Chart types

PACOM offers a great variety of charts of different types, showing different features in different ways. Here we present a table with all of them, with a short description and the type of graphical representation(s) available for each of them:

Chart name	Description	Type of graphical representation
1	Number of identifications	PSMs/Peptides/Proteins	Shows the number of PSMs, Peptides and Proteins in the same chart.	Line chart
2		Peptide number	Shows the number of Peptides.	Bar chart / stacked bar chart / pie chart
3		Number of different peptides per protein	Shows the number of different peptide sequences per protein.	Bar chart / Stacked bar chart
4		Protein number	Shows the number of Proteins.	Bar chart / Stacked bar chart / Pie chart
5		Single hit proteins	Shows the number of proteins identified just with one PSM.	Bar chart / Stacked bar chart / Pie chart
6		Protein sensitivity and specificity	After entering a list of true positive proteins, it shows the sensitivity, accuracy, specificity, precision, fraction of true negatives and error rate.	Bar chart
7	Overlapping	Peptide overlapping	Shows a Venn diagram representing the overlapping of the peptides.	Venn diagram
8		Protein overlapping	Shows a Venn diagram representing the overlapping of the proteins.	Venn diagram
9	Scores	Peptide score comparison	Each point represents the score of the same peptide in two different datasets.	Scatter plot
10		Peptide score distribution	Shows the distribution of a selected peptide score.	Histogram in a line chart
11		Protein score comparison	Each point represents the score of the same protein in two different datasets.	Scatter plot
12		Protein score distribution	Shows the distribution of a selected protein score.	Histogram in a line chart
13	Protein features	Protein words cloud	Taking all protein descriptions, it represents each word depending on its frequency in the dataset. The more frequent the word is, the bigger is represented.	Word cloud
14		Protein group type distribution	Shows the number of proteins or protein groups that are classified in each protein group category.	Bar chart / Stacked bar chart
15		Number of exclusive proteins	Number of proteins identified only in each dataset.	Combined line and bar chart
16		Protein repeatability	Number of proteins detected once, twice…etc, in each dataset.	Stacked bar chart
17		Protein coverage	Protein coverage	Shows the average protein sequence coverage.	Stacked bar chart with error bars
18			Protein coverage distribution	Shows the distribution of protein coverages over the dataset.	Histogram in a line chart
19	Peptide features	Miscleavages distribution	Shows the number of peptides containing no miscleavages, one, two, etc…	Bar chart / Stacked bar chart
20		Peptide mass distribution	Shows the distribution of masses (in Da) of the peptides.	Histogram in a line chart
21		Peptide length distribution	Giving a range of lengths, shows the number of peptides for each length in between that length range.	Bar chart / Stacked bar chart
22		Peptide charge distribution	Shows the number of peptides for each detected charge state.	Bar chart / Stacked bar chart
23		Peptide mass error	For each PSM, shows the difference between the experimental and observed m/z values against the experimental m/z values.	Scatter plot
24		Peptide retention time distribution	Distribution of the number of peptides by its retention time.	Histogram in a line chart
25		Peptide retention time comparison	Each point represents the retention time for the same peptide in two different datasets.	Scatter plot
26		Single retention time comparison	For each selected PSM, shows the retention time in each dataset, allowing multiple selections.	Bar chart
27		Number of exclusive peptides	Number of peptides identified only in each dataset.	Combined line and bar chart
28		Peptide repeatability	Number of peptides detected once, twice…etc, in each dataset.	Stacked bar chart
29		Peptide modifications	Peptide modification distribution	Number of peptides detected with one, two, three, etc… PTM positions of a given type of PTM.	Bar chart / Stacked chart
30			Peptide monitoring	Number of times that a given peptide sequence is detected in each dataset. Multiple peptide selections are possible.	Bar chart
31			Number of modified peptides	Number of peptides containing at least one amino acid modified with a given PTM. Multiple PTM selection are allowed.	Bar chart / Stacked bar chart
32			Number of modified sites	Number of PTM sites of a given PTM in each dataset. Multiple PTM selection are allowed.	Bar chart / Stacked bar chart
33	Heat-maps	Protein heat-map	Heat-map representing if a given protein is detected or not in all datasets.	Heat-map chart
34		Number of peptides per protein heat-map	Heat-map representing the number of peptides explaining each protein in each dataset.	Heat-map chart
35		Peptide heat-map	Heat-map representing the number of times each peptide is detected in all datasets.	Heat-map chart
36		Peptide presence heat-map	Given a list of peptides of interest introduced by the user, it represents the number of times each one is detected over the datasets.	Heat-map chart
37	False discovery rates	False discovery rates	Shows the number of protein/peptides/PSMs identified for each FDR value.	Line chart
38		FDRs vs Scores / # proteins vs Score	Shows the best scores versus the FDR values and the number of proteins detected at different score thresholds.	Line chart
39	Human genes and chromosomes	Human chromosome coverage	Shows the proportion of proteins detected versus the total number of encoded proteins in each human chromosome, per each dataset.	Bar chart / Spider plot
40		Proteins and genes per chromosome	Shows the number of different proteins and genes identified that are encoded in each chromosome.	Bar chart / Pie chart
41		Peptides and PSMs per chromosome	Shows the number of peptides and PSMs identified mapping to proteins encoded in each human chromosome.	Bar chart / Pie chart
42	Peptide counting	Peptide counting ratio histogram	Histogram of the distribution of the spectral count ratio between two datasets	Histogram in a bar chart
43		Peptide counting ratio vs score	For each peptide, the spectral count ratio between two datasets vs the score of the peptide in each dataset.	Scatter plot
44	Metadata	Spectrometers	Shows a table with the spectrometers information used in each dataset.	Table
45		Input parameters	Shows a table with the values of the input parameters of the search engine (required in MIAPE)	Table