Summary

MaxQuant Search Summary

MaxQuant Search Summary

MaxQuant Version: 1.6.7.0, 11

Search Date: 04/12/2020 23:09:48, 9

FASTA File: /home/huffman.r/FASTA/SwissProt_human_09042017.fasta, 1

Experiment Map

Map of raw file names to short names

MaxQuant Parameters

MaxQuant Search Parameters

MaxQuant Experiment Summary

MaxQuant experiment summary statistics

Chromatography

Elution profile: FWHM

Plotting the distrution of elution profile widths at half the maximum intensity value for each peak.

Identification frequency across gradient

Plotting the frequency of peptide identification across the chromatographic gradient.

Retention length of peptides at base

Plotting the retention length of identified peptide peaks at the base.

Ion Sampling

Apex Offset

Plotting the distance from the peak of the elution profile the MS2 events were executed.

MS1 Intensity for identified ions

Plotting the MS1 intensity for all identified ions across runs.

MS1 Intensity for z>1 ions

Plotting the MS1 intensity for all peptide-like ions observed (not necessarily sent to MS2) across runs.

MS1 Intensity for identified ions in common

Plotting the MS1 intensity for all common identified ions across runs.

MS1 Intensity for all ions

Plotting the MS1 intensity for all ions observed (not necessarily sent to MS2) across runs.

Injection times, PSM resulting

Plotting distribution of injection times for MS2 events that did result in a PSM.

Injection times, no PSM resulting

Plotting distribution of injection times for MS2 events that did not result in a PSM.

Peptide Identifications

Miscleavage rate

Plotting frequency of peptide miscleavages.

Miscleavage rate percentage

Percentages of missed cleavages - measure the efficiency of protein digest

Number of Confident Identifications

Plotting the number of peptides identified at each given confidence level.

Precursor Ion Fraction (PIF)

The distribution of PIFs for identified peptides across all sets, where PIF is a measure of coisolation (1 = pure, 0 = impure).

Fractional ID Rate

Fractional rate of confident PSMs and PSMs from all MS2 scan events

Total ID Rate

Number of MSMS scans, PSMs, and confident PSMs

Contamination

Number of ions by charge state

Plotting the frequency of charge states observed. This will give an if you are seeing mostly peptides or non-peptide species

TIC of ions by charge state

Plotting the TIC of charge states observed. This will give an idea if you are seeing mostly peptides or non-peptide species

MS1 Intensity, +1 ions

Plotting the intensity distribution of +1 ions, a diagnostic of non-peptide contaminants

m/z Distribution for +1 ions

Plotting the m/z distribution of +1 ions, a diagnostic of non-peptide contaminants

Intensity of z=1 across gradient

Plotting the intensity of z=1 ions observed. This will give an if you are seeing mostly peptides or non-peptide species and where they occur in the gradient

SCoPE-MS Diagnostics

Fraction of Missing Data per TMT Channel

This plot displays the fraction of missing values per reporter ion per run per TMT channel, reported as 0 by MaxQuant.

Reporter Ion Intensities vs. Carrier Intensities

Comparing the reporter ion intensities for all TMT channels to the carrier channel, chosen automatically as the most intense channel (median intensity).

## [1] "Plot failed to render. Reason: Error: Please select a single experiment\n"

Reporter ion intensity

Plotting the TMT reporter intensities for a single run.

## [1] "Plot failed to render. Reason: Error: All arguments must be named\n"

Relative reporter ion intensity

Plotting the TMT reporter intensities for a single run, normalized by the channel with the highest mean reporter ion intensity.

## [1] "Plot failed to render. Reason: Error: Please select a single experiment\n"

Reporter ion channel correlations

Plotting all pairwise TMT reporter ion intensity channel correlations (Pearson) for a single run.

## [1] "Plot failed to render. Reason: Error: Please select a single experiment\n"

DART-ID

Error Probability Update

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.

## [1] "Plot failed to render. Reason: Error: Provide evidence.txt from DART-ID output, with updated dart_PEP column. Visit https://dart-id.slavovlab.net/ for more information about DART-ID\n"

Increase in Confident PSMs

Fold-change increase of PSMs at given confidence thresholds (in this case, FDR thresholds)

## [1] "Plot failed to render. Reason: Error: Provide evidence.txt from DART-ID output, with updated dart_PEP column.  Visit https://dart-id.slavovlab.net/ for more information about DART-ID\n"

RT Alignment Error

Alignment Error (Predicted RT - Observed RT) for the RT Alignment in DART-ID

## [1] "Plot failed to render. Reason: Error: Provide evidence.txt from DART-ID output, with residual RT column [residual]. Visit https://dart-id.slavovlab.net/ for more information about DART-ID\n"

Peptide Identification Increase by Experiment

Increased number of peptide IDs per experiment, relative to existing IDs before DART-ID

## [1] "Plot failed to render. Reason: Error: Provide evidence.txt from DART-ID output, with updated dart_PEP column. Visit https://dart-id.slavovlab.net/ for more information about DART-ID\n"

Fractional ID Rate

Fractional rate of confident PSMs and PSMs from all MS2 scan events

## [1] "Plot failed to render. Reason: Error: Provide evidence.txt from DART-ID output, with updated dart_PEP column. Visit https://dart-id.slavovlab.net/ for more information about DART-ID\n"

Total ID Rate

Number of MSMS scans, PSMs, and confident PSMs

## [1] "Plot failed to render. Reason: Error: Provide evidence.txt from DART-ID output, with updated dart_PEP column. Visit https://dart-id.slavovlab.net/ for more information about DART-ID\n"