I only have raw data. What software can I use to process it to determine the protein sequence?

Parsing protein sequences from RAW data (e.g., files obtained through mass spectrometers) typically requires specialized mass spectrometry data analysis software and database search tools. Here are some recommended software options:

 

1. Common Software Tools

1. Tools for Raw Data Processing

（1）Thermo Fisher Xcalibur/Proteome Discoverer

• Specifically designed for Thermo Fisher mass spectrometers, can directly read RAW data.

• Proteome Discoverer supports database searches and outputs protein identification results.

• If using mass spectrometers from other brands, you may need other specific software or tools for data conversion.

 

（2）MSConvert (ProteoWizard)

A free open-source tool that can convert RAW files to standard formats like mzML, mzXML, facilitating analysis in other software.

 

2. Tools for Database Searching and Protein Identification

（1）Mascot

• A commercial database search tool supporting various mass spectrometry data.

• Requires a reference protein database, such as UniProt, for use.

 

（2）MaxQuant

• A free and powerful mass spectrometry data analysis tool, widely used in proteomics research.

• Includes the built-in Andromeda search engine for database searching and protein identification.

• Supports common modification analysis (e.g., phosphorylation, acetylation).

 

（3）SEQUEST (Thermo Fisher Proteome Discoverer)

• Built into Proteome Discoverer, a classic search engine for the Thermo system.

• Very compatible with RAW data, can directly parse and search proteins.

 

（4）PEAKS

• Focused on de novo sequencing and database searching.

• Can directly infer protein sequences from raw data, particularly useful when no database is available.

 

（5）Byonic

Especially suitable for analyzing modified proteins (e.g., glycosylation or phosphorylation), supports high-resolution mass spectrometry data.

 

3. Tools for Subsequent Result Analysis

（1）Perseus

Used to process MaxQuant output results for further statistical analysis, visualization, and functional enrichment analysis.

 

（2）Skyline

A powerful quantitative mass spectrometry data analysis tool that can be used to verify protein identification results.

 

2. Database Preparation

Common databases include:

1、UniProt：A global standard protein sequence database.

2、NCBI RefSeq：A comprehensive nucleic acid and protein database.

3、Swiss-Prot：Manually annotated and high-precision database.

4. Custom Database:If the research subject is a specific species or the experiment design is unique, a custom protein database can be generated using the genome data of that species.

 

3. Special Case: De Novo Sequencing without a Database

If there is no existing database for the target sample's sequence (e.g., a new species or mutant protein), de novo sequencing tools can be used to directly infer protein sequences from mass spectrometry data:

1、PEAKS：Supports de novo sequencing.

2、Novor：Focused on efficient de novo protein sequence inference.

3、DeNovoGUI：Open source software for directly inferring sequences from mass spectrometry data.

 

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