Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching

Slawski, Martin; Hussong, Rene; Tholey, Andreas; Jakoby, Thomas; Gregorius, Barbara; Hildebrandt, Andreas; Hein, Matthias

doi:10.1186/1471-2105-13-291

Table 1 Mascot results

From: Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching

MALDI Myo 500 fmol	score	cvrg	hits	score	cvrg	hits
l ₁	211.0	0.85	0.94	96.8	0.96	0.04
l ₂	211.0	0.85	0.94	49.6	0.96	0.04
lasso	207.0	0.85	1.00	142.0	0.91	0.37
pepex	223.0	0.85	1.00	142.0	0.90	0.17
vendor	223.0	0.85	0.94	174.0	0.90	0.29
wavelet	207.0	0.85	1.00	156.0	0.90	0.14
MALDI Lys 500 fmol	score	cvrg	hits	score	cvrg	hits
l ₁	167.0	0.81	0.57	133.0	0.83	0.37
l ₂	168.0	0.80	0.64	144.0	0.83	0.34
lasso	151.0	0.64	0.77	112.0	0.83	0.37
pepex	172.0	0.80	0.63	135.0	0.83	0.25
vendor	146.0	0.64	0.75	91.4	0.83	0.20
wavelet	127.0	0.58	0.75	113.0	0.81	0.20
MALDI Myo 10 fmol	score	cvrg	hits	score	cvrg	hits
l ₁	211.0	0.85	0.94	82.2	0.95	0.04
l ₂	207.0	0.74	1.00	109.0	0.90	0.14
lasso	195.0	0.77	0.87	146.0	0.85	0.46
pepex	97.8	0.80	0.22	97.8	0.80	0.22
vendor	123.0	0.62	0.62	123.0	0.62	0.62
wavelet	131.0	0.85	0.13	131.0	0.85	0.13
MALDI Lys 10 fmol	score	cvrg	hits	score	cvrg	hits
l ₁	89.0	0.35	1.00	73.7	0.54	0.23
l ₂	89.0	0.35	1.00	35.4	0.72	0.09
lasso	81.9	0.46	0.70	46.0	0.74	0.10
pepex	47.1	0.17	1.00	31.2	0.53	0.12
vendor	62.7	0.23	1.00	43.2	0.34	0.16
wavelet	55.4	0.23	0.45	43.8	0.82	0.10
Orbi Lys 1000 fmol	score	cvrg	hits	score	cvrg	hits
l ₁	149.0	0.70	0.78	138.0	0.80	0.53
l ₂	139.0	0.80	0.50	139.0	0.80	0.50
lasso	159.0	0.63	0.87	120.0	0.81	0.29
wavelet	105.0	0.69	0.44	95.1	0.80	0.23
IT Lys 1000 fmol	score	cvrg	hits	score	cvrg	hits
l ₁	78.7	0.63	0.28	70.9	0.74	0.17
l ₂	82.1	0.72	0.36	35.4	0.85	0.13
lasso	103.0	0.84	0.33	76.8	0.99	0.21
wavelet	107.0	0.79	0.63	69.8	0.99	0.11
Orbi Lys 250 fmol	score	cvrg	hits	score	cvrg	hits
l ₁	107.0	0.63	0.50	100.0	0.80	0.31
l ₂	103.0	0.63	0.52	66.9	0.81	0.14
lasso	108.0	0.63	0.77	107.0	0.80	0.27
wavelet	80.6	0.70	0.22	80.6	0.70	0.22
IT Lys 250fmol	score	cvrg	hits	score	cvrg	hits
l ₁	59.4	0.46	0.16	59.4	0.46	0.16
l ₂	37.0	0.59	0.14	37.0	0.59	0.14
lasso	66.3	0.84	0.20	66.3	0.84	0.20
wavelet	56.3	0.59	0.36	21.3	0.75	0.12

Corresponding Mascot results for the data shown in Figures 4 and 5. The left halves of the tables report the statistics when choosing the threshold(-like) parameter to optimize the score, the right halves when optimizing the coverage (cvrg, given as fraction). The column ‘hits’ contains the fraction of masses that could be matched to peptide masses in the database.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Bioinformatics

Contact us