Database Searching in Mass Spectrometry Based Proteomics

被引：15
|
作者：
Kertesz-Farkas, Attila [1 ]
Reiz, Beata [2 ,3 ]
Myers, Michael P.
Pongor, Sandor [2 ]
机构：
[1] Int Ctr Genet Engn & Biotechnol, Prot Struct & Bioinformat Grp, I-34012 Trieste, Italy
[2] Szeged Biol Ctr, H-6720 Szeged, Hungary
[3] Univ Szeged, Inst Informat, H-6720 Szeged, Hungary
来源：
CURRENT BIOINFORMATICS | 2012年 / 7卷 / 02期
关键词：
Database search; Mass spectrometry; Protein identification; Proteomics; AMINO-ACID-SEQUENCES; PROTEIN IDENTIFICATION; PEPTIDE IDENTIFICATION; SPECTRAL DATA; STATISTICAL SIGNIFICANCE; IMPROVING SENSITIVITY; TANDEM; VALIDATION; MODEL; LIBRARIES;
D O I：
10.2174/157489312800604354
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Bottom-up proteomics (mass spectrometry analysis of peptides obtained by proteolysis and separated by liquid chromatography, (LC-MS/MS)) is one of the most frequently used techniques for identifying and characterizing proteins in biological samples. A key element of the analysis is database searching when the mass spectra of the peptides are compared with a database of theoretically computed (or experimental) peptide spectra. Here we discuss the main computational approaches to spectrum database searching and the statistical analysis of the results.
引用
收藏
页码：221 / 230
页数：10
相关论文
共 50 条
  • [31] Characterizing citrullination by mass spectrometry-based proteomics
    Rebak, A. S.
    Hendriks, I. A.
    Nielsen, M. L.
    PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2023, 378 (1890)
  • [32] The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
    Perez-Riverol, Yasset
    Bai, Jingwen
    Bandla, Chakradhar
    Garcia-Seisdedos, David
    Hewapathirana, Suresh
    Kamatchinathan, Selvakumar
    Kundu, Deepti J.
    Prakash, Ananth
    Frericks-Zipper, Anika
    Eisenacher, Martin
    Walzer, Mathias
    Wang, Shengbo
    Brazma, Alvis
    Vizcaino, Juan Antonio
    NUCLEIC ACIDS RESEARCH, 2022, 50 (D1) : D543 - D552
  • [33] YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research
    Christopher M.Colangelo
    Mark Shifman
    Kei-Hoi Cheung
    Kathryn L.Stone
    Nicholas J.Carriero
    Erol E.Gulcicek
    TuKiet T.Lam
    Terence Wu
    Robert D.Bjornson
    Can Bruce
    Angus C.Nairn
    Jesse Rinehart
    Perry L.Miller
    Kenneth R.Williams
    Genomics,Proteomics & Bioinformatics, 2015, (01) : 25 - 35
  • [34] Mass spectrometry-based proteomics
    Hood, BL
    Veenstra, TD
    Conrads, TP
    ADVANCES IN FERTILITY AND REPRODUCTIVE MEDICINE, 2004, 1266 : 375 - 380
  • [35] From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics
    Lavallee-Adam, Mathieu
    Park, Sung Kyu Robin
    Martinez-Bartolome, Salvador
    He, Lin
    Yates, John R. I. I. I. I.
    JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 2015, 26 (11) : 1820 - 1826
  • [36] A Mass Spectrometry Proteomics Data Management Platform
    Sharma, Vagisha
    Eng, Jimmy K.
    MacCoss, Michael J.
    Riffle, Michael
    MOLECULAR & CELLULAR PROTEOMICS, 2012, 11 (09) : 824 - 831
  • [37] Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics
    Lam, Henry
    Aebersold, Ruedi
    METHODS, 2011, 54 (04) : 424 - 431
  • [38] Mass Spectrometry-Based Proteomics in Clinical Diagnosis of Amyloidosis and Multiple Myeloma: A Review (2012-2024)
    Kratka, Katerina
    Sistik, Pavel
    Olivkova, Ivana
    Kusnierova, Pavlina
    Svagera, Zdenek
    Stejskal, David
    JOURNAL OF MASS SPECTROMETRY, 2025, 60 (03):
  • [39] Tandem Mass Spectrometry with Ultrahigh Mass Accuracy Clarifies Peptide Identification by Database Retrieval
    Boyne, Michael T., II
    Garcia, Benjamin A.
    Li, Mingxi
    Zamdborg, Leonid
    Wenger, Craig D.
    Babai, Shannee
    Kelleher, Neil L.
    JOURNAL OF PROTEOME RESEARCH, 2009, 8 (01) : 374 - 379
  • [40] A Survey of Molecular Descriptors Used in Mass Spectrometry Based Proteomics
    Audain, Enrique
    Sanchez, Aniel
    Vizcaino, Juan Antonio
    Perez-Riverol, Yasset
    CURRENT TOPICS IN MEDICINAL CHEMISTRY, 2014, 14 (03) : 388 - 397
12345