Improving the report from PTX

[ypriverol]

PTX is quite good for generating reports of MQ, we hope to get some ideas from there. The following metrics and styles will be good to be implemented:

• [ ] The Show Help button: a collapsable button that shows a minor description of the metric. (Figure 1). This can help the new users to understand the QC report and the metrics we are computing.
• [ ] The heatmap plot of general metrics for each mzML is quite nice and robust (Figure 2). These metrics can be computed with the qccalculator tool. The idea here is to have a list of metrics per mzML and then compute the heatmap.
• [ ] I think, we should add a section with corresponding subsections where we explore for each mzML file the corresponding metrics see in the repo from 1.3.11 - 1.3.14, 1.3.18, 1.3.19, 1.3.25,

Figure 1:

Figure 2:

[daichengxin]

Hi Yasset, I tested the qccalculator tool. But I found that most of the heat map metrics are not calculated in the tool. Can you check again ?

[daichengxin]

• [ ] [MSMS: MC]: the fraction (0% - 100%) of fully cleaved peptides per Raw file. This is the peptides with misscleavages = 0 / Total number of peptides.
• [ ] [EVD: Charge]: Deviation of the charge 2 proportion from a representative Raw file. Here, we need to check the number of spectra with charge state 2.
• [ ] [MS2 Scans: TopN high]: rewards if TopN was reached on a regular basis. I think we should be able to compute the TopN with qcalculator @mwalzer.
• [ ] [MS2 Scans: TopN over RT]: Rewards uniform (function Uniform) TopN events over time. @mwalzer ?
• [ ] Heatmap score [EVD: ID rate over RT]: Scored using ‘Uniform’ scoring function. It seems that we need to look at the source code of this report. Agree, @daichengxin we should check what means Uniform scoring function.
• [ ] [EVD: RT Peak Width]: Scored using BestKS function, i.e. the D statistic of a Kolmogoriv-Smirnoff test. It seems that we also need to look at the source code of this report.
• [ ] Heatmap score [MS2 Scans: Ion Inj Time]: Linear score as a fraction of MS/MS below the threshold. Note that this threshold needs customization depending on the instrument used (e.g., ITMS vs. FTMS). Where can I extract this information. I think the thresholds can be load from the R package.
• [ ] Heatmap score [MS2 Scans: Intensity]: Linear score (0-100%) between 3 < (TIC / base peak) < 10. we score the ratio BP 10 > TIC (this would be 100% score). If it’s only BP 3 < TIC, we say this MS/MS failed (0%). Anything between 3x and 10x gets a score in between. The score for the Raw file is computed as the median score across all its MS/MS scans. Can qcalculator be use to compute the TIC for each Scan? @qinchunyuan
• [ ] [EVD: MS2 Oversampling]: The percentage of non-oversampled 3D-peaks. @mwalzer
• [ ] [EVD: MS Cal Pre (20.0)]: the centeredness (function CenteredRef) of uncalibrated masses in relation to the search window size. Missing. It seems that we need to look at the source code of this report.
• [ ] [EVD: MS Cal-Post]: The variance and centeredness around zero of the calibrated distribution (function GaussDev). Missing
• [ ] [MSMS: MS2 Cal (Analyzer)]: rewards centeredness around 0 ppm/Da (function Centered). Missing
• [ ] [MS2 Scans: TopN ID over N]: Rewards uniform identification performance across all scan events.
• [ ] [EVD: Pep Missing]: Linear scale of the fraction of missing peptides. Can we compute this using one library based on mzTab.