Merge pull request #138 from bigbio/dev

minor changes in the comments

Author: ypriverol

pmultiqc/modules/quantms/quantms.py

@@ -833,15 +833,22 @@ def draw_ms_information(self):
                 name="MS1 Information",
                 anchor="ms1_information",
                 description="#### MS1 quality control information extracted from the spectrum files",
-                helptext="This plot displays Total Ion Chromatograms (TICs) derived from MS1 scans across all analyzed samples. The x-axis represents retention time, and the y-axis shows the total ion intensity at each time point. Each colored trace corresponds to a different sample."
-                "The TIC provides a global view of the ion signal throughout the LC-MS/MS run, reflecting when compounds elute from the chromatography column. Key aspects to assess include:"
-                "1. Overall intensity pattern: A consistent baseline and similar peak profiles across samples indicate good reproducibility."
-                "2. Major peak alignment: Prominent peaks appearing at similar retention times suggest stable chromatographic performance."
-                "3. Signal-to-noise ratio: High peaks relative to baseline noise reflect better sensitivity."
-                "4. Chromatographic resolution: Sharp, well-separated peaks indicate effective separation."
-                "5. Signal drift: A gradual decline in signal intensity across the run may point to source contamination or chromatography issues."
-                ""
-                "Deviations such as shifted retention times, missing peaks, or inconsistent intensities may signal problems in sample preparation, LC conditions, or mass spectrometer performance that require further investigation.",
+                helptext="""
+                This plot displays Total Ion Chromatograms (TICs) derived from MS1 scans across all analyzed samples. 
+                The x-axis represents retention time, and the y-axis shows the total ion intensity at each time point. 
+                Each colored trace corresponds to a different sample. The TIC provides a global view of the ion signal
+                throughout the LC-MS/MS run, reflecting when compounds elute from the chromatography column. 
+                Key aspects to assess include:
+                
+                * Overall intensity pattern: A consistent baseline and similar peak profiles across samples indicate good reproducibility.
+                * Major peak alignment: Prominent peaks appearing at similar retention times suggest stable chromatographic performance.
+                * Signal-to-noise ratio: High peaks relative to baseline noise reflect better sensitivity.
+                * Chromatographic resolution: Sharp, well-separated peaks indicate effective separation.
+                * Signal drift: A gradual decline in signal intensity across the run may point to source contamination or chromatography issues.
+                
+                Deviations such as shifted retention times, missing peaks, or inconsistent intensities may signal problems 
+                in sample preparation, LC conditions, or mass spectrometer performance that require further investigation.
+                """,
                 plot=ms1_tic_html,
             )
 
@@ -857,14 +864,16 @@ def draw_ms_information(self):
             ms1_bpc_html = linegraph.plot(self.ms1_bpc, ms1_bpc_config)
             self.add_section(
                 description="#### MS1 base peak chromatograms extracted from the spectrum files",
-                helptext="The Base Peak Chromatogram (BPC) displays the intensity of the most abundant ion at each retention"
-                         " time point across your LC-MS run. Unlike the Total Ion Chromatogram (TIC) which shows the summed"
-                         " intensity of all ions, the BPC highlights the strongest signals, providing better visualization"
-                         " of compounds with high abundance while reducing baseline noise. This makes it particularly useful"
-                         " for identifying major components in complex samples, monitoring dominant species, and providing"
-                         " clearer peak visualization when signal-to-noise ratio is a concern. Comparing BPC patterns across"
-                         " samples allows you to evaluate consistency in the detection of high-abundance compounds"
-                         " and can reveal significant variations in sample composition or instrument performance.",
+                helptext="""
+                         The Base Peak Chromatogram (BPC) displays the intensity of the most abundant ion at each retention
+                         time point across your LC-MS run. Unlike the Total Ion Chromatogram (TIC) which shows the summed
+                         intensity of all ions, the BPC highlights the strongest signals, providing better visualization
+                         of compounds with high abundance while reducing baseline noise. This makes it particularly useful
+                         for identifying major components in complex samples, monitoring dominant species, and providing
+                         clearer peak visualization when signal-to-noise ratio is a concern. Comparing BPC patterns across
+                         samples allows you to evaluate consistency in the detection of high-abundance compounds
+                         and can reveal significant variations in sample composition or instrument performance.
+                         """,
                 plot=ms1_bpc_html,
             )
 
@@ -880,25 +889,28 @@ def draw_ms_information(self):
             ms1_peaks_html = linegraph.plot(self.ms1_peaks, ms1_peaks_config)
             self.add_section(
                 description="""#### MS1 Peaks from the spectrum files""",
-                helptext="This plot shows the number of peaks detected in MS1 scans over the course of each sample run."
-                         " The x-axis represents retention time (in minutes), while the y-axis displays the number of"
-                         " distinct ion signals (peaks) identified in each MS1 scan. The MS1 peak count reflects spectral"
-                         " complexity and provides insight into instrument performance during the LC-MS analysis."
-                         " Key aspects to consider include:"
-                         " 1. Overall pattern: Peak counts typically increase during the elution of complex mixtures and"
-                         " decrease during column washing or re-equilibration phases."
-                         " 2. Peak density: Higher counts suggest more complex spectra, potentially indicating a greater"
-                         " number of compounds present at that time point."
-                         " 3. Peak Consistency across samples: Similar profiles among replicates or related samples"
-                         " indicate good analytical reproducibility."
-                         " 4. Sudden drops: Abrupt decreases in peak count may point to transient ionization issues,"
-                         " spray instability, or chromatographic disruptions."
-                         " 5. Baseline values: The minimum peak count observed reflects the level of background noise"
-                         " or instrument sensitivity in the absence of eluting compounds."
-                         ""
-                         " Monitoring MS1 peak counts complements total ion chromatogram (TIC) and base peak chromatogram"
-                         " (BPC) data, offering an additional layer of quality control related to signal complexity,"
-                         " instrument stability, and sample composition.",
+                helptext="""
+                         This plot shows the number of peaks detected in MS1 scans over the course of each sample run.
+                         The x-axis represents retention time (in minutes), while the y-axis displays the number of
+                         distinct ion signals (peaks) identified in each MS1 scan. The MS1 peak count reflects spectral
+                         complexity and provides insight into instrument performance during the LC-MS analysis.
+                         Key aspects to consider include:
+                         
+                         * Overall pattern: Peak counts typically increase during the elution of complex mixtures and
+                         decrease during column washing or re-equilibration phases.
+                         * Peak density: Higher counts suggest more complex spectra, potentially indicating a greater
+                         number of compounds present at that time point."
+                         * Peak Consistency across samples: Similar profiles among replicates or related samples
+                         indicate good analytical reproducibility.
+                         * Sudden drops: Abrupt decreases in peak count may point to transient ionization issues,
+                         spray instability, or chromatographic disruptions.
+                         * Baseline values: The minimum peak count observed reflects the level of background noise
+                         or instrument sensitivity in the absence of eluting compounds.
+                         
+                         Monitoring MS1 peak counts complements total ion chromatogram (TIC) and base peak chromatogram
+                         (BPC) data, offering an additional layer of quality control related to signal complexity,
+                         instrument stability, and sample composition.
+                         """,
                 plot=ms1_peaks_html,
             )
 
@@ -912,13 +924,15 @@ def draw_ms_information(self):
             table_html = table.plot(self.ms1_general_stats, pconfig=tconfig)
             self.add_section(
                 description="#### General stats for MS1 information extracted from the spectrum files",
-                helptext="This table presents general statistics for MS1 information extracted from mass spectrometry data files."
-                         " It displays MS runs with their acquisition dates and times."
-                         " For each file, the table shows two key metrics: TotalCurrent (the sum of all MS1 ion intensities throughout the run) and ScanCurrent (the sum of MS2 ion intensities)."
-                         " These values provide a quick overview of the total ion signals detected during both survey scans (MS1) and fragmentation scans (MS2),"
-                         " allowing for comparison of overall signal intensity across samples. Consistent TotalCurrent and ScanCurrent values across similar samples typically"
-                         " indicate good reproducibility in the mass spectrometry analysis, while significant variations may suggest issues with sample preparation,"
-                         " instrument performance, or ionization efficiency. The blue shading helps visualize the relative intensity differences between samples.",
+                helptext="""
+                         This table presents general statistics for MS1 information extracted from mass spectrometry data files."
+                         It displays MS runs with their acquisition dates and times.
+                         For each file, the table shows two key metrics: TotalCurrent (the sum of all MS1 ion intensities throughout the run) and ScanCurrent (the sum of MS2 ion intensities).
+                         These values provide a quick overview of the total ion signals detected during both survey scans (MS1) and fragmentation scans (MS2),
+                         allowing for comparison of overall signal intensity across samples. Consistent TotalCurrent and ScanCurrent values across similar samples typically
+                         indicate good reproducibility in the mass spectrometry analysis, while significant variations may suggest issues with sample preparation,
+                         instrument performance, or ionization efficiency. The blue shading helps visualize the relative intensity differences between samples.
+                         """,
                 plot=table_html,
             )