MaxQuant Search Summary
MaxQuant Version: 1.6.17.0
Search Date: 04/08/2022 15:24:34
FASTA File: C:/Users/slavovlab/Desktop/AndrewsnPOP_FASTA_v2.fasta
Map of raw file names to short names
MaxQuant Search Parameters
MaxQuant experiment summary statistics
Plotting the distrutions of elution profile widths at half the maximum intensity value for the top ions with max intensity > 8e5.
Plotting the distrution of elution profile widths at half the maximum intensity value for all observed ions.
Plotting the frequency of peptide identification across the chromatographic gradient.
Plotting the retention length of identified peptide peaks at the base.
Plotting the distance from the peak of the elution profile the MS2 events were executed.
Plotting the MS1 intensity for all identified ions across runs.
Plotting the MS1 intensity for all peptide-like ions observed (not necessarily sent to MS2) across runs.
Plotting the precursor intensity for peptides identified in all experiments, normalized to the first experiment
Plotting the MS1 intensity for precursors identified at any level of confidence in all loaded experiments
Plotting the MS1 intensity for all ions observed (not necessarily sent to MS2).
Plotting distribution of MS2 injection times for scans that did result in a PSM.
Plotting distribution of MS2 scans per PSM.
Plotting distribution of MS2 injection times for scans that did not result in a PSM.
Plotting the distributions of MS1 fill times for scans with total ion current greater than the 80th percentile of total ion currents.
Plotting MS2 scans per duty cycle over the active gradient, defined as retention time of first and last confidently IDd peptides (PEP < 0.01).
Identification rate (peptides identified at PEP < 0.01 / all scans) faceted by duty cycle scan order and duty cycle length
Plotting frequency of miscleavages in confidently identified peptides.
Miscleavage rate (percentage) for peptides identified with confidence PEP < 0.01
Plotting the number of peptides identified at each given confidence level.
The distribution of PIFs for identified peptides across all experiments, where PIF is a measure of coisolation (1 = pure, 0 = impure).
Fractional ID rate by binned by MS1 intensity
Fractional rate of confident PSMs and PSMs from all MS2 scan events
Number of MSMS scans, PSMs, and confident PSMs
2D Densities of PSM error probabilities, given by MaxQuant (Spectra) and DART-ID. Points below the 45 degree line indicate boosted confidence (and lowered error probability), and vice versa for above the 45 degree line. Set the PEP slider to 1 to see all PSMs regardless of initial confidence.
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Fold-change increase of PSMs at given confidence thresholds (in this case, FDR thresholds)
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Alignment Error (Predicted RT - Observed RT) for the RT Alignment in DART-ID
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Increased number of peptide IDs per experiment, relative to existing IDs before DART-ID
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Fractional rate of confident PSMs and PSMs from all MS2 scan events
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Number of MSMS scans, PSMs, and confident PSMs
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Number of ions observed during MS1 scans by charge state
Plotting the summed precursor intensity by charge state.
Plotting the intensity distribution of +1 ions.
Plotting the m/z distribution of +1 ions.
Plotting the intensity of z=1 ions observed.
Plotting the intensity of z=1 ions observed.
This plot displays the fraction of missing values per reporter ion per run per TMT channel, reported as 0 by MaxQuant.
This plot displays the intensity of reporter ion per run per TMT channel.
rRI defined as each channel divided by the carrier channel. Carrier channel defined as channel with max median intensity. Plotting the ratio of the mean relative reporter ion signal for miss-cleaved peptides / the same for well-cleaved peptides
Plotting the mean reporter ion intensity for all channels but the carrier. Carrier channel determined as channel with max median intensity.
rRI defined as each channel divided by the carrier channel. Carrier channel defined as channel with max median intensity. Plotting the ratio of the mean relative reporter ion signal for hydrophilic peptides / the same for hydrophobic peptides.
Plotting spearman correlation of carrier channel to all other channels. Carrier channel determined as channel with max median reporter ion intensity.
Plotting the mean reporter ion intensity for spiked in peptides. Carrier channel determined as channel with max median intensity.
Reporter Ion Intensities vs. Carrier Intensities {.plot-title}
Comparing the reporter ion intensities for all TMT channels to the carrier channel, chosen automatically as the most intense channel (median intensity).
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Reporter ion channel spearman correlations {.plot-title}
Plotting all pairwise TMT reporter ion intensity channel correlations (Spearman) for a single run.
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Comparing relative rates of IDs for peptides with, or without the TMT tag. Only compatible with searches performed with TMT as a variable mod (n-terminus and on lysine)
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Labeled / unlabeled precursor ion intensity. Only compatible with searches performed with TMT as a variable mod.
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Percentages of missed cleavages for confidently identified peptides (PEP < 0.01). Efficiency <20% desirable.
Miscleavage rate at arginine and lysine for peptides filtered to PEP < 0.01