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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

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        About MultiQC

        This report was generated using MultiQC, version 1.33

        Video: Using MultiQC Reports MultiQC homepage MultiQC documentation Source code Issue tracker

        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

        MultiQC is developed by Seqera.

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

        Report generated on 2025-12-25, 13:04 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data_temp

        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.https://github.com/bigbio/pmultiqc

        Results Overview

        Summary Table

        This table shows the summary statistics of the submitted data.
        This table shows the summary statistics of the submitted data.
        Showing 1/1 rows and 4/4 columns.
        #MS2 Spectra#Identified MS2 Spectra%Identified MS2 Spectra#Peptides Identified#Proteins Identified
        143179
        69179
        48.32%
        104027
        34377

        HeatMap

        This heatmap provides an overview of the performance of quantms.
        This plot shows the pipeline performance overview.
        Created with MultiQC

        Pipeline Result Statistics

        This plot shows the submitted results
        This plot shows the submitted results. Including the number of identified peptides and the number of identified modified peptides in the submitted results. You can also remove the decoy with the `remove_decoy` parameter.
        Showing 3/3 rows and 4/4 columns.
        Spectra File#Peptide IDs#Unambiguous Peptide IDs#Modified Peptide IDs#Protein (group) IDs
        F10854
        15873
        15873
        6251
        11023
        Q00745
        38147
        38147
        10895
        20108
        cGAS
        51283
        51283
        13523
        23397

        Identification Summary

        Number of Peptides identified Per Protein

        This plot shows the number of peptides per protein in the submitted data
        Proteins supported by more peptide identifications can constitute more confident results.
        Created with MultiQC

        ProteinGroups Count

        Number of protein groups per raw file.
        Based on statistics calculated from mzTab, mzIdentML (mzid), or DIA-NN report files.
        Created with MultiQC

        Peptide ID Count

        Number of unique (i.e. not counted twice) peptide sequences including modifications per Raw file.
        Based on statistics calculated from mzTab, mzIdentML (mzid), or DIA-NN report files.
        Created with MultiQC

        MS/MS Identified

        MS/MS identification rate by Run (or Sample).
        MS/MS identification rate by Run (or Sample) (quantms data from mzTab and mzML files; MaxQuant data from summary.txt)
        Created with MultiQC

        Quantification Analysis

        Peptides Quantification Table

        This plot shows the quantification information of peptides in the final result (mzIdentML).
        The quantification information of peptides is obtained from the mzIdentML. 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. * BestSearchScore: It is equal to max(search_engine_score) for mzIdentML datasets. * 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
        sp|Q8K3M5|CABL2_MOUSE
        AAAAAGGAPGPAPGPSR
        0.0000
        4.9039
        2
        sp|Q9QYL7|ABT1_MOUSE
        AAAAAGGKKGAKYSKDYTEGWVEFR
        0.0000
        5.9731
        3
        sp|Q9D3B1|HACD2_MOUSE
        AAAAATAATKGNGGGSGR
        0.0000
        5.8710
        4
        sp|Q6PG16|HJURP_MOUSE;tr|E9Q4T0|E9Q4T0_MOUSE;tr|E9QKG8|E9QKG8_MOUSE
        AAAALPCQSEHLKRLNPDSPQQSSQKRSISPGCHR
        0.0000
        5.6982
        5
        tr|A0A0R4J0L6|A0A0R4J0L6_MOUSE
        AAAALQLRQTLCPGARVLR
        0.0000
        4.6888
        6
        sp|Q14C51|PTCD3_MOUSE;tr|A0A0U1RQ61|A0A0U1RQ61_MOUSE
        AAAAVAAR
        0.0000
        6.0480
        7
        sp|Q9D6J1|CERS4_MOUSE
        AAACLTNGHTR
        0.0000
        5.7154
        8
        sp|P52431|DPOD1_MOUSE;tr|D6RFB8|D6RFB8_MOUSE
        AAADYAGKQAHVELAER
        0.0000
        5.0073
        9
        sp|Q69ZB3|TSYL5_MOUSE
        AAAEDAWHDEKPPQSPR
        0.0000
        4.2299
        10
        tr|A2AHJ7|A2AHJ7_MOUSE
        AAAEEVVRRRCR
        0.0000
        4.1550
        11
        tr|A0A1Y7VIT9|A0A1Y7VIT9_MOUSE
        AAAELVR
        0.0000
        6.7749
        12
        sp|Q4KUS2|UN13A_MOUSE;tr|H3BJZ7|H3BJZ7_MOUSE;tr|H3BJL3|H3BJL3_MOUSE
        AAAERAQEAEPPK
        0.0000
        5.1633
        13
        sp|Q0VDT2|ZN367_MOUSE
        AAAEWLAKYWEMREQR
        0.0000
        4.0263
        14
        sp|Q8VCF1|CANT1_MOUSE
        AAAGIRPPGYLIHESACWSDTLQRWFFLPRR
        0.0000
        5.5581
        15
        sp|Q8BLY2|SYTC2_MOUSE
        AAAHEPPTQNQEKDTK
        0.0000
        3.9174
        16
        sp|Q9CPW3|RM54_MOUSE
        AAAHLLR
        0.0000
        4.6964
        17
        sp|Q62009|POSTN_MOUSE
        AAAITSDLLESLGR
        0.0000
        4.7159
        18
        sp|Q9D115|ZN706_MOUSE
        AAAKAALIYTCTVCRTQMPDPKTFK
        0.0000
        4.3963
        19
        sp|Q924C5|ALPK3_MOUSE
        AAAKMREIEQSWKHGK
        0.0000
        4.1998
        20
        sp|Q99PU8|DHX30_MOUSE;tr|A0A0G2JGL8|A0A0G2JGL8_MOUSE
        AAALACK
        0.0000
        4.7164
        21
        sp|Q8R3Y5|CS047_MOUSE;tr|A0A087WPA4|A0A087WPA4_MOUSE;tr|A0A087WRI8|A0A087WRI8_MOUSE;tr|A0A0R4J2B5|A0A0R4J2B5_MOUSE;tr|G5E8E3|G5E8E3_MOUSE
        AAALAHR
        0.0004
        6.2399
        22
        sp|Q8CJ27|ASPM_MOUSE
        AAALFIQRWYR
        0.0000
        4.0858
        23
        sp|Q9D113|DNLZ_MOUSE
        AAALGRVEADHYQLVYTCKVCGTR
        0.0000
        5.1654
        24
        sp|Q8BU88|RM22_MOUSE
        AAALLRELGALRVPNLRIWATQTLRVLPPSCIHTSASLDISRKWEKKNK
        0.0000
        5.3391
        25
        sp|Q80VM4|ZN579_MOUSE
        AAALQELQTQASQSPQPPQPLK
        0.0000
        6.3431
        26
        sp|Q8BLF1|NCEH1_MOUSE
        AAALRAR
        0.0000
        5.3443
        27
        sp|P27671|RGRF1_MOUSE
        AAANIIR
        0.0000
        5.1779
        28
        tr|A0A5F8MPH1|A0A5F8MPH1_MOUSE
        AAAPEDR
        0.0000
        6.4133
        29
        sp|P08923|LTK_MOUSE
        AAAPGSGGRGGAAGGGSGWTSRAHSPQAGRSPREGAEGGEGCAEAWAALR
        0.0000
        5.8170
        30
        sp|Q9JIF7|COPB_MOUSE
        AAAQCYIDLIIK
        0.0000
        5.2169
        31
        sp|Q9D0E3|LYSM1_MOUSE
        AAAQKLRK
        0.0000
        5.5579
        32
        sp|Q8C1B7|SEP11_MOUSE;tr|A0A0J9YTY0|A0A0J9YTY0_MOUSE;tr|A0A0J9YUL3|A0A0J9YUL3_MOUSE
        AAAQLLQSQAQQSGAQQTKK
        0.0000
        6.3266
        33
        sp|E9Q5C9|NOLC1_MOUSE;tr|A0A286YDA2|A0A286YDA2_MOUSE;tr|A0A286YDT3|A0A286YDT3_MOUSE;tr|A0A286YDV7|A0A286YDV7_MOUSE
        AAAQTQPADSSDDSSDDSDSSSEEEK
        0.0000
        7.3597
        34
        sp|Q6VUP9|AP2E_MOUSE
        AAARAHDEPPGLLAPPARALGLDPR
        0.0000
        4.8448
        35
        sp|Q9JMI0|ECEL1_MOUSE
        AAARAKLQYMMVMVGYPDFLLKPEAVDKEYEFEVHEKTYFK
        0.0000
        2.9698
        36
        sp|Q8BFR5|EFTU_MOUSE
        AAATLLR
        0.0000
        5.9688
        37
        sp|Q6PAJ1|BCR_MOUSE
        AAATTSQPVLTSQQIETIFFK
        0.0000
        2.1883
        38
        tr|K3W4P7|K3W4P7_MOUSE
        AAATVSIAGRCKSQK
        0.0000
        5.5416
        39
        tr|K3W4P7|K3W4P7_MOUSE
        AAATVSIAGRCKSQKDSQGYCAQYR
        0.0000
        5.6392
        40
        sp|Q80UJ7|RB3GP_MOUSE
        AAAVALPEEELKKSGCPEER
        0.0000
        5.8570
        41
        sp|O89019|INVS_MOUSE;tr|A2AM57|A2AM57_MOUSE
        AAAVIQR
        0.0000
        5.4006
        42
        sp|Q14DK5|HIPL1_MOUSE
        AAAVVCRQLGFAHAVRAAK
        0.0000
        5.9995
        43
        tr|D3Z5T8|D3Z5T8_MOUSE
        AAAWKHR
        0.0000
        5.2440
        44
        tr|E9Q4M2|E9Q4M2_MOUSE;sp|P54310|LIPS_MOUSE
        AAAYGVR
        0.0000
        6.1028
        45
        sp|Q80ZK9|WDTC1_MOUSE;tr|A2AE98|A2AE98_MOUSE
        AAAYMKRKWDGDHYDALRDCLK
        0.0000
        4.8679
        46
        sp|Q6ZWR6|SYNE1_MOUSE;tr|A0A1L1STC6|A0A1L1STC6_MOUSE
        AACDEINGHLMEARYSLSR
        0.0000
        5.1582
        47
        sp|Q9ERK4|XPO2_MOUSE;tr|E9Q1T9|E9Q1T9_MOUSE;tr|F6ZEW4|F6ZEW4_MOUSE
        AACDLVR
        0.0000
        5.0416
        48
        sp|Q99L04|DHRS1_MOUSE
        AACDRLAADCAHELR
        0.0000
        4.9266
        49
        sp|Q9Z0J4|NOS1_MOUSE;tr|F8WGF2|F8WGF2_MOUSE;tr|S4R255|S4R255_MOUSE
        AACDVFCVGDDVNIEKANNSLISNDRSWKRNK
        0.0000
        2.3582
        50
        sp|Q9CQ73|PKP2_MOUSE
        AACGALR
        0.0000
        5.9051
        Expand table

        Protein Quantification Table

        This plot shows the quantification information of proteins in the final result (mzIdentML).
        The quantification information of proteins is obtained from the mzIdentML. The table shows the quantitative level and distribution of proteins 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. * Peptides_Number: Number of peptides per protein. * Average Intensity: Average intensity of each protein sequence (0 or NA ignored).
        Showing 50/50 rows and 3/3 columns.
        ProteinIDProtein NameNumber of PeptidesAverage Intensity
        1
        sp|A0A087WPF7|AUTS2_MOUSE;tr|A0A7N9VSJ5|A0A7N9VSJ5_MOUSE;tr|A0A7P0A163|A0A7P0A163_MOUSE
        3
        5.4331
        2
        sp|A0A087WPF7|AUTS2_MOUSE;tr|A0A7N9VSJ5|A0A7N9VSJ5_MOUSE;tr|A0A7P0A163|A0A7P0A163_MOUSE;tr|E0CZ47|E0CZ47_MOUSE
        3
        6.9017
        3
        sp|A0A087WPF7|AUTS2_MOUSE;tr|A0A7N9VSJ5|A0A7N9VSJ5_MOUSE;tr|A0A7P0A163|A0A7P0A163_MOUSE;tr|E9PZ86|E9PZ86_MOUSE
        8
        5.9310
        4
        sp|A0A087WPF7|AUTS2_MOUSE;tr|A0A7N9VSJ5|A0A7N9VSJ5_MOUSE;tr|A0A7P0A163|A0A7P0A163_MOUSE;tr|E9PZ86|E9PZ86_MOUSE;tr|S4R200|S4R200_MOUSE
        1
        5.9355
        5
        sp|A0A088MLT8|IQIP1_MOUSE;sp|P0DPB4|SCHI1_MOUSE;tr|A0A0A6YXQ5|A0A0A6YXQ5_MOUSE;tr|S4R1J0|S4R1J0_MOUSE
        1
        5.2310
        6
        sp|A0A0A6YXX9|CTSEL_MOUSE;tr|A0A571BGH9|A0A571BGH9_MOUSE;tr|A0A5F8MPV8|A0A5F8MPV8_MOUSE
        2
        5.4538
        7
        sp|A0A0A6YY25|BTBDI_MOUSE
        2
        6.9220
        8
        sp|A0A0B4J1F4|ARRD4_MOUSE
        1
        6.2044
        9
        sp|A0A0B4J1G0|FCG3A_MOUSE
        2
        5.8181
        10
        sp|A0A0B4J1L0|CEA15_MOUSE
        1
        2.6263
        11
        sp|A0A0B4J1N3|GP15L_MOUSE
        2
        5.7969
        12
        sp|A0A0G2JDV3|GBP6_MOUSE;sp|A4UUI3|GBP4_MOUSE;tr|A0A8Q0QEH4|A0A8Q0QEH4_MOUSE;tr|L7N1X8|L7N1X8_MOUSE;tr|Q2V6D6|Q2V6D6_MOUSE
        1
        4.8188
        13
        sp|A0A0G2JDV3|GBP6_MOUSE;sp|A4UUI3|GBP4_MOUSE;tr|Q000W5|Q000W5_MOUSE;tr|Q8BTS3|Q8BTS3_MOUSE;tr|A0A8Q0QEH4|A0A8Q0QEH4_MOUSE;tr|L7N1X8|L7N1X8_MOUSE;tr|Q2V6D6|Q2V6D6_MOUSE
        1
        4.8213
        14
        sp|A0A0G2JDV3|GBP6_MOUSE;tr|A0A8Q0QEH4|A0A8Q0QEH4_MOUSE;tr|L7N1X8|L7N1X8_MOUSE
        1
        4.9218
        15
        sp|A0A0G2JDV3|GBP6_MOUSE;tr|Q000W5|Q000W5_MOUSE;tr|A0A8Q0QEH4|A0A8Q0QEH4_MOUSE;tr|L7N1X8|L7N1X8_MOUSE
        3
        5.6629
        16
        sp|A0A0G2JEB6|CFA47_MOUSE
        6
        5.7070
        17
        sp|A0A0G2JEB6|CFA47_MOUSE;tr|B1AXF0|B1AXF0_MOUSE
        4
        5.7076
        18
        sp|A0A0G2JEB6|CFA47_MOUSE;tr|B1AY26|B1AY26_MOUSE
        5
        5.4346
        19
        sp|A0A0G2JEB6|CFA47_MOUSE;tr|J3QP97|J3QP97_MOUSE
        3
        5.6632
        20
        sp|A0A0M3U1B0|SYC2L_MOUSE
        11
        5.6670
        21
        sp|A0A0M3U1B0|SYC2L_MOUSE;tr|A0A5H1ZRM5|A0A5H1ZRM5_MOUSE
        3
        5.0048
        22
        sp|A0A0U1RPR8|GUC2D_MOUSE;tr|F6VFS9|F6VFS9_MOUSE
        2
        5.7641
        23
        sp|A0A0U1RPR8|GUC2D_MOUSE;tr|F6VFS9|F6VFS9_MOUSE;tr|A0A0U1RPB5|A0A0U1RPB5_MOUSE
        1
        5.1022
        24
        sp|A0A140LHF2|VSXL2_MOUSE
        1
        5.3464
        25
        sp|A0A140LI88|ANR31_MOUSE;tr|A0A4W7PWM5|A0A4W7PWM5_MOUSE;tr|A0A5H1ZRN8|A0A5H1ZRN8_MOUSE
        16
        6.0881
        26
        sp|A0A140LIF8|IRGM2_MOUSE
        2
        6.0264
        27
        sp|A0A140LIF8|IRGM2_MOUSE;sp|Q9DCE9|IRGM3_MOUSE
        2
        4.8763
        28
        sp|A0A140LIJ0|DCST2_MOUSE
        3
        4.9831
        29
        sp|A0A140LIT1|CC194_MOUSE
        3
        5.7282
        30
        sp|A0A1D5RMD1|IQCN_MOUSE
        11
        5.8828
        31
        sp|A0A1D9BZF0|GCNA_MOUSE
        8
        5.7618
        32
        sp|A0A1L1SUL6|TXND6_MOUSE
        5
        5.9314
        33
        sp|A0A1W2P872|NOVA2_MOUSE
        1
        5.5942
        34
        sp|A0A1W2P872|NOVA2_MOUSE;sp|Q9JKN6|NOVA1_MOUSE
        1
        4.9822
        35
        sp|A0A1W2P884|CE85L_MOUSE;tr|E9QA61|E9QA61_MOUSE
        12
        5.6840
        36
        sp|A0A286YDK6|PERC1_MOUSE
        2
        5.4707
        37
        sp|A0A286YEC0|CIROP_MOUSE
        1
        4.4449
        38
        sp|A0A286YEC0|CIROP_MOUSE;tr|A0A2I3BPF0|A0A2I3BPF0_MOUSE
        2
        6.1092
        39
        sp|A0A2R8VHF7|TM249_MOUSE
        1
        5.0194
        40
        sp|A0A338P6K9|QSER1_MOUSE
        8
        6.1907
        41
        sp|A0A571BF63|ANKF1_MOUSE
        3
        5.8031
        42
        sp|A0A571BF63|ANKF1_MOUSE;tr|A0A140LIW7|A0A140LIW7_MOUSE;tr|F6RWQ6|F6RWQ6_MOUSE;tr|F6X7B3|F6X7B3_MOUSE
        6
        5.0316
        43
        sp|A0A571BF63|ANKF1_MOUSE;tr|A0A140LIW7|A0A140LIW7_MOUSE;tr|Q8CDJ6|Q8CDJ6_MOUSE
        1
        2.8010
        44
        sp|A0A571BF63|ANKF1_MOUSE;tr|F6RWQ6|F6RWQ6_MOUSE
        1
        5.6476
        45
        sp|A0A5F8MPE6|CX058_MOUSE
        10
        5.4203
        46
        sp|A0A5F8MPU3|CTSRT_MOUSE
        18
        5.8594
        47
        sp|A0A5F8MPU3|CTSRT_MOUSE;tr|A0A571BEL2|A0A571BEL2_MOUSE
        7
        6.1227
        48
        sp|A0A5K7RLP0|MEIOS_MOUSE
        3
        6.1592
        49
        sp|A0A6I8MX38|TUG1_MOUSE;tr|A0A8Q0QWN6|A0A8Q0QWN6_MOUSE
        2
        5.5627
        50
        sp|A0A7N9VSG0|SPA5L_MOUSE
        2
        5.2918
        Expand table

        MS1 Analysis

        Total Ion Chromatograms

        MS1 quality control information extracted from the spectrum files.
        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.
        Created with MultiQC

        MS1 Base Peak Chromatograms

        MS1 base peak chromatograms extracted from the spectrum files.
        The Base Peak Chromatogram (BPC) displays the intensity of the most abundant ion at each retention time point.
        Created with MultiQC

        MS1 Peaks

        MS1 Peaks from the spectrum files
        This plot shows the number of peaks detected in MS1 scans over the course of each sample run.
        Created with MultiQC

        General stats for MS1 information

        General stats for MS1 information extracted from the spectrum files.
        This table presents general statistics for MS1 information extracted from mass spectrometry data files.
        Showing 3/3 rows and 3/3 columns.
        FileAcquisition Date Timelog10(Total Current)log10(Scan Current)
        F10854
        2018-12-05 19:39:44
        12.0895
        10.2449
        Q00745
        2019-11-28 01:16:23
        13.4335
        12.1113
        cGAS
        2023-04-03 05:06:15
        14.3864
        12.3766

        MS2 and Spectral Stats

        Number of Peaks per MS/MS spectrum

        Histogram of number of peaks per MS/MS spectrum.
        Too few peaks may indicate poor fragmentation; many peaks could indicate noisy spectra.
        Created with MultiQC

        Peak Intensity Distribution

        Histogram of ion intensity vs. frequency for all MS2 spectra.
        High number of low intensity noise peaks expected; disproportionate high signal peaks may indicate issues.
        Created with MultiQC

        Distribution of Precursor Charges

        Bar chart of precursor ion charge distribution.
        Use to identify potential ionization problems or unexpected distributions.
        Created with MultiQC

        Charge-state

        The distribution of the charge-state of the precursor ion.
        Charge distribution by Run (or Sample). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544). The charge distribution should be similar across Raw files. Consistent charge distribution is paramount for comparable 3D-peak intensities across samples.
        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 mzIdentML (or mzML).
        The uncalibrated retention time in minutes in the elution profile of the precursor ion.

        This plot allows to judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization. See [Moruz 2014, DOI: 10.1002/pmic.201400036](https://pubmed.ncbi.nlm.nih.gov/24700534/) for details.

        Created with MultiQC

        MultiQC v1.33 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.