_plot %}

{{ precursor_pca_description }}

{{ precursor_pca_plot | safe }} {% endif %}
{% endif %}
{% if peptide_file %}

Common Peptide TIC

{% if common_peptide_tic_plot %}

{{ common_peptide_tic_description }}

{{ common_peptide_tic_plot | safe }} {% endif %} {% if groupwise_comparison %}

Common Peptide TIC Group CV%

{{ common_peptide_tic_group_cv_description }}

{{ common_peptide_tic_group_cv | safe }} {% endif %}
{% endif %} {% if precursor_file %}

Common Precursor TIC

{% if common_precursor_tic_plot %}

{{ common_precursor_tic_description }}

{{ common_precursor_tic_plot | safe }} {% endif %} {% if groupwise_comparison %}

Common Precursor TIC Group CV%

{{ common_precursor_tic_group_cv_description }}

{{ common_precursor_tic_group_cv | safe }} {% endif %}
{% endif %}
{% if peptide_file or precursor_file %}

No Miscleavages Percentage

{% if percent_miscleavage_plot %}

{{ percent_miscleavage_description }}

{{ percent_miscleavage_plot | safe }} {% endif %}
{% endif %}
{% if irt_plots %}

iRT Intensity Distribution

{% if irt_intensity_plot %}

{{ irt_intensity_description }}

{{ irt_intensity_plot | safe }} {% endif %} {% if irt_intensity_coverage_plot %}

{{ irt_coverage_description }}

{{ irt_intensity_coverage_plot | safe }} {% endif %}
{% endif %} {% if peptide_list %}

Selected Peptide Distribution

{{ selected_peptide_intensity_description }}

{% if selected_peptide_intensity_plot %} {{ selected_peptide_intensity_plot | safe }} {% endif %} {% if selected_peptide_intensity_coverage_plot %} {{ selected_peptide_intensity_coverage_plot | safe }} {% endif %}
{% endif %}