A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry

被引：75

作者：

Li, XJ ^{[1
]}

Pedrioli, PGA ^{[1
]}

Eng, J ^{[1
]}

Martin, D ^{[1
]}

Yi, EC ^{[1
]}

Lee, H ^{[1
]}

Aebersold, R ^{[1
]}

机构：

[1] Inst Syst Biol, Seattle, WA 98103 USA

来源：

ANALYTICAL CHEMISTRY | 2004年 / 76卷 / 13期

关键词：

D O I：

10.1021/ac035375s

中图分类号：

O65 [分析化学];

学科分类号：

070302 ; 081704 ;

摘要：

We present a software tool for visualizing data obtained from analyzing complex peptide mixtures by liquid chromatography (LC) electrospray ionization (EST) mass spectrometry (MS). The data are represented as a two-dimensional density plot. For experiments employing collision-induced dissociation (CID), links are embedded in the image to the CID spectra and the corresponding peptide sequences that are represented by the respective feature. The image provides an intuitive method to evaluate sample quality and the performance of an LC-ESI-MS system and can be used to optimize experimental conditions. Local patterns of the image can also be used to identify chemical contaminants and specific peptide features. Therefore, this software tool may have broad application in MS-based proteomics.

引用

收藏

页码：3856 / 3860

页数：5

相关论文

共 22 条

[1] Mass spectrometry-based proteomics [J].

Aebersold, R ;

Mann, M .

NATURE, 2003, 422 (6928) :198-207

[2] High-throughput global peptide proteomic analysis by combining stable isotope amino acid labeling and data-dependent multiplexed-MS/MS [J].

Berger, SJ ;

Lee, SW ;

Anderson, GA ;

Pasa-Tolic, L ;

Tolic, N ;

Shen, YF ;

Zhao, R ;

Smith, RD .

ANALYTICAL CHEMISTRY, 2002, 74 (19) :4994-5000

[3] A molecular scanner to automate proteomic research and to display proteome images [J].

Binz, PA ;

Müller, M ;

Walther, D ;

Bienvenut, WV ;

Gras, R ;

Hoogland, C ;

Bouchet, G ;

Gasteiger, E ;

Fabbretti, R ;

Gay, S ;

Palagi, P ;

Wilkins, MR ;

Rouge, V ;

Tonella, L ;

Paesano, S ;

Rossellat, G ;

Karmime, A ;

Bairoch, A ;

Sanchez, JC ;

Appel, RD ;

Hochstrasser, DF .

ANALYTICAL CHEMISTRY, 1999, 71 (21) :4981-4988

[4] Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS MS and database searching [J].

Clauser, KR ;

Baker, P ;

Burlingame, AL .

ANALYTICAL CHEMISTRY, 1999, 71 (14) :2871-2882

[5] AN APPROACH TO CORRELATE TANDEM MASS-SPECTRAL DATA OF PEPTIDES WITH AMINO-ACID-SEQUENCES IN A PROTEIN DATABASE [J].

ENG, JK ;

MCCORMACK, AL ;

YATES, JR .

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 1994, 5 (11) :976-989

[6] ELECTROSPRAY IONIZATION FOR MASS-SPECTROMETRY OF LARGE BIOMOLECULES [J].

FENN, JB ;

MANN, M ;

MENG, CK ;

WONG, SF ;

WHITEHOUSE, CM .

SCIENCE, 1989, 246 (4926) :64-71

[7] Abundance ratio-dependent proteomic analysis by mass spectrometry [J].

Griffin, TJ ;

Lock, CM ;

Li, XJ ;

Patel, A ;

Chervetsova, L ;

Lee, H ;

Wright, ME ;

Ranish, JA ;

Chen, SS ;

Aebersold, R .

ANALYTICAL CHEMISTRY, 2003, 75 (04) :867-874

[8] Quantitative analysis of complex protein mixtures using isotope-coded affinity tags [J].

Gygi, SP ;

Rist, B ;

Gerber, SA ;

Turecek, F ;

Gelb, MH ;

Aebersold, R .

NATURE BIOTECHNOLOGY, 1999, 17 (10) :994-999

[9] Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry [J].

Han, DK ;

Eng, J ;

Zhou, HL ;

Aebersold, R .

NATURE BIOTECHNOLOGY, 2001, 19 (10) :946-951

[10] Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography [J].

Hansen, KC ;

Schmitt-Ulms, G ;

Chalkley, RJ ;

Hirsch, J ;

Baldwin, MA ;

Burlingame, AL .

MOLECULAR & CELLULAR PROTEOMICS, 2003, 2 (05) :299-314