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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.31

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-09-13, 05:49 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data

        pmultiqc

        pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, and DIA-NN.URL: https://github.com/bigbio/pmultiqc

        Experimental Design and Metadata

        Experimental Design

        This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.
        You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html
        Showing 3/3 rows and 3/3 columns.
        Sample NameBioReplicateFractionTecReplicate
         
        4_1_2450        		1
         
         ↳ 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450        		11
         
        5_1_2451        		1
         
         ↳ 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A5_1_2451        		11
         
        6_1_2452        		1
         
         ↳ 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A6_1_2452        		11

        Parameters

        This table presents the parameters used in MaxQuant.
        MaxQuant parameters, extracted from parameters.txt, summarizes the settings used for the MaxQuant analysis. Key parameters are MaxQuant version, Re-quantify, Match-between-runs and mass search tolerances. A list of protein database files is also provided, allowing to track database completeness and database version information (if given in the filename).
        Showing 124/124 rows and 2/2 columns.
        No.ParameterValue
        1
        Version
        2.7.2.0
        2
        User name
        wviegener
        3
        Machine name
        supercube005
        4
        Date of writing
        08/10/2025 20:51:04
        5
        Include contaminants
        True
        6
        PSM FDR
        0.0
        7
        PSM FDR Crosslink
        0.0
        8
        Protein FDR
        0.0
        9
        Site FDR
        0.0
        10
        Use Normalized Ratios For Occupancy
        True
        11
        Min. peptide Length
        7
        12
        Min. score for unmodified peptides
        0
        13
        Min. score for modified peptides
        40
        14
        Min. delta score for unmodified peptides
        0
        15
        Min. delta score for modified peptides
        6
        16
        Min. unique peptides
        0
        17
        Min. razor peptides
        1
        18
        Min. peptides
        1
        19
        Use only unmodified peptides and
        True
        20
        Modifications included in protein quantification
        Oxidation (M);Acetyl (Protein N-term)
        21
        Peptides used for protein quantification
        Razor
        22
        Discard unmodified counterpart peptides
        True
        23
        Label min. ratio count
        2
        24
        Use delta score
        False
        25
        iBAQ
        False
        26
        iBAQ log fit
        False
        27
        Match between runs
        False
        28
        Find dependent peptides
        False
        29
        Fasta file
        UP000005640_9606.fasta;UP000005640_9606_additional.fasta;UP000006548_3702.fasta;UP000006548_3702_additional.fasta
        30
        Decoy mode
        revert
        31
        Advanced ratios
        True
        32
        Fixed andromeda index folder
        nan
        33
        Second peptides
        True
        34
        Stabilize large LFQ ratios
        True
        35
        Separate LFQ in parameter groups
        False
        36
        Require MS/MS for LFQ comparisons
        True
        37
        Calculate peak properties
        False
        38
        Main search max. combinations
        200
        39
        Advanced site intensities
        True
        40
        Write msScans table
        False
        41
        Write msmsScans table
        True
        42
        Write ms3Scans table
        True
        43
        Write allPeptides table
        False
        44
        Write mzRange table
        True
        45
        Write DIA fragments table
        False
        46
        Write DIA fragments quant table
        False
        47
        Write pasefMsmsScans table
        True
        48
        Write accumulatedMsmsScans table
        True
        49
        Max. peptide mass [Da]
        4600
        50
        Min. peptide length for unspecific search
        8
        51
        Max. peptide length for unspecific search
        25
        52
        Razor protein FDR
        True
        53
        Disable MD5
        False
        54
        Max mods in site table
        3
        55
        Match unidentified features
        False
        56
        Epsilon score for mutations
        True
        57
        Evaluate variant peptides separately
        True
        58
        Variation mode
        nan
        59
        MS/MS tol. (FTMS)
        20 ppm
        60
        Top MS/MS peaks per Da interval. (FTMS)
        12
        61
        Da interval. (FTMS)
        100
        62
        MS/MS deisotoping (FTMS)
        True
        63
        MS/MS deisotoping tolerance (FTMS)
        7
        64
        MS/MS deisotoping tolerance unit (FTMS)
        ppm
        65
        MS/MS higher charges (FTMS)
        True
        66
        MS/MS water loss (FTMS)
        True
        67
        MS/MS water loss (FTMS for cross link)
        False
        68
        MS/MS ammonia loss (FTMS)
        True
        69
        MS/MS ammonia loss (FTMS for cross link)
        False
        70
        MS/MS dependent losses (FTMS)
        True
        71
        MS/MS recalibration (FTMS)
        False
        72
        MS/MS tol. (ITMS)
        0.5 Da
        73
        Top MS/MS peaks per Da interval. (ITMS)
        8
        74
        Da interval. (ITMS)
        100
        75
        MS/MS deisotoping (ITMS)
        False
        76
        MS/MS deisotoping tolerance (ITMS)
        0.1
        77
        MS/MS deisotoping tolerance unit (ITMS)
        Da
        78
        MS/MS higher charges (ITMS)
        True
        79
        MS/MS water loss (ITMS)
        True
        80
        MS/MS water loss (ITMS for cross link)
        False
        81
        MS/MS ammonia loss (ITMS)
        True
        82
        MS/MS ammonia loss (ITMS for cross link)
        False
        83
        MS/MS dependent losses (ITMS)
        True
        84
        MS/MS recalibration (ITMS)
        False
        85
        MS/MS tol. (TOF)
        25 ppm
        86
        Top MS/MS peaks per Da interval. (TOF)
        16
        87
        Da interval. (TOF)
        100
        88
        MS/MS deisotoping (TOF)
        True
        89
        MS/MS deisotoping tolerance (TOF)
        0.0
        90
        MS/MS deisotoping tolerance unit (TOF)
        Da
        91
        MS/MS higher charges (TOF)
        True
        92
        MS/MS water loss (TOF)
        True
        93
        MS/MS water loss (TOF for cross link)
        False
        94
        MS/MS ammonia loss (TOF)
        True
        95
        MS/MS ammonia loss (TOF for cross link)
        False
        96
        MS/MS dependent losses (TOF)
        True
        97
        MS/MS recalibration (TOF)
        False
        98
        MS/MS tol. (ASTRAL)
        25 ppm
        99
        Top MS/MS peaks per Da interval. (ASTRAL)
        16
        100
        Da interval. (ASTRAL)
        100
        101
        MS/MS deisotoping (ASTRAL)
        True
        102
        MS/MS deisotoping tolerance (ASTRAL)
        0.0
        103
        MS/MS deisotoping tolerance unit (ASTRAL)
        Da
        104
        MS/MS higher charges (ASTRAL)
        True
        105
        MS/MS water loss (ASTRAL)
        True
        106
        MS/MS water loss (ASTRAL for cross link)
        False
        107
        MS/MS ammonia loss (ASTRAL)
        True
        108
        MS/MS ammonia loss (ASTRAL for cross link)
        False
        109
        MS/MS dependent losses (ASTRAL)
        True
        110
        MS/MS recalibration (ASTRAL)
        False
        111
        MS/MS tol. (UNKNOWN)
        20 ppm
        112
        Top MS/MS peaks per Da interval. (UNKNOWN)
        12
        113
        Da interval. (UNKNOWN)
        100
        114
        MS/MS deisotoping (UNKNOWN)
        True
        115
        MS/MS deisotoping tolerance (UNKNOWN)
        7
        116
        MS/MS deisotoping tolerance unit (UNKNOWN)
        ppm
        117
        MS/MS higher charges (UNKNOWN)
        True
        118
        MS/MS water loss (UNKNOWN)
        True
        119
        MS/MS water loss (UNKNOWN for cross link)
        False
        120
        MS/MS ammonia loss (UNKNOWN)
        True
        121
        MS/MS ammonia loss (UNKNOWN for cross link)
        False
        122
        MS/MS dependent losses (UNKNOWN)
        True
        123
        MS/MS recalibration (UNKNOWN)
        False
        124
        Site tables
        nan

        Identification Summary

        Number of Peptides identified Per Protein

        This plot shows the number of peptides per protein in the MaxQuant data.
        This statistic is extracted from the proteinGroups.txt file. Proteins supported by more peptide identifications can constitute more confident results.
        Created with MultiQC

        ProteinGroups Count

        [Excludes Contaminants] Number of Protein groups (after FDR) per Raw file.
        If MBR was enabled, three categories ('Genuine (Exclusive)', 'Genuine + Transferred', 'Transferred (Exclusive)' are shown, so the user can judge the gain that MBR provides. Here, 'Transferred (Exclusive)' means that this protein group has peptide evidence which originates only from transferred peptide IDs. The quantification is (of course) always from the local Raw file. Proteins in the 'Genuine + Transferred' category have peptide evidence from within the Raw file by MS/MS, but at the same time also peptide IDs transferred to this Raw file using MBR were used. It is not unusual to see the 'Genuine + Transferred' category be the rather large, since a protein group usually has peptide evidence from both sources. To see of MBR worked, it is better to look at the two MBR-related metrics. If MBR would be switched off, you can expect to see the number of protein groups corresponding to 'Genuine (Exclusive)' + 'Genuine + Transferred'. In general, if the MBR gain is low and the MBR scores are bad (see the two MBR-related metrics), MBR should be switched off for the Raw files which are affected (could be a few or all).
        Created with MultiQC

        Peptide ID Count

        [Excludes Contaminants] Number of unique (i.e. not counted twice) peptide sequences including modifications (after FDR) per Raw file.
        If MBR was enabled, three categories ('Genuine (Exclusive)', 'Genuine + Transferred', 'Transferred (Exclusive)' are shown, so the user can judge the gain that MBR provides. Peptides in the 'Genuine + Transferred' category were identified within the Raw file by MS/MS, but at the same time also transferred to this Raw file using MBR. This ID transfer can be correct (e.g. in case of different charge states), or incorrect -- see MBR-related metrics to tell the difference. Ideally, the 'Genuine + Transferred' category should be rather small, the other two should be large. If MBR would be switched off, you can expect to see the number of peptides corresponding to 'Genuine (Exclusive)' + 'Genuine + Transferred'. In general, if the MBR gain is low and the MBR scores are bad (see the two MBR-related metrics), MBR should be switched off for the Raw files which are affected (could be a few or all).
        Created with MultiQC

        Contaminants

        Top5 Contaminants Per Raw File

        The five most abundant external protein contaminants by Raw file
        pmultiqc will explicitly show the five most abundant external protein contaminants (as detected via MaxQuant's contaminants FASTA file) by Raw file, and summarize the remaining contaminants as 'other'. This allows to track down which proteins exactly contaminate your sample. Low contamination is obviously better. If you see less than 5 contaminants, it either means there are actually less, or that one (or more) of the shortened contaminant names subsume multiple of the top5 contaminants (since they start with the same prefix).
        Created with MultiQC

        Potential Contaminants Per File

        Potential contaminants per group from proteinGroups.txt.
        External protein contamination should be controlled for, therefore MaxQuant ships with a comprehensive, yet customizable protein contamination database, which is searched by MaxQuant by default. A contamination plot derived from the proteinGroups (PG) table, showing the fraction of total protein intensity attributable to contaminants. Note that this plot is based on experimental groups, and therefore may not correspond 1:1 to Raw files.
        Created with MultiQC

        Quantification Analysis

        Intensity Distribution

        Intensity boxplots by experimental groups. Groups are user-defined during MaxQuant configuration. This plot displays a (customizable) threshold line for the desired mean intensity of proteins. Groups which underperform here, are likely to also suffer from a worse MS/MS id rate and higher contamination due to the lack of total protein loaded/detected. If possible, all groups should show a high and consistent amount of total protein. The height of the bar correlates to the number of proteins with non-zero abundance.
        Created with MultiQC

        LFQ Intensity Distribution

        Label-free quantification (LFQ) intensity boxplots by experimental groups.
        Label-free quantification (LFQ) intensity boxplots by experimental groups. Groups are user-defined during MaxQuant configuration. This plot displays a (customizable) threshold line for the desired mean of LFQ intensity of proteins. Raw files which underperform in *Raw* intensity, are likely to show an *increased* mean here, since only high-abundance proteins are recovered and quantifyable by MaxQuant in this Raw file. The remaining proteins are likely to receive an LFQ value of 0 (i.e. do not contribute to the distribution). The height of the bar correlates to the number of proteins with non-zero abundance.
        Created with MultiQC

        Peptide Intensity Distribution

        Peptide precursor intensity per Raw file from evidence.txt WITHOUT match-between-runs evidence.
        Peptide precursor intensity per Raw file from evidence.txt WITHOUT match-between-runs evidence. Low peptide intensity usually goes hand in hand with low MS/MS identifcation rates and unfavourable signal/noise ratios, which makes signal detection harder. Also instrument acquisition time increases for trapping instruments. Failing to reach the intensity threshold is usually due to unfavorable column conditions, inadequate column loading or ionization issues. If the study is not a dilution series or pulsed SILAC experiment, we would expect every condition to have about the same median log-intensity (of 2%1.1f). The relative standard deviation (RSD) gives an indication about reproducibility across files and should be below 5%%.
        Created with MultiQC

        PCA of Raw Intensity

        [Excludes Contaminants] Principal components plots of experimental groups (as defined during MaxQuant configuration).
        This plot is shown only if more than one experimental group was defined. If LFQ was activated in MaxQuant, an additional PCA plot for LFQ intensities is shown. Similarly, if iTRAQ/TMT reporter intensities are detected. Since experimental groups and Raw files do not necessarily correspond 1:1, this plot cannot use the abbreviated Raw file names, but instead must rely on automatic shortening of group names.
        Created with MultiQC

        PCA of LFQ Intensity

        [Excludes Contaminants] Principal components plots of experimental groups (as defined during MaxQuant configuration).
        This plot is shown only if more than one experimental group was defined. If LFQ was activated in MaxQuant, an additional PCA plot for LFQ intensities is shown. Similarly, if iTRAQ/TMT reporter intensities are detected. Since experimental groups and Raw files do not necessarily correspond 1:1, this plot cannot use the abbreviated Raw file names, but instead must rely on automatic shortening of group names.
        Created with MultiQC

        Peptides Quantification Table

        This plot shows the quantification information of peptides in the final result (evidence.txt).
        The quantification information of peptides is obtained from the evidence.txt. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms. Contaminants have been removed from the data by filtering using the 'Potential contaminant' field. * BestSearchScore: maximum score (Andromeda score). * Average Intensity: Average intensity of each peptide sequence (0 or NA ignored).
        Showing 50/50 rows and 4/4 columns.
        PeptideIDProtein NamePeptide SequenceBest Search ScoreAverage Intensity
        1
        P36578;H3BM89;H3BU31
        AAAAAAALQAK
        161.1800
        4.4932
        2
        Q8WUQ7-2;Q8WUQ7
        AAAAALSQQQSLQER
        63.7890
        2.4939
        3
        A0A182DWI4;E9PN30;Q9BQE4
        AAAAVEPDVVVK
        84.0580
        2.6657
        4
        Q8WWH5
        AAAAVVAAAAR
        47.1370
        2.5108
        5
        O95159
        AAADSDPNLDPLMNPHIR
        80.8750
        2.4607
        6
        Q6P2E9;Q6P2E9-2;I3L2F4
        AAADTLQGPMQAAYR
        80.8820
        3.2962
        7
        E9PQY2;Q9NQP4
        AAAEDVNVTFEDQQK
        104.5400
        3.4109
        8
        O15357
        AAAEELLAR
        63.7880
        3.3416
        9
        P30260;P30260-2
        AAAEGLMSLLR
        88.8620
        3.2454
        10
        Q01780;Q01780-2
        AAAEQAISVR
        136.0100
        3.1720
        11
        A0A8V8TLM6;P02786;A0A8V8TM41;G3V0E5;A0A8V8TLN0;A0A8V8TM46;A0A8V8TN37
        AAAEVAGQFVIK
        125.8900
        3.8313
        12
        P07954-2;P07954;A0A804HI24;A0A804HKE6
        AAAEVNQDYGLDPK
        156.2100
        3.7888
        13
        Q9Y490
        AAAFEEQENETVVVK
        101.9600
        3.1901
        14
        O94826
        AAAFEQLQK
        125.8900
        3.6887
        15
        Q96L58
        AAAFLAVLVASAPR
        60.0260
        2.3909
        16
        Q9H9Y2;X6R7Q1
        AAAFPPGFSISEIK
        56.6810
        2.8300
        17
        Q9BQG0;Q9BQG0-2;I3L1L3
        AAAFQHLLLLVGIHLLK
        116.3400
        3.2287
        18
        Q96S52;K7EN97
        AAAGAAATHLEVAR
        60.1310
        2.8166
        19
        P35221-2;P35221;G3XAM7;E5RIB1;E5RG03;E5RGY6;E5RJ41;E5RHV7
        AAAGEFADDPCSSVK
        91.0600
        3.2960
        20
        Q96C19;H0Y4Y4
        AAAGELQEDSGLCVLAR
        123.9300
        3.6631
        21
        Q9H3U1;A0A1W2PNX8;Q9H3U1-2;Q9H3U1-3
        AAAGGLAMLTSMR
        131.8900
        3.4807
        22
        G5EA36;I3L328
        AAAGLMSLLR
        78.2960
        3.1183
        23
        A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37
        AAAIGIDLGTTYSCVGVFQHGK
        131.8800
        3.7363
        24
        Q8TAE8
        AAALAAAVAQDPAASGAPSS
        81.0880
        3.0420
        25
        Q8IYS1
        AAALASGCTVEIK
        138.1200
        3.4165
        26
        A0A8I5QKQ8;O15269;A0A8I5KUM4;A0A2R8Y4S0;A0A2R8Y6A2;O15269-2
        AAALASLKK
        64.9040
        2.4581
        27
        Q14008;Q14008-3;Q14008-2
        AAALATVNAWAEQTGMK
        103.8000
        2.9852
        28
        Q8N0Z6
        AAALDPAWPEPR
        81.1860
        2.8836
        29
        P31948;P31948-2;P31948-3;H0YGI8
        AAALEAMK
        79.2700
        3.0417
        30
        P31948;P31948-2;P31948-3;H0YGI8
        AAALEAMKDYTK
        111.9800
        3.1725
        31
        P31948;P31948-2;F5H783;F5GXD8
        AAALEFLNR
        146.8700
        4.2265
        32
        P31948;P31948-2;F5H783;F5GXD8
        AAALEFLNRFEEAK
        100.9500
        3.1519
        33
        Q13423;A0A590UJM2;A0A590UK29;E9PCX7;A0A590UJI3
        AAALEQFK
        81.4080
        3.1788
        34
        Q13470;Q13470-2;I3L334
        AAALSGGLLSDPELQR
        62.9320
        2.7468
        35
        O60716;O60716-21;O60716-10;O60716-9;O60716-13;O60716-2;O60716-3;C9JZR2;A0A669KB05;O60716-11;H0YC95;O60716-19;O60716-5;O60716-17;O60716-18;A0A669KB62;O60716-8;O60716-7;O60716-14;O60716-6;O60716-24;O60716-12;O60716-23;O60716-4;O60716-15;O60716-16;O60716-20;O60716-22;O60716-26;O60716-29;O60716-25;O60716-27;O60716-30;O60716-28;O60716-31;O60716-32;A0A804HK15;A0A804HIL4
        AAALVLQTIWGYK
        153.8000
        3.5405
        36
        A0A3B3IRK3;A0A8V8TQQ2;A0A8V8TQP7;H7C5F7;A0A8V8TQ43;A0A8V8TRG3;B4DGY6;A0A8V8TQN7;A0A8V8TRH3;A0A0C4DGW0;A0A8V8TQN2;A0A8V8TQM3;Q9NV92
        AAAMAAAAAETSQR
        83.7650
        2.8485
        37
        Q14498-2;Q14498;Q14498-3;G3XAC6;A0A0U1RQH7;H0Y4X3
        AAAMANNLQK
        85.7110
        3.3252
        38
        A0A8J9AUI2;Q15042;Q15042-4
        AAAMTPPEEELKR
        43.6000
        2.9106
        39
        C9JRZ6;Q9NX63;A0A286YEX5;F8WAR4
        AAANEQLTR
        84.2000
        2.7965
        40
        A0A286YFD6;P31350;P31350-2;A0A7P0SBL1
        AAAPGVEDEPLLR
        74.4660
        3.6212
        41
        P53618;E9PP73
        AAAQCYIDLIIK
        131.8800
        3.4922
        42
        D6RGI3;D6RER5;Q9NVA2;Q9NVA2-2;H0Y961;H0Y9G8
        AAAQLLQSQAQQSGAQQTK
        50.7610
        2.4474
        43
        O14981
        AAAQQLGEVVK
        95.5110
        2.9890
        44
        O95801
        AAAQYYLGNFR
        110.8600
        3.4352
        45
        A0A8I5QJC9;A0A8I5KY07;A0A8I5KRP1;A0A8I5KRK1;A0A8I5KYQ0;A0A8I5KZB3;Q9H2M9;A0A8I5KWJ9;A0A8I5QJG4;A0A8I5KUS2
        AAASGNENIQPPPLAYK
        69.3470
        3.0709
        46
        Q9P1Y5;Q9P1Y5-2
        AAASLAWVLR
        84.6830
        2.7828
        47
        Q5JPU2;P08559;P08559-2;P08559-4;P08559-3
        AAASTDYYK
        63.1510
        3.1247
        48
        Q99733;Q99733-2;C9J6D1;A8MXH2;E9PKT8;C9JZI7;H0YCI4
        AAATAEEPDPK
        109.0700
        3.5712
        49
        P49006
        AAATPESQEPQAK
        139.0200
        3.6938
        50
        P09327;B4DV78
        AAATTAQEYLK
        66.6020
        3.3613

        Protein Quantification Table

        This plot shows the quantification information of proteins in the final result (evidence.txt).
        The quantification information of peptides is obtained from the evidence.txt. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms. Contaminants have been removed from the data by filtering using the 'Potential contaminant' field. * Peptides_Number: The number of peptides for each protein. * Average Intensity: Average intensity of each protein (0 or NA ignored).
        Showing 50/50 rows and 3/3 columns.
        ProteinIDProtein NameNumber of PeptidesAverage Intensity
        1
        A0A024QZX5;A0A087X1N8;P35237;A0A2R8YD12
        8
        3.4630
        2
        A0A024QZX5;A0A087X1N8;P35237;A0A2R8YD12;A0A2R8Y6A7
        7
        3.7022
        3
        A0A024QZX5;A0A087X1N8;P35237;A0A2R8YD12;A0A2R8Y6A7;P50452;A0A1B0GU38;P50452-2;C9JVA8;H7BXK7;C9JTJ8
        1
        3.8874
        4
        A0A024QZX5;A0A087X1N8;P35237;A0A2R8YDD0;A0A2R8Y517
        1
        4.1155
        5
        A0A024R161;Q9H1X3-3;F2Z3D1;J3QR79;Q9H1X3
        1
        2.0759
        6
        A0A024R161;Q9H1X3-3;P50151
        1
        3.0184
        7
        A0A024R4E5;C9JIZ1;C9J5E5;C9JZI8;C9JES8;C9JHZ8;C9JHS7;C9JK79;C9JT62;C9JHN6;C9JEJ8;C9JBS3
        1
        3.4740
        8
        A0A024R4E5;Q00341;H7C0A4
        2
        3.7892
        9
        A0A024R4E5;Q00341;Q00341-2
        1
        3.4131
        10
        A0A024R4E5;Q00341;Q00341-2;C9JIZ1;C9J5E5;C9JZI8;C9JES8;C9JHZ8;C9JHS7
        1
        3.1645
        11
        A0A024R4E5;Q00341;Q00341-2;C9JIZ1;C9J5E5;C9JZI8;C9JES8;C9JHZ8;C9JHS7;C9JK79;C9JT62
        1
        2.9139
        12
        A0A024R4E5;Q00341;Q00341-2;C9JIZ1;C9J5E5;C9JZI8;C9JES8;C9JHZ8;C9JHS7;C9JK79;C9JT62;C9JHN6;C9JEJ8;C9JBS3;C9JQ82
        1
        2.8056
        13
        A0A024R4E5;Q00341;Q00341-2;C9JIZ1;C9J5E5;C9JZI8;C9JES8;C9JHZ8;C9JHS7;C9JK79;C9JT62;C9JHN6;C9JEJ8;C9JBS3;C9JQ82;C9JMQ6
        2
        3.2138
        14
        A0A024R4E5;Q00341;Q00341-2;H0Y394
        6
        3.0600
        15
        A0A024R4E5;Q00341;Q00341-2;H0Y394;H7BZC3
        3
        3.0777
        16
        A0A024R4E5;Q00341;Q00341-2;H0Y394;H7BZC3;H7C2D1
        3
        3.0758
        17
        A0A024R4E5;Q00341;Q00341-2;H0Y394;H7C0A4
        8
        3.1484
        18
        A0A024R4E5;Q00341;Q00341-2;H0Y394;H7C0A4;C9JIZ1
        1
        3.3312
        19
        A0A024R4E5;Q00341;Q00341-2;H0Y394;H7C0A4;C9JIZ1;C9J5E5
        1
        3.3157
        20
        A0A024R4E5;Q00341;Q00341-2;H0Y394;H7C0A4;C9JIZ1;C9J5E5;C9JZI8
        1
        3.0445
        21
        A0A024R4E5;Q00341;Q00341-2;H0Y394;H7C2D1
        1
        3.1812
        22
        A0A024R4E5;Q00341;Q00341-2;H0Y394;H7C3D0
        1
        3.3016
        23
        A0A024R4E5;Q00341;Q00341-2;H7C0A4;C9JIZ1;C9J5E5;C9JZI8;C9JES8;C9JHZ8
        1
        2.9099
        24
        A0A024R4E5;Q00341;Q00341-2;H7C0A4;C9JIZ1;C9J5E5;C9JZI8;C9JES8;C9JHZ8;C9JHS7
        2
        3.2709
        25
        A0A024R4E5;Q00341;Q00341-2;H7C3D0
        1
        2.9887
        26
        A0A024R571;Q9H4M9
        3
        3.1472
        27
        A0A024R571;Q9H4M9;C9J2Z4
        4
        3.2469
        28
        A0A024R571;Q9H4M9;C9JC03;C9J2Z4
        5
        3.1790
        29
        A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8
        5
        3.3572
        30
        A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8;Q9H223
        2
        3.3359
        31
        A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1
        4
        3.3599
        32
        A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1;Q9NZN4
        1
        3.8361
        33
        A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739
        5
        3.0699
        34
        A0A024RA52;P25787;A0A7I2V2H3
        4
        3.5245
        35
        A0A024RA52;P25787;A0A7I2V2H3;A0A7I2YQP7;C9JCK5
        2
        2.8563
        36
        A0A024RA52;P25787;A0A7I2V2H3;H3BT36
        2
        3.8149
        37
        A0A024RA52;P25787;A0A7I2YQP7;C9JCK5
        2
        3.3619
        38
        A0A067XG54;A0A804HIW2;Q8NB49-2;Q8NB49-3;Q8NB49-4;Q8NB49
        3
        2.6076
        39
        A0A075B6F9;Q9Y314
        2
        2.9876
        40
        A0A075B6F9;Q9Y314;M0R3B2
        1
        3.0345
        41
        A0A075B6F9;Q9Y314;M0R3B2;A0A075B797
        1
        3.2546
        42
        A0A075B6F9;Q9Y314;M0R3B2;M0R1K2;A0A075B797
        1
        3.1492
        43
        A0A075B6F9;Q9Y314;M0R3B2;M0R1K2;A0A075B797;M0QX85
        1
        3.4443
        44
        A0A075B6F9;Q9Y314;M0R3B2;M0R1K2;M0QX85;M0R1T7
        1
        2.6600
        45
        A0A075B6T1;Q9C0C7-4;Q9C0C7-2;Q9C0C7-3;Q9C0C7;Q9C0C7-5
        3
        3.1249
        46
        A0A075B6T1;Q9C0C7-4;Q9C0C7-2;Q9C0C7-3;Q9C0C7;Q9C0C7-5;Q9C0C7-6
        4
        2.4667
        47
        A0A075B6T4;Q9NVX7;Q9NVX7-2
        3
        2.7975
        48
        A0A075B730;P58107
        63
        3.3030
        49
        A0A075B730;P58107;Q15149-4;A0A8I5KUE3;A0A8I5KYZ1;E9PMV1;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-2;Q15149;A0A8I5KSD5;Q15149-3;H0YDN1
        6
        3.7537
        50
        A0A075B763;Q8WWW0-3;Q8WWW0
        1
        2.4824

        MS2 and Spectral Stats

        Charge-state of Per File

        The distribution of the charge-state of the precursor ion, excluding potential contaminants.
        The distribution of the charge-state of the precursor ion, excluding potential contaminants.
        Created with MultiQC

        MS/MS Counts Per 3D-peak

        An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.
        For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.
        Created with MultiQC

        RT Quality Control

        IDs over RT

        Distribution of retention time, derived from the evidence table.
        The uncalibrated retention time in minutes in the elution profile of the precursor ion, and does not include potential contaminants.
        Created with MultiQC

        Peak width over RT

        Distribution of widths of peptide elution peaks, derived from the evidence table.
        The distribution of the widths of peptide elution peaks, derived from the evidence table and excluding potential contaminants, is one parameter of optimal and reproducible chromatographic separation.
        Created with MultiQC

        MultiQC v1.31 - Written by Phil Ewels, available on GitHub.

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