## {{analysis.name}}

MS1 Mass Accuracy: {{analysis.parameters.mass_error_tolerance * (10 ** 6)}} PPM
Grouping Tolerance: {{analysis.parameters.grouping_error_tolerance * (10 ** 6)}} PPM
MSn Mass Accuracy: {{analysis.parameters.fragment_error_tolerance * (10 ** 6)}} PPM
Minimum `q`-Value For Clustering: {{analysis.parameters.psm_fdr_threshold}}
MSn Scoring Model: {%- if analysis.parameters.tandem_scoring_model is is_type %} {{analysis.parameters.tandem_scoring_model.__name__}} {%- else %} {{analysis.parameters.tandem_scoring_model.__class__.__name__}} {%- endif %}
{% if 'fdr_estimation_strategy' in analysis.parameters %} FDR Strategy: {{analysis.parameters.fdr_estimation_strategy.name}} {% endif %}
Glycopeptide Hypothesis: {{hypothesis.name}}

{% if "fasta_file" in hypothesis.parameters %}
- FASTA File: {{hypothesis.parameters['fasta_file']}}
{% elif "mzid_file" in hypothesis.parameters %}
- mzIdentML File: {{hypothesis.parameters['mzid_file']}}
{% endif %} {% if "enzymes" in hypothesis.parameters %}
- Enzymes: {{hypothesis.parameters['enzymes'] | unique | join(", ")}}
{% endif %} {% if 'constant_modifications' in hypothesis.parameters%}
- Constant Modifications

{% for modrule in hypothesis.parameters['constant_modifications'] %} {% for rule_text in modrule | modification_specs %}
- {{rule_text}}
{% endfor %} {% endfor %}

{% endif %} {% if 'variable_modifications' in hypothesis.parameters%}
- Variable Modifications

{% for modrule in hypothesis.parameters['variable_modifications'] %} {% for rule_text in modrule | modification_specs %}
- {{rule_text}}
{% endfor %} {% endfor %}

{% endif %}

Sample Searched: {{sample_run.name}}
{% if renderer.fdr_estimator is not none %}
{% for panel in renderer.fdr_estimator_plot() %} {{panel | safe}} {% endfor %}
{%- endif %} {% if renderer.retention_time_model is not none %}

Width Range | Mean Interval Error | R2
--- | --- | ---
{{ "%0.3f" % renderer.retention_time_model.width_range.lower }} - {{ "%0.3f" % renderer.retention_time_model.width_range.upper }} minutes | {{ "%0.3f" % renderer.retention_time_model.interval_padding }} | {{ "%0.3f" % renderer.retention_time_model.R2() }}

{% for panel in renderer.retention_time_model_plot() %} {{panel | safe}} {% endfor %}
{%- endif %}

Protein | Matched Glycopeptides
--- | ---
{% for row in protein_index %}
{{row.protein_name}} | {{row.identified_glycopeptide_count}}
{% endfor %}

{% for i, glycoprotein in glycoprotein_iterator %}
0 %} style='display: none;' {% endif %} >
{% include "protein-heading.templ" %} {% if not use_dynamic_display_mode or (use_dynamic_display_mode and glycoprotein.identified_glycopeptides|length > 1) %}
{{renderer.draw_glycoforms(glycoprotein)}}
{% endif %} {% include "glycopeptide-table.templ" %}
{% for site_type, axis in renderer.site_specific_abundance_plots(glycoprotein).items() %}
{{axis|safe}}
{% endfor %}
{% for glycopeptide in glycoprotein.identified_glycopeptides|sort(reverse=True, attribute='-q_value,ms2_score') %} {% include "glycopeptide-detail-entry.templ" %} {% endfor %}
{% endfor %}