Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry

*McKusick-Nathans Institute for Genetic Medicine and Departments of Biological Chemistry, Pathology, and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;
^†Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark;
^‡Agilent Technologies, Santa Clara, CA 95052; and
^§Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India

Communicated by Paul Talalay, Johns Hopkins University School of Medicine, Baltimore, MD, December 25, 2006 (received for review November 1, 2006)

Footnotes

^¶To whom correspondence should be addressed. E-mail: pandey{at}jhmi.edu
Author contributions: H.M. and A.P. designed research; H.M., N.T., and S.M. performed research; H.M., D.M.H., S.M., and A.P. analyzed data; and H.M. and A.P. wrote the paper.
Conflict of interest statement: D.M.H. and N.T. are employees of Agilent Technologies. All other authors have declared no conflict of interest.
This article contains supporting information online at www.pnas.org/cgi/content/full/0611217104/DC1.
Abbreviations:
CID,
collision-induced dissociation;
ETD,
electron transfer dissociation;
MS/MS,
tandem MS;
LC,
liquid chromatography.
Freely available online through the PNAS open access option.

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Jul 2007	16	71	63
Aug 2007	34	80	77
Sep 2007	66	89	105
Oct 2007	76	115	124
Nov 2007	40	76	90
Dec 2007	62	67	81
Total 2007	1208	1277	1924
Jan 2008	68	82	97
Feb 2008	65	97	87
Mar 2008	72	89	95
Apr 2008	57	69	88
May 2008	55	86	83
Jun 2008	129	66	92
Jul 2008	166	27	79
Aug 2008	100	39	53
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Oct 2008	183	45	77
Nov 2008	114	34	75
Dec 2008	95	33	61
Total 2008	1255	704	947
Jan 2009	111	40	69
Feb 2009	104	25	68
Mar 2009	89	63	89
Apr 2009	79	57	88
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Jun 2009	70	52	77
Jul 2009	59	54	56
Aug 2009	60	37	35
Sep 2009	50	36	43
Oct 2009	60	48	59
Nov 2009	79	44	82
Dec 2009	42	30	32
Total 2009	877	527	750
Jan 2010	70	35	57
Feb 2010	67	34	45
Mar 2010	54	32	32
Apr 2010	50	41	48
May 2010	59	46	37
Jun 2010	61	49	34
Jul 2010	41	43	23
Aug 2010	62	35	36
Sep 2010	45	33	30
Oct 2010	58	53	37
Nov 2010	60	38	34
Dec 2010	61	47	40
Total 2010	688	486	453
Jan 2011	44	31	30
Feb 2011	48	23	22
Mar 2011	60	40	41
Apr 2011	36	18	37
May 2011	64	26	38
Jun 2011	40	45	49
Jul 2011	77	27	45
Aug 2011	77	28	24
Sep 2011	95	30	51
Oct 2011	106	51	46
Nov 2011	84	46	40
Dec 2011	57	23	38
Total 2011	788	388	461
Jan 2012	68	28	30
Feb 2012	93	48	57
Mar 2012	77	55	68
Apr 2012	80	51	51
May 2012	67	38	46
Jun 2012	56	27	45
Jul 2012	59	23	36
Aug 2012	32	18	34
Sep 2012	53	15	31
Oct 2012	49	11	28
Nov 2012	61	25	39
Dec 2012	32	16	24
Total 2012	727	355	489
Jan 2013	66	26	39
Feb 2013	63	17	29
Mar 2013	79	20	36
Apr 2013	54	9	24
May 2013	55	17	29
Jun 2013	23	13	18
Jul 2013	38	14	20
Aug 2013	27	16	31
Sep 2013	40	13	27
Oct 2013	42	17	37
Nov 2013	32	20	20
Dec 2013	39	16	33
Total 2013	558	198	343
Jan 2014	41	14	28
Feb 2014	55	23	35
Mar 2014	63	16	35
Apr 2014	54	15	36
May 2014	44	13	38
Jun 2014	44	13	42
Jul 2014	267	23	48
Aug 2014	301	25	27
Sep 2014	63	24	13
Oct 2014	55	29	37
Nov 2014	48	16	31
Dec 2014	41	25	27
Total 2014	1076	236	397
Jan 2015	36	12	19
Feb 2015	38	11	20
Mar 2015	48	28	42
Apr 2015	44	18	29
May 2015	31	18	24
Jun 2015	22	12	20
Jul 2015	25	12	27
Aug 2015	27	13	24
Sep 2015	45	7	18
Oct 2015	34	11	21
Nov 2015	28	9	24
Dec 2015	27	17	23
Total 2015	405	168	291
Jan 2016	32	13	29
Feb 2016	40	14	33
Mar 2016	40	18	26
Apr 2016	46	16	47
May 2016	25	11	13
Jun 2016	24	24	16
Jul 2016	39	18	12
Aug 2016	33	16	14
Sep 2016	34	12	17
Oct 2016	45	21	16
Nov 2016	43	23	18
Dec 2016	46	4	15
Total 2016	447	190	256
Jan 2017	39	11	12
Feb 2017	38	13	21
Mar 2017	41	13	20
Apr 2017	30	14	18
May 2017	29	16	17
Jun 2017	22	15	13
Jul 2017	35	8	21
Aug 2017	22	13	20
Sep 2017	23	9	11
Oct 2017	30	16	7
Nov 2017	30	8	10
Dec 2017	12	7	6
Total 2017	351	143	176
Jan 2018	21	6	16
Feb 2018	30	36	17
Mar 2018	33	25	7
Apr 2018	27	22	7
May 2018	35	23	13
Jun 2018	27	21	10
Jul 2018	31	29	7
Aug 2018	26	33	3
Sep 2018	46	36	8
Oct 2018	7	48	10
Nov 2018	7	39	8
Dec 2018	5	28	12
Total 2018	295	346	118
Jan 2019	14	44	11
Feb 2019	8	26	11
Mar 2019	12	27	14
Apr 2019	18	60	19
May 2019	10	36	15
Jun 2019	10	29	12
Jul 2019	10	24	16
Aug 2019	4	27	10
Sep 2019	7	14	7
Oct 2019	11	31	13
Nov 2019	6	31	8
Dec 2019	4	27	10
Total 2019	114	376	146
Jan 2020	5	31	23
Feb 2020	3	23	7
Mar 2020	1	24	10
Apr 2020	10	37	16
May 2020	6	22	8
Jun 2020	1	18	6
Jul 2020	3	10	3
Aug 2020	4	10	6
Sep 2020	6	21	6
Oct 2020	11	26	26
Nov 2020	16	23	14
Dec 2020	14	14	8
Total 2020	80	259	133
Jan 2021	12	21	15
Feb 2021	4	21	8
Total 2021	16	42	23
Total	8885	5695	6907