CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data Using Restricted Search Space and Intelligent Random Sampling

Pencarian berdasarkan :

SEMUA Pengarang Subjek ISBN/ISSN Pencarian Spesifik

Pencarian terakhir:

e-journal

CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data Using Restricted Search Space and Intelligent Random Sampling

Fahad Saeed - Nama Orang; Jason D. Hoffert - Nama Orang; Mark A. Knepper - Nama Orang;

High-throughput mass spectrometers can produce massive amounts of redundant data at an astonishing rate with many of them having poor signal-to-noise (S/N) ratio. These low S/N ratio spectra may not get interpreted using conventional spectra-todatabase matching techniques. In this paper, we present an efficient algorithm, CAMS-RS (Clustering Algorithm for Mass Spectra using Restricted Space and Sampling) for clustering of raw mass spectrometry data. CAMS-RS utilizes a novel metric (called F-set)
that exploits the temporal and spatial patterns to accurately assess similarity between two given spectra. The F-set similarity metric is independent of the retention time and allows clustering of mass spectrometry data from independent LC-MS/MS runs. A novel restricted search space strategy is devised to limit the comparisons of the number of spectra. An intelligent sampling method is executed on individual bins that allow merging of the results to make the final clusters. Our experiments, using experimentally
generated data sets, show that the proposed algorithm is able to cluster spectra with high accuracy and is helpful in interpreting low S/N ratio spectra. The CAMS-RS algorithm is highly scalable with increasing number of spectra and our implementation allows clustering of up to a million spectra within minutes.
Index Terms—Mass spectrometry, clustering, proteomics, search space

Ketersediaan

Tidak ada salinan data

Informasi Detail

Judul Seri: IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
No. Panggil: -
Penerbit: New York : IEEE., 2014
Deskripsi Fisik: IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. 1, JANUARY/FEBRUARY 2014
Bahasa: English
ISBN/ISSN: 1545-5963
Klasifikasi: -
Tipe Isi: -
Tipe Media: -
Tipe Pembawa: -
Edisi: VOL. 11, NO. 1, JANUARY/FEBRUARY 2014
Subjek: BIOLOGI
Info Detail Spesifik: -
Pernyataan Tanggungjawab: Yuli/Agus

Versi lain/terkait

Tidak tersedia versi lain

Lampiran Berkas

FULL TEXT. CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data Using Restricted Search Space and Intelligent Random Sampling

Komentar

Anda harus masuk sebelum memberikan komentar