UIMF Library

This software package includes a library of C# functions to create, modify and extract data from UIMF files. UIMF files are SQLite databases of mass spectrometry data acquired at Pacific Northwest National Laboratory (PNNL).

NuGet

The UIMFLibrary is available on NuGet at:

• https://www.nuget.org/packages/UIMFLibrary/

Continuous Integration

The latest version of the application may be available on the AppVeyor CI server, but builds are deleted after 6 months.

How to use the UIMFLibrary in C#:

• Use the NuGet package manager to add a reference to the UIMFLibrary
  • Note that it depends on System.Data.SQLite

using UIMFLibrary;

• Declare the DataReader and DataWriter classes in your main code:
• Now the functions can be called as such:

UIMFReader DataReader = new UIMFReader(filePath);
DataReader.GetSpectrum(frameNumber, DataReader.FrameType.MS1, scanNumber, out var mzArray, out var intensityArray)
    ......

UIMFWriter DataWriter = new UIMFWriter(filePath);
DataWriter.CreateTables();

How to use the UIMFLibrary in C++:

• Copy UIMFLibrary.dll and System.Data.SQLite.DLL from either
  • UIMFLibrary\bin\x86
  • UIMFLibrary\bin\x64
• Open the Solution Explorer, add UIMFLibrary to your Project/References
• Add this using statement at the top of your code:

using namespace UIMFLibrary;

• In your .h file, declare the DataReader and DataWriter classes:

gcroot<UIMFReader*> ReadUIMF;
gcroot<UIMFWriter*> WriteUIMF;

• In you .cpp file, instantantiate the reader and the writer:

• Now the functions can be called as such:

ReadUIMF = new UIMFReader(filePath);
ReadUIMF->GetSpectrum(frameNumber, scanNumber, mzArray, intensityArray);
  ......

WriteUIMF = new UIMFWriter(filePath);
WriteUIMF->CreateTables();

Examples

To see examples of how to create, modify, and extract data out of the database, refer to the UIMFLibrary_Demo solution (see GitHub)

UIMF database structure:

Tables in a UIMF database file:

Table Name	Description	Comments
Global_Params	Global parameters	Parameters that apply to the entire UIMF file, with one row per parameter
Frame_Param_Keys	Description of the frame parameters in Frame_Params	Each frame parameter has a unique parameter id
Frame_Params	Parameters that apply to each frame	Each frame will have a series of parameters listed, with one parameter per row
Frame_Scans	Description of each mass spectrum, including BPI and TIC plus the ion intensities	Intensities are stored as binary blobs
Log_Entries	Log messages	Optional table
Bin_Intensities	Selected ion chromatograms for each m/z bin	Optional Table tracking the intensity at a given m/z in every scan of every frame
Global_Parameters	Legacy global parameters table	Wide table with a single row
Frame_Parameters	Legacy frame parameters table	Wide table with one row per frame

The UIMFWriter can optionally populate the legacy tables, but their use was phased out starting in 2015.

Global_Params

Column Name	Data Type	Comment
ParamID	int	Global parameter ID
ParamName	string	Parameter name
ParamValue	int	Parameter value
ParamDataType	string	Data type for the parameter
ParamDescription	string	Description of the parameter

Frame_Param_Keys

Column Name	Data Type	Comment
ParamID	int	Frame parameter ID
ParamName	string	Parameter name
ParamDataType	string	Data type for the parameter
ParamDescription	string	Description of the parameter

Frame_Params

Column Name	Data Type	Comment
FrameNum	int	Frame number
ParamID	int	Frame parameter ID
ParamValue	int	Parameter value

Frame_Scans table

Column Name	Data Type	Comment
FrameNum	int	Contains the frame number
ScanNum	short	Contains the TOF pulse number the spectra are located in
NonZeroCount	int	Nonzero intensities
BPI	double/float/int	Base Peak Intensity per Scan
BPI_MZ	double	m/z associated with BPI
TIC	double/float/int	Total Ion Chromatogram per Scan
Intensities	binary (BLOB)	Intensities in compressed binary format

Log_Entries table

Column Name	Data Type	Comment
Entry_ID	int	Log entry ID
Posted_By	string	Log source
Posting_Time	string	DateTime
Type	string	Message type
Message	string	Log message

Bin_Intensities table

Column Name	Data Type	Comment
MZ_BIN	integer	Bin number. Convert to m/z using ConvertBinToMZ in UIMFDataReader
INTENSITIES	binary (BLOB)	Intensities for the given m/z across scans (for all frames)

Legacy Global_Parameters table

Column Name	Data Type	Comment
DateStarted	string	Date Experiment was acquired
NumFrames	int	Number of frames in dataset
TimeOffset	int	Offset from 0. All bin numbers must be offset by this amount
BinWidth	double	Width of TOF bins (in ns)
Bins	int	Total TOF bins in a frame
TOFCorrectionTime	float	Time Delay correction
FrameDataBlobVersion	float	Version of FrameDataBlob in table Frame_Parameters
ScanDataBlobVersion	float	Version of ScanInfoBlob in table Frame_Parameters
TOFIntensityType	string	Data type of intensity in each TOF record (ADC is int/TDC is short/FOLDED is float)
DatasetType	string	Type of dataset (HMS/HMSMS/HMS-MSn)
Prescan_TOFPulses	int	Prescan TOP Pulses
Prescan_Accumulations	int	Prescan Accumulations
Prescan_TICThreshold	int	Prescan TIC Threshold
Prescan_Continuous	bool	Prescan continous mode (True or False)
Prescan_Profile	string	Prescan Profile File Name
Instrument_Name	string	Instrument name

Legacy Frame_Parameters table

Column Name	Data Type	Comment
FrameNum	int	(Primary Key) Frame number
StartTime	double	Start time of frame
Duration	double	Duration of frame
Accumulations	short	Number of collected and summed acquisitions in a frame
FrameType	short	Bitmap: 0=MS (Legacy); 1=MS (Regular); 2=MS/MS (Frag); 3=Calibration; 4=Prescan
Scans	int	Number of TOF scans
IMFProfile	string	File name for IMF Profile
TOFLOsses	double	TOF Losses
AverageTOFLength	double	Average time between TOF trigger pulses
CalibrationSlope	double	Value of k0
CalibrationIntercept	double	Value of t0
a2	double	secondary coefficients for residual mass error correction
b2	double	secondary coefficients for residual mass error correction
c2	double	secondary coefficients for residual mass error correction
d2	double	secondary coefficients for residual mass error correction
e2	double	secondary coefficients for residual mass error correction
f2	double	secondary coefficients for residual mass error correction
Temperature	double	Ambient temperature
voltHVRack1	double	HVRack Voltage
voltHVRack2	double	HVRack Voltage
voltHVRack3	double	HVRack Voltage
voltHVRack4	double	HVRack Voltage
voltCapInlet	double	Capilary Inlet Voltage
voltEntranceIFTIn	double	IFT In Voltage
voltEntranceIFTOut	double	IFT Out Voltage
voltEntranceCondLmt	double	Cond Limit Voltage
voltTrapOut	double	Trap Out Voltage
voltTrapIn	double	Trap In Voltage
voltJetDist	double	Jet Disruptor Voltage
voltQuad1	double	Fragmentation Quadrupole Voltage
voltCond1	double	Fragmentation Conductance Voltage
voltQuad2	double	Fragmentation Quadrupole Voltage
voltCond2	double	Fragmentation Conductance Voltage
voltIMSOut	double	IMS Out Voltage
voltExitIFTIn	double	IFT In Voltage
voltExitIFTOut	double	IFT Out Voltage
voltExitCondLimit	double	Cond Limit Voltage
PressureFront	double	Pressure at front of Drift Tube
PressureBack	double	Pressure at back of Drift Tube
MPBitOrder	short	Determines original size of bit sequence
FragmentationProfile	binary (BLOB)	Voltage profile used in fragmentation, Length number of Scans
HighPressureFunnelPressure	double	High pressure funnel pressure
IonFunnelTrapPressure	double	Ion funnel trap pressure
QuadrupolePressure	double	Quadrupole pressure
ESIVoltage	double	Electrospray voltage
FloatVolage	double	Float voltage
CALIBRATIONDONE	int	Set to 1 after a frame has been calibrated
Decoded	int	Set to 1 after a frame has been decoded

Contacts

Written by PNNL Staff for the Department of Energy (PNNL, Richland, WA)
Copyright 2009, Battelle Memorial Institute. All Rights Reserved.

Contributors include:
Kevin Crowell, Bill Danielson, Bryson Gibbons, Matthew Monroe, Spencer Prost, Yan Shi, Anuj Shah, Gordon Slysz

E-mail: matthew.monroe@pnnl.gov or proteomics@pnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/UIMF-Library

License

Licensed under the Educational Community License, Version 2.0 (the "License"); you may not use this program except in compliance with the License. You may obtain a copy of the License at

https://opensource.org/licenses/ECL-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.