Agilent MSProfile.bin File Structure

This file format contains Agilent HRMS data.

The HRMS data is encoded across several files in a subdirectory named AcqData:

File	Information
MSTS.xml	Number of retention times
MSScan.xsd	File structure of MSScan.bin
MSScan.bin	Offsets and compression info for MSProfile.bin
MSMassCal.bin	Calibration info for masses
MSProfile.bin	Mz and intensity values

MSTS.xml is an XML document that contains several NumOfScans elements, whose values summed together give the total number of retention times. This is useful for parsing subsequent files.

<TimeSegment TimeSegmentID="2">
    <StartTime>1.04351666666667</StartTime>
    <EndTime>7.99746666666667</EndTime>
    <NumOfScans>2095</NumOfScans>
    <FixedCycleLength>0</FixedCycleLength>
</TimeSegment>

MSScan.xsd is an XML document that defines the structure of the MSScan.bin binary using elements that are assigned simple and complex types.

A simple type translates directly into a little-endian number type. For example:

<xs:element name="TIC" type="xs:double"/>

A complex type is comprised of simple types and other complex types. The following example shows a heavily simplified version of a complex type that contains another complex type.

<xs:complexType name="ScanRecordType">
    <xs:sequence>
        <xs:element name="ScanTime" type="xs:double"/>
        <xs:element name="SpectrumParamValues" type="SpectrumParamsType"/>
    </xs:sequence>
</xs:complexType>
<xs:complexType name="SpectrumParamsType">
    <xs:sequence>
        <xs:element name="SpectrumOffset" type="xs:long"/>
        <xs:element name="ByteCount" type="xs:int"/>
        <xs:element name="PointCount" type="xs:int"/>
        <xs:element name="UncompressedByteCount" type="xs:int"/>
    </xs:sequence>
</xs:complexType>

The root type is the complex type ScanRecordType.

MSScan.bin is a binary that contains a data segment in the format defined by ScanRecordType for each retention time. These data segments begin at offset 0x58.

The simplified example above would correspond to the following data segment structure:

Purpose	Data Type
Retention time	Double
Offset of data in MSProfile.bin	Unsigned long
Length of compressed data segment	Unsigned int
Number of mz-intensity pairs	Unsigned int
Length of decompressed data segment	Unsigned int

Although it is a simplified example, the table above contains the key information about a MSProfile.bin binary that is stored in MSScan.bin.

MSMassCal.bin is a binary that contains a data segment of 10 little-endian doubles for each retention time. The first 2 doubles are used as calibration numbers for the mz values recorded at the corresponding retention time. The purpose of the other 8 doubles is currently unknown. The data segments begin at offset 0x4c.

MSProfile.bin is a binary that has been compressed using the LZF algorithm. The length of the decompressed data is required for LZF decompression.

This file format is comprised of a data segment for each retention time. Assume little-endianness.

Each data segment begins with 2 doubles that hold the smallest mz value and the mz delta value, before calibration. The resulting mz range may be unusable without calibration because the values can be very large.

Let the corresponding 2 calibration numbers from MSMassCal.bin be coeff and base. The calibration formula for each mz is (coeff * (mz - base))^2.

The rest of the data segment consists of the intensities as unsigned integers. Recall that the number of intensities is stored in MSScan.bin.

The entirety of the file can be visualized by the following diagram. The inner segments are not drawn to scale.

+-------------+----------+-----------+-----------+-----------+-----------+-----------+
| smallest mz | mz delta | intensity | intensity | intensity | intensity | intensity |
+-------------+----------+-----------+-----------+-----------+-----------+-----------+
| smallest mz | mz delta | intensity | intensity | intensity | intensity | intensity |
+-------------+----------+-----------+-----------+-----------+-----------+-----------+
| smallest mz | mz delta | intensity | intensity | intensity | intensity | intensity |
+-------------+----------+-----------+-----------+-----------+-----------+-----------+
|                          repeats for every retention time                          |
+------------------------------------------------------------------------------------+