Case 1
A user investigates whether or not 3 experimentally measured peptides, which she/he believes play an important role, are unique for a protein.
The peptides are:
"STELLA",  "SARTW",  "ARTARTS" 

Step A.

In the "Peptide Sequence Search" mode, at the "Search by a List of Peptide Sequences" area, the user submits the sequences 

Step B.

    The application returns the following :

1

Protein AC	Protein Description	Peptide	Molecular Mass
Q4KMX7	Protein FAM106A Homo sapiens	STELLA Click to check across species Click to check enzymatic digestion	632.34

Step C.

The user finds that the peptide STELLA is a core unique peptide (CUP) which belongs only to protein Q4KMX7.

Step D.

By clicking on the link "Click to check across species" the user finds that the peptide STELLA is also unique in 10 other species apart from Humans, getting the information of the corresponding proteins (see table below).

Index	Species	Protein	Description
1	XANOR	Q5H616	Probable ubiquinone biosynthesis protein ubiB Xanthomonas oryzae pv. oryzae
2	HUMAN	Q4KMX7	Protein FAM106A Homo sapiens
3	BPT4	P04521	Exonuclease subunit 1 Bacteriophage T4
4	SHISO	P16943	Insertion element IS630 uncharacterized 39 kDa protein Shigella sonnei PE=4 SV=1
5	NOCSI	P77816	Steroid Delta-isomerase Nocardioides simplex
6	NITEU	Q82TW6	DNA ligase Nitrosomonas europaea
7	XANOM	Q2P8Q0	Probable ubiquinone biosynthesis protein ubiB Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
8	YARLI	P34229	Fatty acid synthase subunit beta Yarrowia lipolytica
9	ACIAC	A1TP97	Trans-aconitate 2-methyltransferase Acidovorax avenae subsp. citrulli (strain AAC00-1)
10	WHEAT	Q42430	Zinc finger protein 1 Triticum aestivum PE=2 SV=1
11	ECOLI	P39285	Uncharacterized mscS family protein yjeP Escherichia coli (strain K12)

Step E.

By clicking on the link "Click to check enzymatic digestion" the user finds the unique peptide sequences when Q4KMX7 is digested with enzymes (see table below).

Enzyme	Position	Peptide Sequence	Molecular Mass
Trypsin	K or R in C term	GTLSIAYCLMSSVSTSSEAIMSTELLANYCHSSLHVCICISSFPNETGNHDSFPGAVVSI SDQPTDQCK	7282.30
Arg-C	R in C term	GTLSIAYCLMSSVSTSSEAIMSTELLANYCHSSLHVCICISSFPNETGNHDSFPGAVVSI SDQPTDQCKLAAKELPLR	8273.92
Chymotrypsin	F or Y or W or L in C term	-	-
Formic Acid	D in C term	PVILISLHEAVRFSFAFSFPRGTLSIAYCLMSSVSTSSEAIMSTELLANYCHSSLHVCIC ISSFPNETGNHD	7836.75
Lys-C	K in C term	MLPSTMFLVHLPLSTNRLHCLRNTSLESCLCSFVHLNHPLHISDPVILISLHEAVRFSFA FSFPRGTLSIAYCLMSSVSTSSEAIMSTELLANYCHSSLHVCICISSFPNETGNHDSFPG AVVSISDQPTDQCK	14704.12
PepsinA	F or L in C term	-	-
TrypChymo	F or Y or W or L or K or R in C term	-	-
V8-DE	D or E in C term	-	-
Asp-N	D in N term	DPVILISLHEAVRFSFAFSFPRGTLSIAYCLMSSVSTSSEAIMSTELLANYCHSSLHVCI CISSFPNETGNH	7836.75
Asp-N_ambic	D or E in N term	-	-

Step F.

Now the user continues the investigation with the second peptide (SARTW) which is found to be not a CUP. By clicking on the link "Check for other sequences containing or included in SARTW" the user searches for the corresponding unique subsequences or supersequences. (see table below).

Index	Protein	Description	Supersequence	Molecular Mass
1	Q5R3K3	Protein FAM26F Homo sapiens	LSARTW Click to check across species Click to check enymatic digestion	732.39
			SARTWR Click to check across species Click to check enymatic digestion	775.41
2	Q8N394	Transmembrane and TPR repeat-containing protein 2 Homo sapiens	YSARTW Click to check across species Click to check enymatic digestion	782.37

It comes that SARTW has no core unique subsequences and thus it is not a unique sequence. 

However, there are 2 core unique supersequences of SARTW in protein  Q5R3K3 and 1 core unique supersequence of SARTW in protein Q8N394 

Thus, SARTW is part of 3 core unique sequences.

Step G.

The user continues the investigation with the third peptide (ARTARTS) which is found to be not a CUP. By clicking on the link "Check for other sequences containing or included in ARTARTS" the user searches for the corresponding unique subsequences or supersequences. (see table below).

Index	Protein	Description	Subsequence	Molecular Mass
1	Q7Z6M4	mTERF domain-containing protein 2 Homo sapiens	ARTART Click to check across species Click to check enymatic digestion	674.38

It comes that ARTARTS is a unique sequence since it has a core unique subsequence (ARTART) in protein Q7Z6M4 . 

Case 2
A user investigates whether or not a list of molecular masses contains unique molecular masses for a protein.
These molecular masses are: 2345, 2500, 2800, 3015, 3100 Da.

Case 3
A user investigates whether or not around 3000 Da and in a range of 2 Da
are there any unique molecular masses.

Case 4
A user investigates whether or not the candidate biomarkers Von Willebrand Factor (P04275)
and Cathepsin B (P07858) have unique peptide sequences and masses.