User Guide

Input File Format

MGF File

DeepMASS accepts mgf files containing one or multiple MS/MS spectra. The Mascot Generic Format (MGF) is a standard file format used to store mass spectrometry (MS) data, particularly tandem mass spectrometry (MS/MS) data.

Structure of MGF Files:

Header Information: Optional metadata about the MS data, including instrument parameters, acquisition settings, and other experimental details.
BEGIN IONS: Marks the beginning of the MS/MS data section.
Spectrum Information: Parameters and a list of mass-to-charge ratio (m/z) and intensity pairs.
Peak Data: Describes the mass spectrum with m/z and intensity pairs.
END IONS: Marks the end of the MS/MS data section for a specific spectrum.

Essential DeepMASS input information includes:

CHARGE: Number of charges of the precursor ion.
PRECURSOR_MZ: Precursor ion's mass-to-charge ratio.
COMPOUND_NAME: Identifier for the compound.
IONMODE: Ionization mode of the precursor ion.
ADDUCT: Type of adduct of the precursor ion.

At least one of the following is necessary for DeepMASS inputs:

FORMULA: Molecular formula of the compound.
PARENT_MASS: Monoisotopic mass of the compound.

Here's a simplified example of an MGF file:

    BEGIN IONS
    CHARGE=1-
    PRECURSOR_MZ=194.04588176800002
    COMPOUND_NAME=challenge_255
    CHALLENGE=CASMI2016_Challenge-006
    FORMULA=C9H9NO4
    SMILES=CC(=O)NC1=CC=C(O)C(=C1)C(O)=O
    INCHIKEY=GEFDRROBUCULOD-UHFFFAOYSA-N
    ADDUCT=[M-H]-
    IONMODE=negative
    PARENT_MASS=195.053157768
    132.0454 0.006008828855732822 
    134.0245 0.0022295306804225633 
    149.0483 0.00297960480724686 
    150.056 1.0 
    194.0459 0.36915136378467533 
    END IONS

    BEGIN IONS
    CHARGE=1+
    PRECURSOR_MZ=223.970551912
    COMPOUND_NAME=challenge_368
    CHALLENGE=CASMI2016_Challenge-119
    FORMULA=C9H6BrNO
    SMILES=BrC1=CC2=C(NC(=O)C=C2)C=C1
    INCHIKEY=YLAFBGATSQRSTB-UHFFFAOYSA-N
    ADDUCT=[M+H]+
    IONMODE=positive
    PARENT_MASS=222.963275912
    127.0418 0.01388754827761238 
    145.0524 0.0058134492435322465 
    205.9602 0.1043324271433068 
    223.9708 1.0 
    END IONS

MSP File

DeepMASS also accepts msp files, which contain one or multiple MS/MS spectra.

Structure of MSP Files:

Name: A descriptor or identifier for the spectrum, often the compound name.
Num Peaks: The number of mass-to-charge ratio (m/z) and intensity pairs that follow.
Peak Data: Describes the mass spectrum with m/z and intensity pairs listed.

Essential DeepMASS input information includes:

CHARGE: Number of charges of the precursor ion.
PRECURSOR_MZ: Precursor ion's mass-to-charge ratio.
COMPOUND_NAME: Identifier for the compound.
IONMODE: Ionization mode of the precursor ion.
ADDUCT: Type of adduct of the precursor ion.

At least one of the following is necessary for DeepMASS inputs:

FORMULA: Molecular formula of the compound.
PARENT_MASS: Monoisotopic mass of the compound.

Here's a simplified example of an MSP file with multiple spectra:

    Name: challenge_255
    PrecursorMZ: 194.04588176800002
    ExactMass: 195.053157768
    Formula: C9H9NO4
    Ion_mode: negative
    Adduct: [M-H]-
    Num Peaks: 5
    132.0454 0.0060
    134.0245 0.0022
    149.0483 0.0030
    150.0560 1.0
    194.0459 0.3692

    Name: challenge_368
    PrecursorMZ: 223.970551912
    ExactMass: 222.963275912
    Formula: C9H6BrNO
    Ion_mode: positive
    Adduct: [M+H]+
    Num Peaks: 4
    127.0418 0.0139
    145.0524 0.0058
    205.9602 0.1043
    223.9708 1.0

MAT File

DeepMASS accepts mat files which contain detailed information about MS/MS spectra. The file format is the same as MS-Finder used, which also contains isotopical information.

Here's a simplified example of an MAT file with multiple spectra:

    NAME: L-Glutamic acid
    SCANNUMBER: 1228
    RETENTIONTIME: 5.8845
    PRECURSORMZ: 148.0424
    PRECURSORTYPE: [M+H]+
    IONMODE: Positive
    SPECTRUMTYPE: Profile
    INTENSITY: 10818.72
    FORMULA: C5H9NO4
    ONTOLOGY: 
    INCHIKEY: WHUUTDBJXJRKMK-VKHMYHEASA-N
    SMILES: 
    MSTYPE: MS1
    Num Peaks: 5
    148.04244   17967
    149.04424   1255
    150.03773   1096
    151.04014   113
    152.07201   68
    MSTYPE: MS2
    Num Peaks: 7
    44.97939    304
    61.00939    32
    73.78966    70
    74.00583    7225
    76.82613    13
    87.01311    80
    120.01151   988

Output File Format

The output is CSV file contains information about ranked annotated chemical structures. The columns provide details about each compound, including its title, molecular formula, structure, and scores related to formula and structure predictions.

Columns Description:

Title: The name of the compound.
MolecularFormula: The molecular formula of the compound, indicating the number and type of atoms present.
CanonicalSMILES: The Canonical Simplified Molecular Input Line Entry System (SMILES) string, representing the structure of the compound.
InChIKey: The International Chemical Identifier Key, a unique alphanumeric string to identify the compound.
Database IDs: Identifiers from various databases where the compound is registered.
Formula Score: A score indicating the accuracy or confidence in the predicted molecular formula.
Structure Score: A score indicating the accuracy or confidence in the predicted molecular structure.
Consensus Score: An overall score combining the formula and structure scores, reflecting the overall confidence in the compound identification.

Here's a simplified example of an output file:

	Title	MolecularFormula	CanonicalSMILES	InChIKey	Database IDs	Formula Score	Structure Score	Consensus Score
0	"Acetic acid N',N'-dimethylhydrazide"	C4H10N2O	CC(=O)NN(C)C	SLIKWWJXVUHCPJ-UHFFFAOYSA-N	NIST:CAS6233041	1.0	0.9999999991779194	0.9999999994245434
1	N-(2-Aminoethyl)acetamide	C4H10N2O	CC(=O)NCCN	DAKZISABEDGGSV-UHFFFAOYSA-N	PMHub:MS000036761	1.0	0.957735969543063	0.970415178680144
2	N-Propylurea	C4H10N2O	CCCNC(N)=O	ZQZJKHIIQFPZCS-UHFFFAOYSA-N	BloodExp:CID12303;;HMDB0255240	1.0	0.940423010788881	0.9582961075522167
3	"2-Amino-N,N-dimethylacetamide"	C4H10N2O	CN(C)C(=O)CN	KNVRBEGQERGQRP-UHFFFAOYSA-N	NIST:CAS1857198	1.0	0.8933594423863824	0.9253516096704677
4	4-Aminobutanamide	C4H10N2O	NCCCC(N)=O	WCVPFJVXEXJFLB-UHFFFAOYSA-N	NIST:CAS3251089	1.0	0.8222707059586819	0.8755894941710773
5	"1,1,3-Trimethylurea"	C4H10N2O	CNC(=O)N(C)C	COSWCAGTKRUTQV-UHFFFAOYSA-N	NIST:CAS632144	1.0	0.7851222117039512	0.8495855481927659
6	Methylpropylnitrosamine	C4H10N2O	CCCN(C)N=O	ITBDKUCVKYSWMF-UHFFFAOYSA-N	BloodExp:CID13545	1.0	0.7422341116397019	0.8195638781477912
7	(2S)-2-(Methylamino)propanamide	C4H10N2O	CNC@@HC(N)=O	QKNFFJHHPCWXTH-VKHMYHEASA-N	NIST:CAS55988120	1.0	0.7230225309588504	0.8061157716711953
8	N-nitrosodiethylamine	C4H10N2O	CCN(CC)N=O	WBNQDOYYEUMPFS-UHFFFAOYSA-N	CHEBI:34873;;BloodExp:CID5921;;C14422;;PMHub:MS000007343;;DTXSID2021028	1.0	0.7174501691978581	0.8022151184385007
9	ISOPROPYLUREA	C4H10N2O	CC(C)NC(=N)O	LZMATGARSSLFMQ-UHFFFAOYSA-N	PMHub:MS000231594;;NIST:CAS691601	1.0	0.6049047550645834	0.7234333285452084

Export MS/MS file from MS-DIAL

To export an MGF (Mascot Generic Format) file from MS-DIAL processing results, follow these steps:

A) Peak list export B) Alignment result export C) Molecular spectrum networking export D) Copy screenshot to clipboard (emf) E) Parameter export (Tab-delimited text) F) Export as lipoquality database format G) Export normalization result

A) Peak list export: You can get the peak list information of each sample including retention time, m/z, MS/MS spectra information, and so on. Available formats are MSP, MGF or Text.

Step1. Choose an export folder path. Step2. Choose files which you want to export and click button "Add ->". Step3. Select export format. Step4. Click the export button.

B) Alignment result export: You can get data matrix or spectral information.

Step1. Choose an export folder path. Step2. Choose an alignment file which you want to export. Step3. Select export format if you want to export the representative spectra. Step4. Click the export button.

Export MS/MS file from XCMS

To export MS/MS data into an MGF (Mascot Generic Format) file from XCMS result, we can use the combineSpectra function. For more details see the documentation of the consensusSpectrum function in the MSnbase R package. Refer this script to define a function exportSpectraToMGF to convert the spectra data into MGF format.

    exportSpectraToMGF <- function(spectra, file) {
        mgf_data <- lapply(spectra, function(sp) {
            list(
                TITLE = paste("Scan", sp@scanIndex),
                RTINSECONDS = sp@rtime,
                PEPMASS = c(sp@precursorMz, sp@precursorIntensity),
                CHARGE = sp@precursorCharge,
                MZ = sp@mz,
                INTENSITY = sp@intensity
            )
        })
        con <- file(file, "w")
        for (spectrum in mgf_data) {
            cat("BEGIN IONS\n", file = con)
            cat(paste("TITLE=", spectrum$TITLE, sep = ""), "\n", file = con)
            cat(paste("RTINSECONDS=", spectrum$RTINSECONDS, sep = ""), "\n", file = con)
            cat(paste("PEPMASS=", paste(spectrum$PEPMASS, collapse = " "), sep = ""), "\n", file = con)
            cat(paste("CHARGE=", spectrum$CHARGE, sep = ""), "\n", file = con)
            for (i in seq_along(spectrum$MZ)) {
                cat(paste(spectrum$MZ[i], spectrum$INTENSITY[i], sep = " "), "\n", file = con)
            }
            cat("END IONS\n\n", file = con)
        }
        close(con)
    }