AirdSDK 2.0.3.1-beta1

What is Aird?

Aird is a new format for mass spectrometry data storage. It is an opensource and computation-oriented format with controllable precision, flexible indexing strategies, and high compression rate for m/z and intensity pairs. Aird provides a novel compressor call ZDPD for m/z data compression,which makes up an amazing compression rate. Compared with Zip, m/z data is about 55% lower in the Aird on average. Aird is a computational friendly algorithm. Through SIMD optimization, the decoding speed of Aird is much higher than that of Zip. <br/> Aird SDK is a developer tool written in Java. It is convenient for developers who want to read the spectrum data in the Aird file quickly. With the high performance of reading and excellent compression rate, developer can develop a lot of application based on Aird for data visualization and analysis.

Citation

1. Lu, M., An, S., Wang, R. et al. Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time. BMC Bioinformatics 23, 35 (2022)

2. Wang,J. et al. StackZDPD: a novel encoding scheme for mass spectrometry data optimized for speed and compression ratio. Scientific Reports, 12, 5384.(2022)

AirdPro

You should use the AirdPro client to transfer the vendor files into Aird format.<br/> You can download the AirdPro from the github: <br/> https://github.com/CSi-Studio/AirdPro/releases/ <br/> After downloading, unzip the file, click the AirdPro.exe to start the AirdPro Application AirdPro is written in C#, it is also an opensource project. Simple UI is provided by AirdPro for people to convert the vendor file to the Aird file quickly.

What does Aird format like?

Aird Index File Suffix: .json <br/> Aird Data File Suffix: .aird <br/> Aird Index File and Aird Data File show be stored in the same directory with the same file name but with different suffix, so that AirdScanUtil class can scan both of the two files with the same file name;<br/> When dealing with Spectra, we advise that you should process with SWATH Window one by one so that we can control the Memory

Maven for Java SDK

<dependency>
    <groupId>net.csibio.aird</groupId>
    <artifactId>aird-sdk</artifactId>
    <version>2.0.3.1</version>
</dependency>

Nuget for C# SDK

Search "AirdSDK" in Nuget Package Manager

Main API Class

AirdManager is the entry level class. You can also use the Parsers under the parser package. Aird-SDK 1.1.X is currently support three types of MS file.

• DIA/SWATH
• DDA
• PRM
• DIA_PASEF
• DDA_PASEF
• Common type like mzXML

Demo code: see SampleCode.java in the project

MetaData JSON Schema

refer in the root package of the project: AirdMetaData.json

Detail Description

AirdInfo

Compressor

WindowRange

BlockIndex

Instrument

DataProcessing

Software

ParentFile

MobiInfo

Sample Code

Detail sample code. See net.csibio.aird.sample.SampleCode

Scan Aird files from target directory

    List<File> files = AirdScanUtil.scanIndexFiles("E:\\data\\SGS");
    files.forEach(file -> {
        AirdManager.getInstance().load(file.getPath());
    });

Load Aird Info into memory

    DIAParser diaParser = new DIAParser("\\FilePath\\file.json");
    DDAParser ddaParser = new DDAParser("\\FilePath\\file.json");
    DDAPasefParser ddaPasefParser = new DDAPasefParser("\\FilePath\\file.json");
    DIAPasefParser diaPasefParser = new DIAPasefParser("\\FilePath\\file.json");
    PRMParser prmParser = new PRMParser("\\FilePath\\file.json");

Read AirdInfo

    AirdInfo airdInfo = parser.getAirdInfo();

Read Spectrum directly

    Spectrum pairs = parser.getSpectrum(0);

Read DIA SWATH block one by one

    airdInfo.getIndexList().forEach(blockIndex -> {
       TreeMap<Float, Spectrum> map = diaParser.getSpectrums(blockIndex);
    });

Read DDA MsCycle

Read all spectra into the memory

    List<DDAMs> cycleList = ddaParser.readAllToMemory();