{% import 'tablemacro.j2' as tm %} Lehtio proteomics QC report

Full QC for {{ searchname }}

Completed on {{ completedate }}


Software

Pipeline DOI: 10.5281/zenodo.3548311 (resolves to latest version)
{{ software}}

Warnings

{% if warnings|length %}
    {% for warn in warnings %}
  • • {{ warn }}
  • {% endfor %}
{% else %}
No warnings
{% endif %}

Protein/peptide level QC

Summary

{{ tm.table(sumtable, tablefieldtitles) }}

Overlap

{% for feat in overlap %}
{{ featnames[feat] }}
{{ tm.table(overlap[feat], tablefieldtitles) }}
{% endfor %}

{% if ptm_summary %}

PTMs

Summary
{{ tm.table(ptmfeatc_summary, ptmtabletitles) }} {% if ptmoverlap %}
Overlap
{{ tm.table(ptmoverlap, ptmtabletitles) }} {% endif %}
PTM site count
{{ tm.table(ptm_summary, ptmtabletitles) }}

{% endif %} {% if normfacs %}

Median centered isobaric normalization factors

{% for feat in normfacs %}
{{ featnames[feat] }}
{{ tm.table(normfacs[feat], tablefieldtitles) }}
{% endfor %}

{% endif %} {% for graphtype in ["featyield", "precursorarea", "isobaric", "normfactors", "nrpsms", "nrpsmsoverlapping", "percentage_onepsm", "ms1nrpeps", "deqms", "pca"] %} {% if graphtype in features['peptides'] or ('proteins' in features and graphtype in features['proteins']) %}

{{ titles[graphtype] }}

{% for feat in features %}
{{ featnames[feat] }}
{{ features[feat][graphtype] }}
{% endfor %}

{% endif %} {% endfor %}
{% if 'proteins' in features %}

Overall protein coverage

{{ features.proteins.coverage }}

{% endif %} {% if ptms|length %} {% include 'ptmqc.j2' %} {% endif %}

PSM level QC

{% if frac == 'frac' %}
{% for graph in psms %}
{{ titles[graph] }}
{{ psms[graph] }}
{% endfor %}
{% else %} {% for graph in psms %}
{{ titles[graph] }}
{{ psms[graph] }} {% endfor %} {% endif %}
{% for graph in ppsms[firstplate] %}

{{ titles[graph] }}

{% for plate, graphs in ppsms|dictsort %}
Plate: {{ plate }}
{{ ppsms[plate][graph] }}
{% endfor %}
{% endfor %}