期刊
JOURNAL OF PROTEOME RESEARCH
卷 20, 期 8, 页码 4068-4074出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.1c00379
关键词
proteomics; glycomics; glycoproteomics; de novo; tandem MS; mass spectrometry
资金
- NSF [1933305]
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1933305] Funding Source: National Science Foundation
Glycans are important in biochemical processes, but the computational interpretation of glycans in mass spectrometry analysis can be challenging. The C++ implementation of the Sweet-SEQer algorithm, called C-SEQer, outperforms the original algorithm in terms of time and memory usage, making glycan analysis more efficient and effective. The implementation is freely available with an MIT license.
Glycans play an important role in many biochemical processes, including protein function and cell signaling. Mass spectrometry (MS) provides the potential for high-throughput, high-sensitivity analysis of glycans but relies heavily on computational interpretation of experimental results. Open-source, stand-alone algorithms for de novo glycan MS analysis are few. One such algorithm, Sweet-SEQer, is available in Python. Glycan analysis of mass spectra can easily involve high volumes of data where Python's performance in time and memory is a noticeable bottleneck. This manuscript describes C-SEQer, a new implementation of the Sweet-SEQer algorithm in C++, which produces the same output as the original algorithm in approximately 15-fold less time with substantially less memory usage. The implementation is freely available with an MIT license.
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